Plant Breeding, Genetics and Genomics

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agriculture agriculture	3.3	4.9	2011	19.2 Days	CHF 2600
Agronomy agronomy	3.3	6.2	2011	17.6 Days	CHF 2600
Crops crops	-	-	2021	22.1 Days	CHF 1000
Horticulturae horticulturae	3.1	3.5	2015	16.9 Days	CHF 2200
Plants plants	4.0	6.5	2012	18.9 Days	CHF 2700

1 pages, 126 KiB

Open AccessCorrection

Correction: Campuzano-Duque, L.F.; Blair, M.W. Strategies for Robusta Coffee (Coffea canephora) Improvement as a New Crop in Colombia. Agriculture 2022, 12, 1576

by Luis Fernando Campuzano-Duque and Matthew Wohlgemuth Blair

Agriculture 2025, 15(7), 725; https://doi.org/10.3390/agriculture15070725 - 28 Mar 2025

Viewed by 139

Abstract

Parts of Sections 1 and 5 in the original publication [...] Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

16 pages, 1744 KiB

Open AccessArticle

Diallel Analysis: Choosing Parents to Introduce New Variability in a Recurrent Selection Population

by Paulo Henrique Ramos Guimarães, Adriano Pereira de Castro, José Manoel Colombari Filho, Paula Pereira Torga, Paulo Hideo Nakano Rangel and Patrícia Guimarães Santos Melo

Agriculture 2023, 13(7), 1320; https://doi.org/10.3390/agriculture13071320 - 28 Jun 2023

Cited by 3 | Viewed by 2756

Abstract

Selecting appropriate donors and acquiring information about the genetic basis of inheritance is essential for breeding programs. In this study, a diallel cross was produced by crossing 15 progenies with five commercial lines of wide diversity for different rice traits (grain yield, plant [...] Read more.

Selecting appropriate donors and acquiring information about the genetic basis of inheritance is essential for breeding programs. In this study, a diallel cross was produced by crossing 15 progenies with five commercial lines of wide diversity for different rice traits (grain yield, plant height, days to flowering, panicle blast, brown spots, leaf scald, and grain discoloration) in an incomplete crossing design. The 20 parents and the 25 F₂ crosses constituting the diallel cross were evaluated in a triple lattice design for different traits in a field test. The analysis of variance revealed significant differences between parents and their crosses for all traits, showing high variability. The general combining ability (

G C A

) and the specific combining ability (

S C A

) were significant, with a greater contribution of the

S C A

compared to

G C A

for the variation among crosses, indicating that non-additive effects were more prevalent for the traits evaluated. The results suggested that commercial lines such as IRGA 424 and BRS Catiana can be used to improve CNA 12T population. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 7372 KiB

Open AccessArticle

Identification of PAL Gene in Purple Cabbage and Functional Analysis Related to Anthocyanin Synthesis

by Jun Tian, Ru Xu, Kaizhen Chang, Song Yuan, Chenxin Huang, Jinwei Wang, Shuhao Li, Fazhong Liu and Fenglin Zhong

Horticulturae 2023, 9(4), 469; https://doi.org/10.3390/horticulturae9040469 - 7 Apr 2023

Cited by 10 | Viewed by 2690

Abstract

Anthocyanin is a characteristic nutrient of purple cabbage, and phenylalanine ammonia-lyase (PAL) is the rate-limiting enzyme for the synthesis of anthocyanin by the phenylpropane pathway, which is an important part of plant secondary metabolism. In this research, 7 BrPAL, 8 BoPAL, [...] Read more.

Anthocyanin is a characteristic nutrient of purple cabbage, and phenylalanine ammonia-lyase (PAL) is the rate-limiting enzyme for the synthesis of anthocyanin by the phenylpropane pathway, which is an important part of plant secondary metabolism. In this research, 7 BrPAL, 8 BoPAL, and 15 BnPAL genes from genomes of Brassica rapa, Brassica oleracea, and Brassica napus, divided into four subgroups, evolved from 4 PAL genes in Arabidopsis. The amplification and evolution of the BrPAL gene are due to segmental duplication and purifying selection. BrPAL genes clustered in the same clade have similar intron/exon structures and motifs. The cis-regulatory elements are divided into four categories: light, growth and development, stress and hormones. The qRT-PCR assays showed that most BrPAL genes were upregulated by UVA, low temperature and MeJA and downregulated by FR, high temperature, salt, PEG, IAA, ABA and GA, and there was a positive correlation between anthocyanin content and gene expression. This study can be used as a source for the function of the cabbage PAL gene and its molecular mechanism of regulating anthocyanin synthesis and provides a theoretical basis for the molecular breeding of cabbage. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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16 pages, 17570 KiB

Open AccessArticle

Complete Genome of Rose Myrtle, Rhodomyrtus tomentosa, and Its Population Genetics in Thai Peninsula

by Matsapume Detcharoen, Sara Bumrungsri and Supayang Piyawan Voravuthikunchai

Plants 2023, 12(8), 1582; https://doi.org/10.3390/plants12081582 - 7 Apr 2023

Cited by 4 | Viewed by 2234

Abstract

Several parts of rose myrtle, Rhodomyrtus tomentosa, exhibited profound antibacterial and anti-inflammatory activities, suggesting its potential in healthcare and cosmetics applications. During the past few years, the demand for biologically active compounds in the industrial sectors increased. Therefore, gathering comprehensive information on [...] Read more.

Several parts of rose myrtle, Rhodomyrtus tomentosa, exhibited profound antibacterial and anti-inflammatory activities, suggesting its potential in healthcare and cosmetics applications. During the past few years, the demand for biologically active compounds in the industrial sectors increased. Therefore, gathering comprehensive information on all aspects of this plant species is essential. Here, the genome sequencing using short and long reads was used to understand the genome biology of R. tomentosa. Inter-simple sequence repeats (ISSR) and simple sequence repeats (SSR) markers, and geometric morphometrics of the leaves of R. tomentosa collected across Thai Peninsula, were determined for population differentiation analysis. The genome size of R. tomentosa was 442 Mb, and the divergence time between R. tomentosa and Rhodamnia argentea, the white myrtle of eastern Australia, was around 15 million years. No population structure was observed between R. tomentosa on the eastern and western sides of the Thai Peninsula using the ISSR and SSR markers. However, significant differences in leaf size and shape of R. tomentosa were observed in all locations. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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22 pages, 2375 KiB

Open AccessReview

A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation

by Diana Lucia Zuluaga, Emanuela Blanco, Giacomo Mangini, Gabriella Sonnante and Pasquale Luca Curci

Plants 2023, 12(6), 1267; https://doi.org/10.3390/plants12061267 - 10 Mar 2023

Cited by 6 | Viewed by 2624

Abstract

Durum wheat (Triticum turgidum subsp. durum (Desf.) Husn.) is an allotetraploid cereal crop of worldwide importance, given its use for making pasta, couscous, and bulgur. Under climate change scenarios, abiotic (e.g., high and low temperatures, salinity, drought) and biotic (mainly exemplified by [...] Read more.

Durum wheat (Triticum turgidum subsp. durum (Desf.) Husn.) is an allotetraploid cereal crop of worldwide importance, given its use for making pasta, couscous, and bulgur. Under climate change scenarios, abiotic (e.g., high and low temperatures, salinity, drought) and biotic (mainly exemplified by fungal pathogens) stresses represent a significant limit for durum cultivation because they can severely affect yield and grain quality. The advent of next-generation sequencing technologies has brought a huge development in transcriptomic resources with many relevant datasets now available for durum wheat, at various anatomical levels, also focusing on phenological phases and environmental conditions. In this review, we cover all the transcriptomic resources generated on durum wheat to date and focus on the corresponding scientific insights gained into abiotic and biotic stress responses. We describe relevant databases, tools and approaches, including connections with other “omics” that could assist data integration for candidate gene discovery for bio-agronomical traits. The biological knowledge summarized here will ultimately help in accelerating durum wheat breeding. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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21 pages, 814 KiB

Open AccessReview

Sex Chromosomes and Sex Determination in Dioecious Agricultural Plants

by Olga V. Razumova, Oleg S. Alexandrov, Karina D. Bone, Gennady I. Karlov and Mikhail G. Divashuk

Agronomy 2023, 13(2), 540; https://doi.org/10.3390/agronomy13020540 - 14 Feb 2023

Cited by 7 | Viewed by 5447

Abstract

Unlike in animals, dioecy among flowering plants is a rare phenomenon. The vast majority of angiosperm species have a bisexual flower that combines male (androecium) and female (gynoecium) reproductive organs. However, about a quarter of species have dioecious flowers, which can be located [...] Read more.

Unlike in animals, dioecy among flowering plants is a rare phenomenon. The vast majority of angiosperm species have a bisexual flower that combines male (androecium) and female (gynoecium) reproductive organs. However, about a quarter of species have dioecious flowers, which can be located within the same plant (monoecious) or on different plants (dioecious). The flower formation in dioecious plants is determined by various genetic mechanisms. They become more complex from the work of a single gene to the functioning of full-fledged heteromorphic sex chromosomes, which can directly affect sex differentiation or participate in the balance determination of sex (where the formation of male or female flower organs depends on the ratio of X chromosomes to autosomes, for example). In recent years, the development of sequencing techniques, bioinformatics, and molecular biology has led to an increase in interest in the sex determination mechanisms among plants. It is noteworthy that a significant number of dioecious plants have economic value. At the same time, dioeciousness often complicates the growing process. This fact increases the relevance of studies on dioecious crops. In this review, we attempt to summarize the current information on sex chromosomes and the mechanisms of sex determination in dioecious plants, concentrating on species with agricultural importance. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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9 pages, 686 KiB

Open AccessArticle

A Set of Highly Polymorphic Microsatellite Markers for Genetic Diversity Studies in the Genus Origanum

by Marina Alekseeva, Mila Rusanova, Krasimir Rusanov and Ivan Atanassov

Plants 2023, 12(4), 824; https://doi.org/10.3390/plants12040824 - 12 Feb 2023

Cited by 8 | Viewed by 2393

Abstract

This study reports the development of a set of 20 highly polymorphic genomic SSR markers which can be used for both cultivar identification and genetic diversity studies in several Origanum species, including some of the most popular ones like Greek oregano (Origanum [...] Read more.

This study reports the development of a set of 20 highly polymorphic genomic SSR markers which can be used for both cultivar identification and genetic diversity studies in several Origanum species, including some of the most popular ones like Greek oregano (Origanum vulgare L. ssp. hirtum), common oregano (O. vulgare L. ssp. vulgare), and sweet marjoram (O. majorana L.). Analysis of the polymorphic information content (PIC) showed an average PIC value of 0.75 with a minimum of 0.41 and a maximum of 0.89, where 17 of the markers showed PIC values above 0.73. Comparative analysis of the genetic diversity of eight natural populations of Greek oregano in Bulgaria showed that six of the genomic SSR markers revealed significantly higher portions of genetic diversity in the populations, compared to 12 EST SSR markers used in our previous study. We also compared the performance of the same six genomic SSR markers with the results for eight SRAP primer combinations, which showed that SRAP markers captured more precisely the genetic structure in natural populations. The developed highly polymorphic genomic SSR markers can be successfully applied to evaluation of the genetic diversity in the genus Origanum, based on the expected and observed heterozygosity in the populations as well as for easy identification of breeding lines and cultivars based on unique SSR fingerprints. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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13 pages, 2247 KiB

Open AccessEditor’s ChoiceArticle

Multi-Environment Trials and Stability Analysis for Yield-Related Traits of Commercial Rice Cultivars

by Seung Young Lee, Hyun-Sook Lee, Chang-Min Lee, Su-Kyung Ha, Hyang-Mi Park, So-Myeong Lee, Youngho Kwon, Ji-Ung Jeung and Youngjun Mo

Agriculture 2023, 13(2), 256; https://doi.org/10.3390/agriculture13020256 - 20 Jan 2023

Cited by 32 | Viewed by 5981

Abstract

Multi-environment trials (METs) are essential in plant breeding programs to evaluate crop productivity and adaptability in diverse environments. In this study, we demonstrated the practical use of METs to evaluate grain yield and yield-related traits using 276 Korean rice cultivars, divided into three [...] Read more.

Multi-environment trials (METs) are essential in plant breeding programs to evaluate crop productivity and adaptability in diverse environments. In this study, we demonstrated the practical use of METs to evaluate grain yield and yield-related traits using 276 Korean rice cultivars, divided into three maturity groups (81 early-, 90 medium-, and 105 medium–late-maturing cultivars) grown in three regions (Jeonju, Suwon, and Miryang) and two planting seasons (early and regular planting) for two years. Due to the narrow genetic variability of the commercial cultivars, which are cultivated in relatively similar environmental conditions, genotype-by-environment interaction (GEI) effects were not statistically significant. However, genotype and environment evaluation using GGE biplot analysis exhibited distinct patterns of mega-environment formation, winning genotypes, ranking genotypes, discriminating power, and representativeness according to the differences in planting seasons and regions. Moreover, the simultaneous selection of stable high-performance genotypes using a weighted average of absolute scores from the singular-value decomposition of the matrix of BLUPs (WAASB) and a multi-trait stability index (MTSI) revealed six recommended genotypes each for early-maturing (Manho, Namil, Unkwang, Odae 1ho, Sinunbong 1ho, and Jonong) and medium-maturing (Sobi, Cheongdam, Shinbaeg, Boramchal, Mimyeon, and Saemimyeon) cultivars, and four genotypes for medium–late-maturing cultivars (Hanmauem, Dami, Baegseolchal, and Hangangchalbyeo). The winning genotypes of each trait can be used as parents to develop regional specialty cultivars by fine-tuning favorable traits, and recommended genotypes can be utilized as elite climate-resilient parents that can aid breeders in improving yield potential and stability across the planting seasons and regions. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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13 pages, 3217 KiB

Open AccessArticle

Isolation and Expression of Transcription Factors Involved in Somatic Embryo Development by Transcriptome Analysis of Embryogenic Callus of Thuja koraiensis

by Chang Ho Ahn, Jung Yeon Han, Hyeong Soo Park, Hyun Won Yoon, Jung Won Shin, Jeong Min Seo, Hana Lee, Yeoung Ryul Kim, Saeng Geul Baek, Jae Ik Nam, Jung Min Kim and Yong Eui Choi

Horticulturae 2023, 9(2), 131; https://doi.org/10.3390/horticulturae9020131 - 19 Jan 2023

Cited by 6 | Viewed by 2291

Abstract

Thuja koraiensis Nakai (Cupressaceae) is an endangered and ecologically important conifer endemic to Korea. Previously, we established a protocol for micropropagation in T. koraiensis, which involved somatic embryogenesis from embryogenic callus of T. koraiensis. However, the molecular mechanisms underlying somatic embryogenesis [...] Read more.

Thuja koraiensis Nakai (Cupressaceae) is an endangered and ecologically important conifer endemic to Korea. Previously, we established a protocol for micropropagation in T. koraiensis, which involved somatic embryogenesis from embryogenic callus of T. koraiensis. However, the molecular mechanisms underlying somatic embryogenesis remain unclear. Herein, we performed transcriptomic analysis to identify somatic embryogenesis-related genes of T. koraiensis via Illumina RNA sequencing. We conducted de novo transcriptome assembly using a Trinity assembler, which produced 274,077 transcript contigs clustered into 205,843 transcripts (unigenes), with an average length of 825 base pairs. Of all the unigenes, 14.69%, 18.62%, and 7.4% had homologs in the Gene Ontology, NCBI Non-redundant Protein, and NCBI Nucleotide databases, respectively. Among these mRNA sequences, expression of putative embryogenesis-associated transcription factors, namely BABYBOOM (BBM), WUSCHEL-RELATED HOMEOBOX (WOX), and SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK), was analyzed during somatic embryogenesis. RT-PCR analysis revealed that TkBBM, TkWOX, and TkSERK were highly expressed in embryogenic callus and seedling roots, whereas their expression was reduced in seedling leaves. Our findings provide new insights into the roles of BBM, WOX, and SERK in somatic embryogenesis. Our results may serve as a reference for comparative transcriptome analysis in related species and further aid functional genomics studies in conifers. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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17 pages, 648 KiB

Open AccessArticle

Genetic Analysis of Zinc, Iron and Provitamin A Content in Tropical Maize (Zea mays L.)

by Enoobong Udo, Ayodeji Abe, Silvestro Meseka, Wende Mengesha and Abebe Menkir

Agronomy 2023, 13(1), 266; https://doi.org/10.3390/agronomy13010266 - 16 Jan 2023

Cited by 3 | Viewed by 2699

Abstract

Breeding maize with high contents of zinc, iron and provitamin A (PVA) could be effective in mitigating micronutrient deficiency in developing countries with a high reliance on maize-based diets. Information on the mode of inheritance of zinc, iron, PVA and grain yield (GY) [...] Read more.

Breeding maize with high contents of zinc, iron and provitamin A (PVA) could be effective in mitigating micronutrient deficiency in developing countries with a high reliance on maize-based diets. Information on the mode of inheritance of zinc, iron, PVA and grain yield (GY) would facilitate the development of varieties with enhanced contents of these nutrients. Twenty-four yellow to orange maize inbred lines and their 96 F1 hybrids generated using North Carolina Design II, were evaluated alongside four checks for two years at two locations in Nigeria. The effects of environment, hybrid and inbred line were significant for GY and contents of zinc, iron and PVA. The GY, and contents of zinc, iron and PVA of the hybrids ranged from 1.49 to 6.05 t ha⁻¹, 22.51 to 33.33 mg kg⁻¹, 20.04 to 29.65 mg kg⁻¹ and 3.55 to 15.28 µg g⁻¹, respectively. Additive gene effects controlled the accumulation of PVA and Fe, whereas both additive and non-additive gene effects controlled the inheritance of Zn and GY. Inbred lines with high general combining ability for GY and single or multiple micronutrients were identified, and could be used to develop hybrids and synthetics that combine high GY with high micronutrient content. Six hybrids combined high GY with high contents of all three micronutrients, and are recommended for further evaluation and possible release. Our study revealed the feasibility of enriching maize with multiple micronutrients without compromising grain yield. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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14 pages, 915 KiB

Open AccessArticle

Molecular Markers for Detecting Inflorescence Size of Brassica oleracea L. Crops and B. oleracea Complex Species (n = 9) Useful for Breeding of Broccoli (B. oleracea var. italica) and Cauliflower (B. oleracea var. botrytis)

by Simone Treccarichi, Hajer Ben Ammar, Marwen Amari, Riccardo Cali, Alessandro Tribulato and Ferdinando Branca

Plants 2023, 12(2), 407; https://doi.org/10.3390/plants12020407 - 15 Jan 2023

Cited by 20 | Viewed by 3372

Abstract

The gene flow from Brassica oleracea L. wild relatives to B. oleracea vegetable crops have occurred and continue to occur ordinarily in several Mediterranean countries, such as Sicily, representing an important hot spot of diversity for some of them, such as broccoli, cauliflower [...] Read more.

The gene flow from Brassica oleracea L. wild relatives to B. oleracea vegetable crops have occurred and continue to occur ordinarily in several Mediterranean countries, such as Sicily, representing an important hot spot of diversity for some of them, such as broccoli, cauliflower and kale. For detecting and for exploiting the forgotten alleles lost during the domestication processes of the B. oleracea crops, attention has been pointed to the individuation of specific markers for individuating genotypes characterized by hypertrophic inflorescence traits by the marker assisted selection (MAS) during the first plant growing phases after the crosses between broccoli (B. oleracea var. italica)/cauliflower (B. oleracea var. botrytis) with B. oleracea wild relatives (n = 9), reducing the cultivation and evaluation costs. The desired traits often found in several B. oleracea wild relatives are mainly addressed to improve the plant resistance to biotic and abiotic stresses and to increase the organoleptic, nutritive and nutraceutical traits of the products. One of the targeted traits for broccoli and cauliflower breeding is represented by the inflorescences size as is documented by the domestication processes of these two crops. Based on the previous results achieved, the numerical matrix, obtained utilizing five simple sequence repeats (SSRs), was analyzed to assess the relationship among the main inflorescence characteristics and the allelic variation of the SSRs loci analyzed (BoABI1, BoAP1, BoPLD1, BoTHL1 and PBCGSSRBo39), both for the Brassica oleracea and B. oleracea wild relatives (n = 9) accessions set. The main inflorescence morphometric characteristics, such as weight, height, diameter, shape, inflorescence curvature angle and its stem diameter, were registered before the flower anthesis. We analyzed the correlations among the allelic variation of the SSRs primers utilized and the inflorescence morphometric characteristics to individuate genomic regions stimulating the hypertrophy of the reproductive organ. The relationships found explain the diversity among B. oleracea crops and the B. oleracea complex species (n = 9) for the inflorescence size and structure. The individuated markers allow important time reduction during the breeding programs after crossing wild species for transferring useful biotic and abiotic resistances and organoleptic and nutraceutical traits to the B. oleracea crops by MAS. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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16 pages, 16876 KiB

Open AccessArticle

Comparative Analyses of 18 Complete Chloroplast Genomes from Eleven Mangifera Species (Anacardiaceae): Sequence Characteristics and Phylogenomics

by Yaxuan Xin, Wen-Bin Yu, Wichan Eiadthong, Zhengying Cao, Qishao Li, Zhenxin Yang, Wenzhi Zhao and Peiyao Xin

Horticulturae 2023, 9(1), 86; https://doi.org/10.3390/horticulturae9010086 - 9 Jan 2023

Cited by 8 | Viewed by 3040

Abstract

Mangifera plants are tropical fruits that have high economic value and scientific utility. However, the chloroplast genome characteristics and phylogenetic relationships among Mangifera species remain unclear. In this work, we reconstructed maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees using 11 newly [...] Read more.

Mangifera plants are tropical fruits that have high economic value and scientific utility. However, the chloroplast genome characteristics and phylogenetic relationships among Mangifera species remain unclear. In this work, we reconstructed maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees using 11 newly sequenced chloroplast genomes as well as six existing genomes obtained from the National Center for Biotechnology Information (NCBI) database. The chloroplast genomes all had a typical quadripartite structure, with lengths ranging from 157,368 to 158,942 bp. The GC-content in the genomes ranged from 37.8% to 37.9%. We found conserved boundaries comprised of two inverted repeats (IRs), large single-copy (LSC) regions, and small single-copy (SSC) regions. Nucleotide polymorphism analysis revealed three hypervariable regions (ycf4-cemA, rps18-rpl20, and rpl32-ndhF) in the LSC and SSC regions, which could potentially be used as DNA barcodes for Mangifera species. According to our phylogenetic analysis, Mangifera plants were clustered into three clades. Among them, all five samples of M. indica formed a monophyletic group in Clade Ⅰ. Clade Ⅱ included seven Mangifera species and could be further divided into five subclades with 100% branch support values. Clade Ⅲ included two M. persiciforma samples that formed a monophyletic group. Taken together, these results provide a theoretical basis for species determination, in addition to shedding light on the evolution of Mangifera. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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18 pages, 6506 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of NF-Y Gene Family Reveal Its Potential Roles in Stress-Resistance in Chrysanthemum

by Rongqian Hu, Mengru Yin, Aiping Song, Zhiyong Guan, Weimin Fang, Fadi Chen and Jiafu Jiang

Horticulturae 2023, 9(1), 70; https://doi.org/10.3390/horticulturae9010070 - 5 Jan 2023

Cited by 3 | Viewed by 2836

Abstract

Nuclear factor Y (NF-Y) is a class of transcription factors (TFs) with various biological functions that exist in almost all eukaryotes. In plants, heterotrimers composed of different NF-Y subunits are numerous and have different functions that can participate in the regulation of plant [...] Read more.

Nuclear factor Y (NF-Y) is a class of transcription factors (TFs) with various biological functions that exist in almost all eukaryotes. In plants, heterotrimers composed of different NF-Y subunits are numerous and have different functions that can participate in the regulation of plant growth at various stages. However, NF-Y genes have not been systematically analyzed in chrysanthemum, only involving several NF-Y members. In this study, forty-six NF-Y members were identified from the diploid species Chrysanthemum seticuspe, including eight NF-YA members, twenty-one NF-YB members, and seventeen NF-YC members. These NF-Y genes were analyzed for their physicochemical characteristics, multiple alignments, conserved motifs, gene structure, promoter elements, and chromosomal location. Phylogenetic analysis revealed that only two gene pairs in C. seticuspe underwent gene duplication events. The Ka/Ks ratios were both less than one, indicating that the two pairs underwent purifying selection. Promoter element analysis showed that multiple abiotic stress and hormone response elements were present in the CsNF-Y genes, suggesting that these genes play an important role in the response to stress, growth, and development in plants. Further validation of candidate genes in response to drought regulation using RT-qPCR demonstrated that CsNF-Y genes in C. seticuspe play an important role in drought regulation. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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16 pages, 3382 KiB

Open AccessArticle

Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese Cabbage

by Ru Li, Min Tian, Shanshan Nie and Lugang Zhang

Horticulturae 2023, 9(1), 17; https://doi.org/10.3390/horticulturae9010017 - 22 Dec 2022

Cited by 4 | Viewed by 2571

Abstract

As an important genetic improvement technique in current production practice, heterosis is widely used to enhance the productive traits of hybrid progeny from their parents. Alternative splicing (AS) analysis can be used as a method for exploring the molecular manifestations of heterosis. In [...] Read more.

As an important genetic improvement technique in current production practice, heterosis is widely used to enhance the productive traits of hybrid progeny from their parents. Alternative splicing (AS) analysis can be used as a method for exploring the molecular manifestations of heterosis. In our research, 16 hybrids and their parents were utilized to analyze the heterosis performance and AS events. Statistics of plant gross weight (PGW) showed that these hybrids had prominent heterosis, with the mid-parent heterosis values (MPV) ranging from 15.69% to 233.98%. Through pairwise comparison among the female parent, male parent, and hybrid, there were 2980–3205 AS events in each combination, with intron retention being the most common type followed by alternate 3’ splice site, alternative 5’ splice site, skipped exon, and mutually exclusive exon.There were 263–409 differential AS genes (DASGs) between the female parent and the hybrid, and 234–425 DASGs between the male parent and the hybrid in cross combinations. The DASGs were significantly enriched in 33 metabolic pathways in 16 cross combinations, and DASGs of different cross combinations were enriched in different metabolic pathways. Moreover, 76 DASGs in the strong heterosis combinations were identified and significantly enriched in the metabolic pathways related to amino acid metabolism. Further analysis revealed that most of these DASGs in amino acid metabolism were expressed differently in strong heterosis combinations. In addition, the expression levels of BraA06g014310.3C and BraA03g041700.3C in amino acid metabolism significantly correlated with PGW. These results could provide an index for future studies of the genetic and molecular mechanism of heterosis in hybrids. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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12 pages, 1040 KiB

Open AccessArticle

Genetic Resistance of Switchgrass to Rust Evaluated in a Composite Upland × Lowland Population in Lab and Field Settings

by Serge J. Edmé, Nathan A. Palmer, Gautam Sarath, Anthony A. Muhle, Rob Mitchell and Gary Yuen

Agronomy 2022, 12(12), 3137; https://doi.org/10.3390/agronomy12123137 - 10 Dec 2022

Cited by 2 | Viewed by 1770

Abstract

Maintaining low levels of rust incidence (caused by Puccinia novopanici) in switchgrass (Panicum virgatum L.) breeding populations is a priority for the USDA-ARS program engaged in improving cultivars for high biomass yield and quality. Essential to this goal is the unbiased [...] Read more.

Maintaining low levels of rust incidence (caused by Puccinia novopanici) in switchgrass (Panicum virgatum L.) breeding populations is a priority for the USDA-ARS program engaged in improving cultivars for high biomass yield and quality. Essential to this goal is the unbiased and accurate estimation of genetic parameters to predict the merits of parents and progeny. Spores of the fungus were inoculated in greenhouse-grown seedling progeny of 31 half-sib families in generation 2 (Gen 2) of a composite Summer × Kanlow population for evaluation of rust incidence on the leaves with a 0–9 rating scale. Two parents were later chosen to cross and develop a linkage mapping population as Gen 3. The Gen 2, 3, and Kanlow seedlings were transplanted into the field located near Mead, NE, in early June 2020 and laid out as a replicated row–column design with six blocks of single-row plots of five plants each. The field trial was rated in September 2021 and 2022 with a 0–4 scale. Lab and field data were subjected to univariate linear mixed models via the restricted maximum likelihood to extract the variance components needed to predict the breeding values. The additive genetic variation was substantial (p < 0.01), enough to result in high heritability estimates ranging from 0.42 ± 14 to 0.73 ± 0.09 at the individual and family mean levels. This result implies that rust resistance is under strong genetic control to use mass selection for obtaining satisfactory gains. A possible rust incidence x year interaction was detected with a Spearman correlation of breeding values of −0.38, caused by significant rank changes of the Gen 3 genotypes in 2022 (a high heat and drought year). Genetic gains were predicted to reduce rust incidence scores by at least two points on the rating scale when selecting backwards, and by one point when selecting individual candidates as parents of the next generation. Faster gains (31 and 59%) were realized relative to the second generation by respectively selecting the top 10% of the families in Gen 3 or the top 10% of genotypes within this group. Based on these results, strategies for controlling the incidence of rust will be developed to optimize gains in the other traits of economic importance. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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14 pages, 2123 KiB

Open AccessArticle

Development of Simple Sequence REPEAT Markers for Genetic Diversity Analysis Based on the cDNA Sequences of Chinese Yam (Dioscorea spp.)

by Hong Wang, Yue Wang, Lingzhi Xiong, Yingde Chen, Jiali Sun, Changdong Ouyang, Baihua Li, Hanyi Zeng, Xiaorong Chen and Mingbao Luan

Horticulturae 2022, 8(12), 1163; https://doi.org/10.3390/horticulturae8121163 - 7 Dec 2022

Cited by 3 | Viewed by 1713

Abstract

Chinese yam, with its rich taste and high nutritive value, has remained an essential part of Chinese cuisine. As China is rich in yam germplasm resources, understanding the genetic diversity of local varieties, which is important for the proper management, conservation, variety improvement, [...] Read more.

Chinese yam, with its rich taste and high nutritive value, has remained an essential part of Chinese cuisine. As China is rich in yam germplasm resources, understanding the genetic diversity of local varieties, which is important for the proper management, conservation, variety improvement, and sustainable utilization of yam germplasms, is crucial. In this study, an Illumina Hi-seq 2500 sequencing (Illumina, San Diego, CA, USA) system was used to sequence cDNA libraries of root, stem, and leaf tissues of Chinese yam; 14,450 unigenes containing SSR sites were identified from the transcriptome dataset. About half of the SSRs were mononucleotides and approximately 23% were dinucleotides and trinucleotides. In addition, 100 SSR primers were randomly designed for PCR and polymorphism verification. A total of 32 yam materials used in the study were identified by 24 primer pairs. Based on the Qinling-Huaihe River line, the northern and southern germplasms were divided into different taxa, but no clear geographical pattern was observed in the southern germplasms. The 32 germplasms were also divided into three categories using a clustering analysis, with samples in the same group possessing similar morphological characters. These 24 newly identified SSR markers can provide the basis for the genetic identification, diversity analysis, and marker-assisted selection breeding of Dioscoreaceae. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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16 pages, 2516 KiB

Open AccessArticle

Assessing the Effect of a Major Quantitative Locus for Phosphorus Uptake (Pup1) in Rice (O. sativa L.) Grown under a Temperate Region

by Ian Paul Navea, Jae-Hyuk Han, Na-Hyun Shin, O New Lee, Soon-Wook Kwon, Il-Ryong Choi and Joong Hyoun Chin

Agriculture 2022, 12(12), 2056; https://doi.org/10.3390/agriculture12122056 - 30 Nov 2022

Cited by 5 | Viewed by 2326

Abstract

Water and phosphorus (P) fertilizer are two of the most critical inputs in rice cultivation. Irrigation and chemical fertilizers are becoming limiting factors under climate change and urbanization, which is leading to significant losses in yield. The Pup1 quantitative trait locus (QTL) confers [...] Read more.

Water and phosphorus (P) fertilizer are two of the most critical inputs in rice cultivation. Irrigation and chemical fertilizers are becoming limiting factors under climate change and urbanization, which is leading to significant losses in yield. The Pup1 quantitative trait locus (QTL) confers tolerance to P starvation through enhanced early-stage root vigor and P uptake in indica rice grown in the tropics. Whether the QTL works in temperate rice genetic backgrounds grown in temperate regions remains to be elucidated. To address this question, we introgressed the Pup1 QTL into three temperate rice varieties—MS11, TR22183, and Dasanbyeo—using marker-assisted backcrossing and high-density genotyping. The selected lines all harbored the full Pup1 QTL with recurrent parent genome recovery rates ranging from 66.5% to 99.8%. Under the rainfed and P non-supplied conditions, Pup1 introgression lines did not show clear advantages over the recurrent parents in terms of vegetative growth and grain yield per plant, but exhibited enhanced yield responses to P application, except in Dasanbyeo, which a temperate rice that is genetically similar to indica. Our results suggest that Pup1 confers enhanced P uptake in temperate rice and that the efficacy of Pup1 might depend on the subspecific genomic background of the rice, whether it is japonica or indica. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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9 pages, 1031 KiB

Open AccessArticle

QTL Analysis and CAPS Marker Development Linked with Russet in Pear (Pyrus spp.)

by Yumi Kim, Sewon Oh, Hyeondae Han and Daeil Kim

Plants 2022, 11(23), 3196; https://doi.org/10.3390/plants11233196 - 22 Nov 2022

Cited by 2 | Viewed by 1849

Abstract

The fruit skin types of pear (Pyrus spp.) are divided into russet, smooth, and intermediate. One of the important traits in pear breeding programs is russet on pear fruit skin because it affects the commercial value. In the present study, a high-density [...] Read more.

The fruit skin types of pear (Pyrus spp.) are divided into russet, smooth, and intermediate. One of the important traits in pear breeding programs is russet on pear fruit skin because it affects the commercial value. In the present study, a high-density genetic linkage map of ‘Whangkeumbae’ (smooth) × ‘Minibae’ (russet) was constructed. In addition, quantitative trait loci (QTL) analysis was performed to identify russet related QTL and develop a cleaved amplified polymorphism sequence (CAPS) marker. Together with SNPs derived from Axiom Pear 70K Genotyping Array and genotyping-by-sequencing derived SNPs and SSRs generated in previous study, an integrated genetic linkage map of ‘Whangkeumbae’ × ‘Minibae’ was constructed. A total of 1263 markers were anchored in 17 linkage groups (LGs) with a total genetic distance of 1894.02 cM and an average marker density of 1.48 cM. The chromosome coverage of ‘Whangkeumbae’ × ‘Minibae’ map was improved because the SNPs derived from Axiom Pear 70K Genotyping Array were anchored. QTL analysis was performed using previous russet phenotype data evaluated with russet coverage and Hunter a. As a result of QTL analysis, russet coverage- and Hunter a-related QTLs were identified in LG8 of the ‘Whangkeumbae’ × ‘Minibae’ map, and SNPs located in the QTL region were heterozygous in the ‘Minibae’. Although the russet coverage- and Hunter a-related QTLs were commonly detected in LG8, the logarithm of odds values of SNPs in the QTL region were higher in QTL related to russet coverage than to Hunter a. The CAPS marker (CBp08ca01) was developed using an array SNP located in the russet coverage related QTL, and the genotype of CBp08ca01 showed a 1:1 ratio in ‘Whangkeumbae’ × ‘Minibae’ (χ² = 0.65, p > 0.05). ‘Whangkeumbae’ and ‘Minibae’ were thought to have rr and Rr genotypes, respectively, and the genetic factors controlling the russet formation might be located in chromosome 8. The CBp08ca01 was able to select F₁ individuals with less than 30% russet coverage. Thus, it will be a useful tool for marker-assisted selection in pears. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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13 pages, 720 KiB

Open AccessReview

Genetics, Genomics, and Breeding in Melon

by Longlan Xu, Yuhua He, Lingli Tang, Yongyang Xu and Guangwei Zhao

Agronomy 2022, 12(11), 2891; https://doi.org/10.3390/agronomy12112891 - 18 Nov 2022

Cited by 13 | Viewed by 6310

Abstract

Melon is an important horticultural crop worldwide. The high diversity of melon makes it a model plant for various different properties. Some quantitative trait loci or candidates have been discovered, but few were verified as limiting genetic transformation and genome editing systems. Identifying [...] Read more.

Melon is an important horticultural crop worldwide. The high diversity of melon makes it a model plant for various different properties. Some quantitative trait loci or candidates have been discovered, but few were verified as limiting genetic transformation and genome editing systems. Identifying new genetic resources with resistance and special fruit quality traits is imperative to develop effective and useful breeding technologies in melon. This review describes the advances in genetics, genomics, and the breeding of melon and puts forward some recommendations in these areas. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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16 pages, 2331 KiB

Open AccessArticle

Validation of Reference Genes in a Population of Blueberry (Vaccinium corymbosum) Plants Regenerated in Colchicine

by Francisca Valenzuela, Vivían D’Afonseca, Ricardo Hernández, Aleydis Gómez and Ariel D. Arencibia

Plants 2022, 11(19), 2645; https://doi.org/10.3390/plants11192645 - 8 Oct 2022

Cited by 5 | Viewed by 2498

Abstract

For the first time we report the validation of reference genes in plants from a population of blueberry (Vaccinium corymbosum) clones cultured in vitro on a colchicine-supplemented medium. Nodal segment explants of the cultivar Duke were regenerated by organogenesis under different [...] Read more.

For the first time we report the validation of reference genes in plants from a population of blueberry (Vaccinium corymbosum) clones cultured in vitro on a colchicine-supplemented medium. Nodal segment explants of the cultivar Duke were regenerated by organogenesis under different periods of colchicine 1 mg/L exposure (1, 2, 3, 5, 30 days). The clones selected for the study showed variability for phenotypic traits after 2 years of adaptation to field conditions, compared to plants of the donor genotype that were regenerated on a medium without colchicine. Vaccinium myrtillus (GAPDH) and Vaccinium macrocarpon (ATP1, NADH, RPOB and COX2) were used as reference genomes for primer design. The results show that colchicine treatments can cause genomic changes in blueberry plants. At the molecular level, exposure of plants to colchicine in early periods could promote an increase in gene expression of specific genes such as ATP1, COX2, GAPDH, MATK, NADH and RPOB. However, prolonged exposure (30 days) could decrease gene expression of the genes studied. For qPCR assays, the primers designed for ATP1, COX2, GAPDH and MATK genes showed high efficiency. In addition, the GAPDH, ATP1, NADH and COX2 genes showed high stability and could be recommended as potential reference genes for gene expression assays in Vaccinium. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 1449 KiB

Open AccessReview

Strategies for Robusta Coffee (Coffea canephora) Improvement as a New Crop in Colombia

by Luis Fernando Campuzano-Duque and Matthew Wohlgemuth Blair

Agriculture 2022, 12(10), 1576; https://doi.org/10.3390/agriculture12101576 - 29 Sep 2022

Cited by 12 | Viewed by 10514 | Correction

Abstract

Robusta coffee is mostly grown in Africa and Asia and parts of tropical America, but not yet in Colombia. The crop has potential in lowland areas of this traditional Arabica coffee producer. Compared to Arabicas grown in highland areas, the Robustas have more [...] Read more.

Robusta coffee is mostly grown in Africa and Asia and parts of tropical America, but not yet in Colombia. The crop has potential in lowland areas of this traditional Arabica coffee producer. Compared to Arabicas grown in highland areas, the Robustas have more drought and heat tolerance. However, they differ in flavor and have higher caffeine levels. With natural resistance to some of the major pests and diseases of other coffees, such as rust and berry borers, they thrive under harsh conditions. The genetic improvement of Robusta coffee requires the understanding of its genetic resources and a good breeding strategy. This review discusses the traits of interest and selection criteria for breeding and recommends methods of varietal development for Robusta in Colombia. Most of the traits of importance in breeding are quantitative and of low or intermediate heritability. Robusta is an outcrossing species and can suffer from inbreeding depression, so mass and recurrent selection are used, followed by the clonal propagation of best plants. Colombia has limited germplasm only from the Congolese group, so the SG1/Conilon and SG2 genotypes should be introduced with quarantine. Issues to address include the timing of flowering, asynchronous fruit maturation, chemical composition and sensory quality, as well as bean size. Variability for abiotic stress tolerance exists in Robusta genotypes and needs further study. New methods of breeding include hybrid development and recurrent selection. Having adapted varieties of Robusta coffee should promote production in Colombia, as it has in regions of Brazil, and would complement Arabica coffee for this traditional and major producer. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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11 pages, 4769 KiB

Open AccessArticle

Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (Zea mays L. var. ceratina)

by Vinitchan Ruanjaichon, Khin Kyawt Yin, Burin Thunnom, Kanogporn Khammona, Khundej Suriharn, Sakunkan Simla, Chalong Kerdsri, Wanchana Aesomnuk, Arweewut Yongsuwan, Naraporn Chaomueang, Nay Nay Oo, Jintana Unartngam, Siwaret Arikit, Samart Wanchana and Theerayut Toojinda

Agronomy 2022, 12(10), 2289; https://doi.org/10.3390/agronomy12102289 - 23 Sep 2022

Cited by 3 | Viewed by 3477

Abstract

Waxy maize (Zea mays L. var. ceratina) is a special type of maize characterized by a sticky texture when cooked, due to high amylopectin content in the endosperm. Waxy maize is popular in China and Southeast Asia for fresh consumption. Breeding strategies [...] Read more.

Waxy maize (Zea mays L. var. ceratina) is a special type of maize characterized by a sticky texture when cooked, due to high amylopectin content in the endosperm. Waxy maize is popular in China and Southeast Asia for fresh consumption. Breeding strategies have been used to improve the quality of waxy maize, including hybrid breeding by crossing super sweet maize and waxy maize. However, the lack of a marker has limited the efficiency of breeding for the waxy trait, especially because the waxy allele is recessive. In this study, we conducted a genome-wide association study (GWAS) in an association panel consisting of 213 inbred lines and recombinant inbred lines (RILs) of field maize and waxy maize to identify loci associated with the waxy kernel phenotype. The genotypic data were 155,768 SNPs derived from the high-density 600 K maize genotyping array for single-nucleotide polymorphisms (SNPs). The GWAS results identified the qWx9 locus on chromosome 9 (25.06–25.18 Mb) associated with the trait. Based on the most significantly associated SNP (AX-90613979, −log10(P) = 6.8)), which was located on Wx1, a MassArray marker was developed and validated in a panel of 139 maize lines containing waxy maize and sweet maize with different amylose content. The newly developed marker had a significant association with amylose content (R² value of 0.81, p < 0.001) and clearly distinguished between waxy maize and sweet maize lines that had different amylose content. This marker will be useful for maize breeding programs for the waxy trait, as well as for breeding programs for hybrid maize combining the sweetness and waxy traits. The gene-based SNP markers could aid breeders by eliminating the costs and time required to perform lengthy field trials and help to accelerate sweet maize and waxy maize breeding programs. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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18 pages, 2298 KiB

Open AccessArticle

Quantitative Trait Analysis Shows the Potential for Alleles from the Wild Species Arachis batizocoi and A. duranensis to Improve Groundnut Disease Resistance and Yield in East Africa

by Danielle A. Essandoh, Thomas Odong, David K. Okello, Daniel Fonceka, Joël Nguepjop, Aissatou Sambou, Carolina Ballén-Taborda, Carolina Chavarro, David J. Bertioli and Soraya C. M. Leal-Bertioli

Agronomy 2022, 12(9), 2202; https://doi.org/10.3390/agronomy12092202 - 16 Sep 2022

Cited by 8 | Viewed by 2684

Abstract

Diseases are the most important factors reducing groundnut yields worldwide. In East Africa, late leaf spot (LLS) and groundnut rosette disease (GRD) are the most destructive diseases of groundnut. Limited resistance is available in pure pedigree cultivated groundnut lines and novel sources of [...] Read more.

Diseases are the most important factors reducing groundnut yields worldwide. In East Africa, late leaf spot (LLS) and groundnut rosette disease (GRD) are the most destructive diseases of groundnut. Limited resistance is available in pure pedigree cultivated groundnut lines and novel sources of resistance are required to produce resistant new varieties. In this work, 376 interspecific lines from 3 different populations derived from crosses with the wild species A. duranensis, A. ipaënsis, A. batizocoi and A. valida were phenotyped for 2 seasons and across 2 locations, Serere and Nakabango, in Uganda. Several genotypes showed a higher yield, a larger seed, an earlier flowering, and similar resistance to the local cultivar checks. Genotypic data was used to construct a linkage map for the AB-QTL population involving the cross between Fleur11 and [A. batizocoi x A. duranensis]^4x. This linkage map, together with the phenotypic data was used to identify quantitative trait loci controlling disease resistance. These lines will be useful in combining good agronomic traits and stacking disease resistance to improve the groundnut crop in sub-Saharan Africa. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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20 pages, 2453 KiB

Open AccessArticle

High-Density Genetic Linkage Map Construction and QTLs Identification Associated with Four Leaf-Related Traits in Lady’s Slipper Orchids (Paphiopedilum concolor × Paphiopedilum hirsutissimum)

by Dong-Mei Li and Gen-Fa Zhu

Horticulturae 2022, 8(9), 842; https://doi.org/10.3390/horticulturae8090842 - 14 Sep 2022

Cited by 5 | Viewed by 2485

Abstract

Lady’s slipper orchids (Paphiopedilum spp.) are highly valuable within the flower industry. Recently, both Paphiopedilum concolor and Paphiopedilum hirsutissimum (2n = 2x = 26) have been widely used for hybrid parents, ornamental, and economic purposes. However, high-density genetic maps and leaf traits [...] Read more.

Lady’s slipper orchids (Paphiopedilum spp.) are highly valuable within the flower industry. Recently, both Paphiopedilum concolor and Paphiopedilum hirsutissimum (2n = 2x = 26) have been widely used for hybrid parents, ornamental, and economic purposes. However, high-density genetic maps and leaf traits related to quantitative trait loci (QTLs) in these two Paphiopedilum species have been poorly studied. Herein, an interspecific F1 population of 95 individuals was developed from the cross between P. concolor and P. hirsutissimum with contrasting leaf length (LL), leaf width (LW), leaf thickness (LT), and leaf number (LN). RNA extracted from the F1 population and their parents was subjected to high-throughput RNA sequencing. Approximately 745.59 Gb of clean data were generated, and were assembled into 349,730 transcripts and 185,089 unigenes. In total, 165,196 high-resolution polymorphic single nucleotide polymorphism (SNP) markers were initially identified. Finally, 8410 SNP markers satisfied the requirements and were used to construct a genetic map. The integrated map contained 13 linkage groups (LGs) and spanned 1616.18 cM, with an average distance of 0.19 cM between adjacent markers. QTL analysis in the F1 population identified 12 QTLs linked to four leaf-related traits, including LL, LW, LT, and LN. These QTLs by composition interval mapping, explained 11.86% to 21.58% of the phenotypic variance, and were distributed on eight LGs, but not on LGs 4, 6, 8, 12, and 13. Furthermore, 25 unigenes were identified via BLAST searches between the SNP markers in the QTL regions and our assembled transcriptome, of which 11 unigenes were enriched with 59 gene ontology (GO) terms. The information generated in this study will be useful for candidate genes for further molecular regulation studies on leaf traits, future marker-assisted selection of leaf ornamental improvement breeding, genome assembly, and comparative genome analyses. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 1828 KiB

Open AccessArticle

Detection of Candidate Loci and Genes Related to Phosphorus Efficiency at Maturity through a Genome-Wide Association Study in Soybean

by Qing Wang, Lihua Ning, Wenqing Yu, Wei Zhao, Fang Huang, Deyue Yu, Hui Wang and Hao Cheng

Agronomy 2022, 12(9), 2031; https://doi.org/10.3390/agronomy12092031 - 26 Aug 2022

Cited by 5 | Viewed by 2208

Abstract

Phosphorus (P) deficiency is one of the major factors limiting soybean production, and approximately 90% of P absorbed by plants occurs during the reproductive stage. Thus, it is important to understand the genetic mechanism underlying soybean low-P tolerance, especially in the mature period. [...] Read more.

Phosphorus (P) deficiency is one of the major factors limiting soybean production, and approximately 90% of P absorbed by plants occurs during the reproductive stage. Thus, it is important to understand the genetic mechanism underlying soybean low-P tolerance, especially in the mature period. Here, we evaluated six P-efficiency-related traits at maturity of 219 soybean accessions, namely, plant height (PH), node number of the main shoot (NN), branch number of the main shoot (BN), pod number per plant (PN), 100-seed weight (100SW), and seed yield per plant (SY), under normal-phosphorus (NP) and low-phosphorus (LP) conditions across two environments. Then, a genome-wide association study (GWAS) in conjunction with a high-density NJAU 355 K SoySNP array was performed. As a result, 27 P-efficiency-related single nucleotide polymorphisms (SNPs) were identified. Furthermore, two repeated SNPs, AX-93897192 and AX-93897200, located on chromosome 19 that were associated with both PH and NN were considered as stable SNPs associated with P deficiency, and the candidate gene GmABCG39 was identified. This work will be helpful in breeding high-P-efficiency soybean varieties. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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11 pages, 1115 KiB

Open AccessArticle

Identification of Novel Broad-Spectrum Leaf Rust Resistance Sources from Khapli Wheat Landraces

by K. Raghunandan, Jatin Tanwar, Shivanagouda N. Patil, Ajay Kumar Chandra, Sandhya Tyagi, Priyanka Agarwal, Niharika Mallick, Niranjana Murukan, Jyoti Kumari, Tanmaya Kumar Sahu, Sherry R. Jacob, Atul Kumar, Suresh Yadav, Sneha Nyamgoud, Vinod, Amit Kumar Singh and Shailendra Kumar Jha

Plants 2022, 11(15), 1965; https://doi.org/10.3390/plants11151965 - 28 Jul 2022

Cited by 11 | Viewed by 2495

Abstract

Wheat leaf rust caused by Puccinia triticina Eriks is an important disease that causes yield losses of up to 40% in susceptible varieties. Tetraploid emmer wheat (T. turgidum ssp. Dicoccum), commonly called Khapli wheat in India, is known to have [...] Read more.

Wheat leaf rust caused by Puccinia triticina Eriks is an important disease that causes yield losses of up to 40% in susceptible varieties. Tetraploid emmer wheat (T. turgidum ssp. Dicoccum), commonly called Khapli wheat in India, is known to have evolved from wild emmer (Triticum turgidum var. dicoccoides), and harbors a good number of leaf rust resistance genes. In the present study, we are reporting on the screening of one hundred and twenty-three dicoccum wheat germplasm accessions against the leaf rust pathotype 77-5. Among these, an average of 45.50% of the germplasms were resistant, 46.74% were susceptible, and 8.53% had mesothetic reactions. Further, selected germplasm lines with accession numbers IC138898, IC47022, IC535116, IC535133, IC535139, IC551396, and IC534144 showed high level of resistance against the eighteen prevalent pathotypes. The infection type varied from “;”, “;N”, “;N1” to “;NC”. PCR-based analysis of the resistant dicoccum lines with SSR marker gwm508 linked to the Lr53 gene, a leaf rust resistance gene effective against all the prevalent pathotypes of leaf rust in India and identified from a T. turgidum var. dicoccoides germplasm, indicated that Lr53 is not present in the selected accessions. Moreover, we have also generated 35K SNP genotyping data of seven lines and the susceptible control, Mandsaur Local, to study their relationships. The GDIRT tool based on homozygous genotypic differences revealed that the seven genotypes are unique to each other and may carry different resistance genes for leaf rust. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 2768 KiB

Open AccessArticle

Genetic Mapping and Identification of the Gibberellin 3-Oxidase Gene GA3ox Leading to a GA-Deficient Dwarf Phenotype in Pumpkin (Cucurbita moschata D.)

by Ziyang Min, Xinjun Hu, Xiaoxia Han, Yongqi Li, Jiajia Li, Duanhua Wang, Longjun Sun and Xiaowu Sun

Agronomy 2022, 12(8), 1779; https://doi.org/10.3390/agronomy12081779 - 28 Jul 2022

Cited by 6 | Viewed by 2676

Abstract

Plant height is an important indicator in the ideal plant model and contributes to optimizing yield and lodging resistance. The emergence of a dwarfing phenotype provides an opportunity for plant height improvement. In a previous study, we identified a dwarf mutant Si1 in [...] Read more.

Plant height is an important indicator in the ideal plant model and contributes to optimizing yield and lodging resistance. The emergence of a dwarfing phenotype provides an opportunity for plant height improvement. In a previous study, we identified a dwarf mutant Si1 in pumpkin (Cucurbita moschata D.) obtained by ethyl methane sulfonate (EMS) mutagenesis of the inbred line N87. Phenotype identification for Si1 revealed a decrease in cell size and shorter internodes than those of wild type. Genetic analysis revealed that the dwarf mutant trait was controlled by a single recessive gene, CmaSI1. By bulked segregant analysis (BSA) and subsequent fine mapping, we mapped the CmaSI1 locus to a 463 kb region on chromosome 8 that contained 28 annotated genes in the F₂ population. Only one nonsynonymous single nucleotide polymorphism (SNP) in CmoCh08G006170 was obtained according to whole-genome resequencing of the two parents. CmoCh08G006170, a homolog of Arabidopsis gibberellin 3-beta hydroxylase (GA3ox), is a key enzyme in the regulation of bioactive gibberellins (GAs). RNA-seq analysis and qRT-PCR showed that the expression level of CmoCh08G006170 in stems of Si1 was changed compared with that of wild type. The dwarf phenotype could be restored by exogenous GA₃ treatment, suggesting that Si1 is a GA-deficient mutant. The above results demonstrated that CmoCh08G006170 may be the candidate gene controlling the dwarf phenotype. This study provides an important theoretical basis for the genetic regulation of vine length and crop breeding in pumpkin. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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16 pages, 2351 KiB

Open AccessArticle

Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids by indica-japonica Hybridization in Rice

by Jayanth Kallugudi, Vikram Jeet Singh, Kunnumal Kurungara Vinod, Subbaiyan Gopala Krishnan, Shekharappa Nandakumar, Brijesh Kumar Dixit, Ranjith Kumar Ellur, Haritha Bollinedi, Mariappan Nagarajan, Amit Kumar, Mridul Chakraborti, Rakesh Kumar Seth, Tapan Kumar Mondal, Prolay Kumar Bhowmick and Ashok Kumar Singh

Plants 2022, 11(15), 1930; https://doi.org/10.3390/plants11151930 - 26 Jul 2022

Cited by 7 | Viewed by 2289

Abstract

The exploitation of heterosis through intersubspecific hybridisation between indica and japonica has been a major breeding target in rice, but is marred by the cross incompatibility between the genomes. Wide compatibility (WC) is a triallelic system at the S5 locus on chromosome 6 [...] Read more.

The exploitation of heterosis through intersubspecific hybridisation between indica and japonica has been a major breeding target in rice, but is marred by the cross incompatibility between the genomes. Wide compatibility (WC) is a triallelic system at the S5 locus on chromosome 6 that ensures the specificity of hybridisation within and between indica and japonica. The S5n allele that favours intercrossing is sparsely distributed in the rice gene pool and therefore warrants identification of diverse WC sources to develop superior intersubspecific hybrids. In this study, we have identified several novel WC sources through the marker-assisted screening of a large set of 950 rice genotypes. Seventeen percent of the genotypes carried S5n, which fell into two subpopulations. The WC genotypes showed wide phenotypic and genotypic variability, including both indica and japonica lines. Based on phenotypic performance, the WC varieties were grouped into three clusters. A subset of 41 WC varieties was used to develop 164 hybrids, of which WC/japonica hybrids showed relative superiority over WC/indica hybrids. The multilocation evaluation of hybrids indicated that hybrids derived from WC varieties, such as IRG137, IRG143, OYR128, and IRGC10658, were higher yielding across all the three different locations. Most of the hybrids showed the stability of performance across locations. The identified diverse set of wide compatible varieties (WCVs) can be used in the development of intersubspecific hybrids and also for parental line development in hybrid rice breeding. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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17 pages, 5226 KiB

Open AccessArticle

Genome-Wide Identification and Expression Pattern Analysis of the TCP Gene Family in Radish (Raphanus sativus L.)

by Yi Mei, Zhe Liu, Jiaqiu Zheng, Weiwei Wang, Yanxia Zu, Yongcheng Wu, Lina Zhang, Ruchao Feng and Feng Shen

Horticulturae 2022, 8(7), 656; https://doi.org/10.3390/horticulturae8070656 - 19 Jul 2022

Cited by 1 | Viewed by 2489

Abstract

TCP transcription factors are a unique transcription family in higher plants, and play important roles in plant development, responses to environmental stresses and phytohormones. Radish is an important crop and widely cultivated worldwide. However, genome-wide identification and expression analysis of TCP family in [...] Read more.

TCP transcription factors are a unique transcription family in higher plants, and play important roles in plant development, responses to environmental stresses and phytohormones. Radish is an important crop and widely cultivated worldwide. However, genome-wide identification and expression analysis of TCP family in radish has not been reported yet. In this study, 32 RsTCP genes were identified from the whole genome. Phylogenetic analysis showed that the RsTCP family can be divided into two major groups and three subgroups, namely Class I (PCF), Class II (CIN), and Class II (CYC/TB1). Chromosome mapping showed that 32 genes were distributed on all nine chromosomes of radish. Transcriptome data indicated that the transcription of RsTCP genes differed between tissues and developmental stages. Multiple phytohormone-related cis-acting elements in the promoter region of RsTCPs and several post-translational modification sites in RsTCP protein sequences were identified. The real-time quantitative PCR (RT-qPCR) analysis indicated that several RsTCP genes changed significantly in response to the treatments, including low temperature, drought, salt, gibberellin (GA₃), and abscisic acid. Among them, RsTCP16 showed significantly higher levels in leaves than in other radish tissues, and the transcription of RsTCP16 was significantly upregulated under the five treatments, especially during low temperature, salt shock, and GA₃ response, suggesting that RsTCP16 could be involved in the development of radish leaves and the response to stress. In summary, these results provided a basis for further exploring the molecular mechanism of RsTCP genes in radish. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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13 pages, 1552 KiB

Open AccessArticle

Characterization of the NGP4A Gene in Regulating Grain Number Per Panicle of Rice (Oryza sativa L.)

by Yanhong Chen, Wanling Yang, Minmin Zhao, Gumu Ding, Yi Zhou, Jiankun Xie and Fantao Zhang

Agronomy 2022, 12(7), 1549; https://doi.org/10.3390/agronomy12071549 - 28 Jun 2022

Cited by 21 | Viewed by 2199

Abstract

Grain number per panicle (GNPP) is a major factor influencing rice yield (Oryza sativa L.). However, the molecular mechanisms of GNPP determination are not well understood. A rice GNPP mutant, ngp4a, was isolated from an ethyl methanesulfonate-mutagenized rice library of japonica Nipponbare. [...] Read more.

Grain number per panicle (GNPP) is a major factor influencing rice yield (Oryza sativa L.). However, the molecular mechanisms of GNPP determination are not well understood. A rice GNPP mutant, ngp4a, was isolated from an ethyl methanesulfonate-mutagenized rice library of japonica Nipponbare. ngp4a produced fewer grains than wild-type plants at maturity as the number of secondary branches decreased significantly. The mutant phenotype of ngp4a was controlled by a recessive nuclear gene, which was fine-mapped into a 155.2 kb region on chromosome 4. One GNPP-related gene, Gnp4/LAX2 (LOC_Os04g32510), was found in the mapped region. The deletion of 3-bp nucleotides in the first exon of NGP4A resulted in a threonine residue loss. The mutation in NGP4A was responsible for the mutant phenotype of ngp4a. These results suggest that NGP4A is a new allele for Gnp4 and LAX2, while the mutant phenotype and underlying causation differed. Notably, transcriptome analysis revealed that NGP4A could regulate GNPP determination through the phenylpropanoid biosynthesis and mitogen-activated protein kinase signaling pathways. Our results further elucidated the vital roles of Gnp4/LAX2 in GNPP determination, providing a new genetic resource and theoretical basis to further explore the molecular mechanisms of GNPP in rice. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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14 pages, 1836 KiB

Open AccessArticle

Genetic Diversity and Structure of Persian Walnut (Juglans regia L.) in Pakistan: Implications for Conservation

by Ephie A. Magige, Peng-Zhen Fan, Moses C. Wambulwa, Richard Milne, Zeng-Yuan Wu, Ya-Huang Luo, Raees Khan, Hong-Yu Wu, Hai-Ling Qi, Guang-Fu Zhu, Debabrata Maity, Ikramullah Khan, Lian-Ming Gao and Jie Liu

Plants 2022, 11(13), 1652; https://doi.org/10.3390/plants11131652 - 22 Jun 2022

Cited by 21 | Viewed by 4037

Abstract

Persian (Common) walnut (Juglans regia L.) is a famous fruit tree species valued for its nutritious nuts and high-quality wood. Although walnut is widely distributed and plays an important role in the economy and culture of Pakistan, the genetic diversity and structure [...] Read more.

Persian (Common) walnut (Juglans regia L.) is a famous fruit tree species valued for its nutritious nuts and high-quality wood. Although walnut is widely distributed and plays an important role in the economy and culture of Pakistan, the genetic diversity and structure of its populations in the country remains poorly understood. Therefore, using 31 nuclear microsatellites, we assessed the genetic diversity and population structure of 12 walnut populations sampled across Pakistan. We also implemented the geostatistical IDW technique in ArcGIS to reveal “hotspots” of genetic diversity. Generally, the studied populations registered relatively low indices of genetic diversity (N_A = 3.839, H_O = 0.558, U_HE = 0.580), and eight populations had positive inbreeding coefficient (F_IS) values. Low among-population differentiation was indicated by AMOVA, pairwise F_ST and D_C. STRUCTURE, PCoA and neighbor joining (NJ) analysis revealed a general lack of clear clustering in the populations except that one population in Upper Dir was clearly genetically distinct from the rest. Furthermore, the Mantel test showed no correlation between the geographic and genetic distance (r = 0.14, p = 0.22), while barrier analysis suggested three statistically significant genetic barriers. Finally, the spatial interpolation results indicated that populations in Ziarat, Kashmir, Dir, Swat, Chitral, and upper Dir had high intrapopulation genetic diversity, suggesting the need to conserve populations in those areas. The results from this study will be important for future breeding improvement and conservation of walnuts in Pakistan. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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18 pages, 922 KiB

Open AccessArticle

Improving the Carotenoid Content in Maize by Using Isonuclear Lines

by Roxana Elena Calugar, Edward Muntean, Andrei Varga, Carmen Daniela Vana, Voichita Virginia Has, Nicolae Tritean and Loredana Anca Ceclan

Plants 2022, 11(13), 1632; https://doi.org/10.3390/plants11131632 - 21 Jun 2022

Cited by 7 | Viewed by 2090

Abstract

Carotenoids are important biologically active compounds in the human diet due to their role in maintaining a proper health status. Maize (Zea mays L.) is one of the main crops worldwide, in terms of production quantity, yield and harvested area, as it [...] Read more.

Carotenoids are important biologically active compounds in the human diet due to their role in maintaining a proper health status. Maize (Zea mays L.) is one of the main crops worldwide, in terms of production quantity, yield and harvested area, as it is also an important source of carotenoids in human nutrition worldwide. Increasing the carotenoid content of maize grains is one of the major targets of the research into maize breeding; in this context, the aim of this study was to establish the influence of some fertile cytoplasm on the carotenoid content in inbred lines and hybrids. Twenty-five isonuclear lines and 100 hybrids were studied for the genetic determinism involved in the transmission of four target carotenoids: lutein, zeaxanthin, β-cryptoxanthin and β-carotene. The analysis of carotenoids was carried out using high performance liquid chromatography using a Flexar system with UV-VIS detection. The obtained data revealed that the cytoplasms did not have a significant influence on the carotenoid content of the inbred lines; larger differences were attributed to the cytoplasm × nucleus interaction. For hybrids, the cytoplasmic nuclear interactions have a significant influence on the content of lutein, zeaxanthin and β-cryptoxanthin. For the cytoplasm × nucleus × tester interactions, significant differences were identified for all traits. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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13 pages, 352 KiB

Open AccessReview

Haploid Induction in Tomato (Solanum lycopersicum L.) via Gynogenesis

by Ivan Maryn Marin-Montes, Juan Enrique Rodríguez-Pérez, Alejandrina Robledo-Paz, Eulogio de la Cruz-Torres, Aureliano Peña-Lomelí and Jaime Sahagún-Castellanos

Plants 2022, 11(12), 1595; https://doi.org/10.3390/plants11121595 - 17 Jun 2022

Cited by 10 | Viewed by 5163

Abstract

The generation of new hybrid varieties of tomato (Solanum lycopersicum L.) is the most widely used breeding method for this species and requires at least seven self-fertilization cycles to generate stable parent lines. The development of doubled haploids aims at obtaining completely [...] Read more.

The generation of new hybrid varieties of tomato (Solanum lycopersicum L.) is the most widely used breeding method for this species and requires at least seven self-fertilization cycles to generate stable parent lines. The development of doubled haploids aims at obtaining completely homozygous lines in a single generation, although, to date, routine commercial application has not been possible in this species. In contrast, obtaining doubled haploid lines via gynogenesis has been successfully implemented in recalcitrant crops such as melon, cucumber, pumpkin, loquat and walnut. This review provides an overview of the requirements and advantages of gynogenesis as an inducer of haploidy in different agricultural crops, with the purpose of assessing the potential for its application in tomato breeding. Successful cases of gynogenesis variants involving in vitro culture of unfertilized ovules, use of ⁶⁰Co-irradiated pollen, in vivo haploid inducers and wide hybridization are presented, suggesting that these methodologies could be implemented in tomato breeding programs to obtain doubled haploids. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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18 pages, 2448 KiB

Open AccessArticle

Comparative Genetic Diversity Analysis for Biomass Allocation and Drought Tolerance in Wheat

by Kwame W. Shamuyarira, Hussein Shimelis, Isack Mathew, Admire Shayanowako, Rebecca Zengeni and Vincent Chaplot

Agronomy 2022, 12(6), 1457; https://doi.org/10.3390/agronomy12061457 - 17 Jun 2022

Cited by 1 | Viewed by 2698

Abstract

Genetic diversity is invaluable in developing climate-smart and drought-adapted wheat varieties. The aim of this study was to determine the extent of genetic variation present in wheat germplasm collections for biomass allocation and drought tolerance based on complementary phenotypic and root attributes and [...] Read more.

Genetic diversity is invaluable in developing climate-smart and drought-adapted wheat varieties. The aim of this study was to determine the extent of genetic variation present in wheat germplasm collections for biomass allocation and drought tolerance based on complementary phenotypic and root attributes and high-density single nucleotide polymorphism (SNP) markers to select breeding parents. A total of 97 bread wheat (Triticum aestivum L.) genotypes were evaluated in field and greenhouse trials under drought-stressed and non-stressed conditions. The molecular variance analysis showed that the intrapopulation variance was very high at 99%, with a small minimal inter-population variance (1%). The genetic distance, polymorphic information content and expected heterozygosity were 0.20–0.88, 0.24–1.00 and 0.29–0.58, respectively. The cluster analysis based on SNP data showed that 44% and 28% of the assessed genotypes maintained their genetic groups when compared to hierarchical clusters under drought-stressed and non-stressed phenotypic data, respectively. The joint analysis using genotypic and phenotypic data resolved three heterotic groups and allowed the selection of genotypes BW140, BW152, BW157, BW162, LM30, LM47, LM48, LM52, LM54 and LM70. The selected genotypes were the most genetically divergent with high root biomass and grain yield and are recommended for production or breeding. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 4904 KiB

Open AccessArticle

Cloning and Functional Analysis of NtMYB9 in ‘Jinzhanyintai’ of Narcissus tazetta var. chinensis

by Keke Fan, Yanjun Ma, Yanting Chang, Xiaomeng Hu, Wenbo Zhang, Yayun Deng, Mengsi Xia, Zehui Jiang and Tao Hu

Horticulturae 2022, 8(6), 528; https://doi.org/10.3390/horticulturae8060528 - 15 Jun 2022

Cited by 1 | Viewed by 2147

Abstract

Narcissus tazetta var. chinensis M.Roem. (Chinese Narcissus) is a traditional and famous flower in China, and its corona shows a transition from green to yellow with the opening of flowers, which is of great ornamental value. To investigate the molecular mechanism of the [...] Read more.

Narcissus tazetta var. chinensis M.Roem. (Chinese Narcissus) is a traditional and famous flower in China, and its corona shows a transition from green to yellow with the opening of flowers, which is of great ornamental value. To investigate the molecular mechanism of the corona color-forming in the Chinese Narcissus, in this study, a MYB gene was screened from the transcriptome of the corona by bioinformatics analysis methods, named NtMYB9. The expression level of the NtMYB9 gene was significantly higher in the corona than in the tepal, filament, ovary and leaf, and reached the highest level at the fourth period of complete coloration of the corona. The full-length sequence of the NtMYB9 coding region was cloned using the corona cDNA as a template. Sequence analysis revealed that NtMYB9 protein contained R2 and R3 domains, phylogenetic tree analysis showed that the NtMYB9 protein was most closely related to flavonol activators. Subcellular localization showed that NtMYB9 was localized in the nucleus. The overexpression of NtMYB9 gene into tobacco leaves and the expression level of seven enzyme genes related to the flavonoid biosynthesis pathway were significantly up-regulated. The transient transformation of Petunia × hybrida (Petunia) and Phalaenopsis aphrodite (Phalaenopsis) significantly revealed that the NtMYB9 gene could turn flowers yellow. These results suggest that the NtMYB9 gene is involved in the positive regulation of flavonoid biosynthesis in the Chinese Narcissus and may promote the synthesis of flavonols. In conclusion, these findings provide a valuable resource for further studies on the regulatory mechanism of the flavonoid biosynthesis pathway, and they are also beneficial to the molecular breeding of Chinese Narcissus. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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14 pages, 2932 KiB

Open AccessArticle

Genome-Wide Characterization of Laccase Gene Family from Turnip and Chinese Cabbage and the Role in Xylem Lignification in Hypocotyls

by Jing Wen, Yuanyuan Liu, Shuda Yang, Yongping Yang and Chuntao Wang

Horticulturae 2022, 8(6), 522; https://doi.org/10.3390/horticulturae8060522 - 15 Jun 2022

Cited by 3 | Viewed by 2509

Abstract

The turnip and the Chinese cabbage belong to the Brassica rapa subspecies, yet they have evolved marked differences in morphology. The turnip has a distinct swelled taproot, while the Chinese cabbage has a big leafy head. The turnip’s taproot is developed mainly by [...] Read more.

The turnip and the Chinese cabbage belong to the Brassica rapa subspecies, yet they have evolved marked differences in morphology. The turnip has a distinct swelled taproot, while the Chinese cabbage has a big leafy head. The turnip’s taproot is developed mainly by the hypocotyl. To explore the taproot formation, we firstly compared the vascular structure of the hypocotyl during the early developmental stages of the turnip and the Chinese cabbage, finding that there were observable differences in the number of xylem cells and the cell-wall lignification in the hypocotyl vascular tissues after the transition from primary to secondary growth. Laccases (LAC) play an important role in lignification by polymerizing monolignols in the cell wall, however, it is not clear whether differences in the lignification levels in the hypocotyl xylem cell walls are related to the genetic variations of the LAC gene family, between the turnip and the Chinese cabbage. Therefore, we systematically characterized the LAC genes from the turnip and the Chinese cabbage, and 27 LAC genes were identified in each. These LAC genes can be divided into six groups, and each LAC in the turnip is closely adjacent to that in the Chinese cabbage. Gene structure, conserved motif, and chromosomal localization were highly conserved between the turnip and the Chinese cabbage. We also compared the expression pattern of the laccases in the different tissues and hypocotyl’s early development stage, and the results clearly showed the different profiles between the turnip and the Chinese cabbage. Following a comprehensive analysis of these results, we predicted that LAC17.1 and LAC17.3 are two candidate genes that participate in the regulation of lignin synthesis during taproot formation. Our results provide a valuable clue for uncovering the regulation mechanism of the lower lignification level in the turnip’s hypocotyl and fundamental information for further studies of the LAC gene family in Brassica rapa. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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13 pages, 552 KiB

Open AccessArticle

Genetic Analysis of Fruit Traits in Wolfberry (Lycium L.) by the Major Gene Plus Polygene Model

by Xiaoyue Ren, Haoxia Li, Yue Yin, Linyuan Duan, Yajun Wang, Xiaojie Liang, Ru Wan, Ting Huang, Bo Zhang, Wanpeng Xi, Wei An and Jianhua Zhao

Agronomy 2022, 12(6), 1403; https://doi.org/10.3390/agronomy12061403 - 11 Jun 2022

Cited by 5 | Viewed by 2055

Abstract

The fruit diameter (FD), fruit length (FL), fruit peduncle length (FPL), fruit weight (FW) and fruit index (FI, FL/FD) are important quantitative traits in wolfberry fruit, and also one of the most important goals of variety breeding; however, the inheritance of these traits [...] Read more.

The fruit diameter (FD), fruit length (FL), fruit peduncle length (FPL), fruit weight (FW) and fruit index (FI, FL/FD) are important quantitative traits in wolfberry fruit, and also one of the most important goals of variety breeding; however, the inheritance of these traits has not been studied to date. In this study, the genetic analysis of these five fruit traits was undertaken for four pairs of F₁ hybrid populations (CI, CII, CIII and CIV) using the major gene and polygene mixed inheritance model. The results showed that the five fruit traits exhibited super-parent segregation in four hybrid combinations, and five traits of progeny with abundant genetic diversity. In CII, CIII and CIV, the mid-parental heterosis ratio (RH_m%) of FD, FL, FPL and FI was greater than 0 with positive heterosis. FD, FL and FI in CI, CII and CIII were controlled by one pair of additive-dominant major genes (A-1). However, in CIV, FD was controlled by two pairs of additive-dominant alleles (B-6) and FL was best fitted to polygenic control (A-0). In addition, it was found that FPL in CI, CIII and CIV was controlled by one or two pairs of additive-dominant major genes (A-1, B-6, B-1), and FW in CIII and CIV was also controlled by one or two pairs of additive-dominant major gene controls (A-1, B-1). For FD, FPL, FW and FI in CIII and FPL and FW in CII, the major genes heritability was over 50%, indicating that these traits are affected by both genes and the environment, and that the selection of these traits should be considered in later generations due to the large effect of environmental factors. Therefore, this study provides a theoretical basis for QTL mapping and early selection of hybrid breeding of Lycium fruits. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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17 pages, 3478 KiB

Open AccessReview

The Structure, Function, and Regulation of Starch Synthesis Enzymes SSIII with Emphasis on Maize

by Guowu Yu, Yuanzhu Gaoyang, Lun Liu, Noman Shoaib, Yawen Deng, Na Zhang, Yangping Li and Yubi Huang

Agronomy 2022, 12(6), 1359; https://doi.org/10.3390/agronomy12061359 - 3 Jun 2022

Cited by 9 | Viewed by 6235

Abstract

Starch biosynthesis is a complex and highly controlled process that requires coordinated activities among multiple enzymes. Starch synthase III (SSIII) is the largest protein in the starch synthase complex and its function is to lengthen long-chain amylopectin in starch synthesis. It potentially affects [...] Read more.

Starch biosynthesis is a complex and highly controlled process that requires coordinated activities among multiple enzymes. Starch synthase III (SSIII) is the largest protein in the starch synthase complex and its function is to lengthen long-chain amylopectin in starch synthesis. It potentially affects the activity of other key enzymes in starch synthesis through protein–protein interactions; therefore, its function and regulation play a predominant role in starch synthesis. In this review, we summarized the main research of SSIII including its biochemical characteristics, structural features, expression atlas, and regulation means. Structural features and expressional analysis indicated that SSIIIa is the main functional protein in maize endosperm rather than SSIIIb-a and SSIIIb-b, even though they are similar in the tertiary structures. The regulation investigation of SSIIIa showed that there are 13 transcription factors that control the transcription of SSIIIa. Interaction network analysis showed that SSIIIa could be involved with ten other key enzymes in starch synthesis. In conclusion, this review considerably extends our understanding of SSIII and provides the theoretical basis for improving starch synthesis by SSIII in maize. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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12 pages, 3655 KiB

Open AccessArticle

An Identification and Expression Analysis of the ABCG Genes Related to Benzaldehyde Transportation among Three Prunus Species

by Ruijie Hao, Jun Chang, Chen Qiu and Shuting Yang

Horticulturae 2022, 8(6), 475; https://doi.org/10.3390/horticulturae8060475 - 26 May 2022

Cited by 4 | Viewed by 2251

Abstract

The plants of Prunus mostly bloom in early spring, and the flowers of various species possess their individual floral scent characteristics; Prunus mume, especially, can volatilize a large amount of benzenoid compounds into the air during the flowering phase. In order to [...] Read more.

The plants of Prunus mostly bloom in early spring, and the flowers of various species possess their individual floral scent characteristics; Prunus mume, especially, can volatilize a large amount of benzenoid compounds into the air during the flowering phase. In order to elucidate the molecular basis of the differences in the volatile capacity of aromatic substances among Prunus flowers, the endogenous and the headspace volatile components and the expression of ABCG genes were studied among P. mume, P. armeniaca, and P. persica. We detected the floral components in the three species by gas chromatography-mass spectrometry (GC-MS), and we found that benzaldehyde was the key component. Meanwhile, the volatilization efficiency of benzaldehyde in P. mume and P. armeniaca were much higher than that in P. persica. Furthermore, 130, 135, and 133 ABC family members from P. mume, P. armeniaca, and P. persica were identified, respectively. WGCNA analysis demonstrated that candidate ABCG genes were positively correlated with benzaldehyde volatilization efficiency. Moreover, quantitative Real-time PCR indicated that ABCG17 was more likely to be involved in the transmembrane transport of benzaldehyde. This study aimed to provide a theoretical basis for elucidating the transmembrane transport of benzaldehyde and to further the valuable information for fragrant flower breeding in Prunus. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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21 pages, 4019 KiB

Open AccessArticle

Genetic Mapping to Detect Stringent QTLs Using 1k-RiCA SNP Genotyping Platform from the New Landrace Associated with Salt Tolerance at the Seedling Stage in Rice

by Sheikh Maniruzzaman, Mohammad Akhlasur Rahman, Mehfuz Hasan, Mohammad Golam Rasul, Abul Hossain Molla, Hasina Khatun and Salma Akter

Plants 2022, 11(11), 1409; https://doi.org/10.3390/plants11111409 - 26 May 2022

Cited by 5 | Viewed by 2985

Abstract

Rice is the world’s most important food crop, providing the daily calorie intake for more than half of the world’s population. Rice breeding has always been preoccupied with maximizing yield potential. However, numerous abiotic factors, such as salt, cold, drought, and heat, significantly [...] Read more.

Rice is the world’s most important food crop, providing the daily calorie intake for more than half of the world’s population. Rice breeding has always been preoccupied with maximizing yield potential. However, numerous abiotic factors, such as salt, cold, drought, and heat, significantly reduce rice productivity. Salinity, one of the major abiotic stresses, reduces rice yield worldwide. This study was conducted to determine new quantitative trait loci (QTLs) that regulate salt tolerance in rice seedlings. One F_2:3 mapping population was derived from a cross between BRRI dhan49 (a popular but sensitive rainfed rice variety) and Akundi (a salt-tolerant rice landrace in Bangladesh used as a donor parent). The 1k-Rice Custom Amplicon (1k-RiCA) single-nucleotide polymorphism (SNP) markers were used to genotype this mapping population. After removing segregation distortion and monomorphic markers, 884 SNPs generated a 1526.8 cM-long genetic linkage map with a mean marker density of 1.7 cM for the 12 linkage groups. By exploiting QGene and ICIM-ADD, a sum of 15 QTLs for nine traits was identified in salt stress on seven chromosomes. Four important genomic loci were identified (qSES1, qSL1, qSUR1 and qRL1) on chromosome 1. Out of these 15 QTLs, 14 QTLs are unique, as no other study has mapped in the same chromosomal location. We also detected 15 putative candidate genes and their functions. The ICIM-EPI approach identified 43 significant pairwise epistasis interactions between regions associated with and unassociated with QTLs. Apart from more well-known donors, Akundi serves as an important new donor source for global salt tolerance breeding initiatives, including Bangladesh. The introgression of the novel QTLs identified in this study will accelerate the development of new salt-tolerant varieties that are highly resistant to salt stress using marker-enabled breeding. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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5 pages, 473 KiB

Open AccessCommunication

Evidence That 2n Eggs Explain Partial Hybrids between Medicago sativa and Medicago arborea

by Edwin Bingham and John Irwin

Plants 2022, 11(10), 1380; https://doi.org/10.3390/plants11101380 - 23 May 2022

Cited by 2 | Viewed by 1939

Abstract

Selected genotypes of alfalfa (Medicago sativa) produce partial hybrids in sexual crosses with Medicago arborea, as reported in Plants (2013). The hybrids contain mostly alfalfa DNA and traits, but also contain DNA and traits from M. arborea. It was [...] Read more.

Selected genotypes of alfalfa (Medicago sativa) produce partial hybrids in sexual crosses with Medicago arborea, as reported in Plants (2013). The hybrids contain mostly alfalfa DNA and traits, but also contain DNA and traits from M. arborea. It was proposed in 2008 that the partial hybrids could be explained by fertilization of 2n eggs in alfalfa by normal pollen from M. arborea, followed by partial loss of M. arborea chromosomes during embryogenesis. In this paper, we confirm the presence of 2n eggs in the first alfalfa parents that produced hybrids. The test for 2n eggs involved pollinating 4x alfalfa with pollen from 8x alfalfa. The production of 8x progeny in the cross proved that selected alfalfa parents produced 2n eggs. Thus, 2n eggs appear to explain how the partial hybrids (hereafter hybrids) contain mostly alfalfa DNA and traits. However, two of the six alfalfa plants that did not hybridize with M. arborea also had 2n eggs. Thus, although 2n eggs explain the alfalfa content of hybrids, 2n eggs are not the only factor involved in weakening the hybridization barrier, and in transferring genes to alfalfa from M. arborea. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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22 pages, 2740 KiB

Open AccessArticle

Combining Ability and Heterotic Patterns of Tropical Early-Maturing Maize Inbred Lines under Individual and Combined Heat and Drought Environments

by Alimatu Sadia Osuman, Baffour Badu-Apraku, Beatrice Elohor Ifie, Charles Nelimor, Pangirayi Tongoona, Ebenezer Obeng-Bio, Benjamin Karikari and Eric Yirenkyi Danquah

Plants 2022, 11(10), 1365; https://doi.org/10.3390/plants11101365 - 20 May 2022

Cited by 8 | Viewed by 2735

Abstract

Information on combining ability and heterotic patterns of multiple stress-tolerant inbred lines are fundamental prerequisites for devising appropriate breeding strategies for the development of climate-resilient maize hybrids. In the present study, we evaluated 150 single cross hybrids derived from the North Carolina Design [...] Read more.

Information on combining ability and heterotic patterns of multiple stress-tolerant inbred lines are fundamental prerequisites for devising appropriate breeding strategies for the development of climate-resilient maize hybrids. In the present study, we evaluated 150 single cross hybrids derived from the North Carolina Design II (NCD II) along with six commercial checks under terminal drought stress (TDS), heat stress (HS), and combined drought and heat stress (CHDS)conditions. The objectives of the study were to: (i) determine the combining ability of the inbred lines and identify the best testers across the stresses; (ii) classify the inbred lines into heterotic groups (HGs) based on the general combining ability of multiple traits (HGCAMT) and sequencing-based diversity array technology (DArTseq) and (iii) assess the performance and stability of the lines in hybrid combinations. The inbred lines showed significantly (p < 0.01 and p < 0.05) positive and negative general combining ability (GCA) and specific combining ability (SCA) effects for grain yield (GY) and most other measured traits. The inbred line TZEI 135 displayed relatively larger positive GCA effects for GY when mated either as male or female and was identified as the best tester. TZEI 135 × TZEI 182 was identified as the best single-cross tester across environments. Results of the assessment of the relative importance of GCA and SCA effects revealed the predominance of additive gene action over the non-additive. Six HGs of inbreds were identified using the HGCAMT and three, based on the DArTseq marker genetic distance method, were the most efficient. The best hybrids in this study significantly out-yielded the best checks by 21, 46, and 70% under CHDS, HS, and TDS, respectively. These hybrids should be extensively tested in on-farm trials for possible commercialization in sub-Saharan Africa. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 2348 KiB

Open AccessArticle

Introgression of Resistance to Multiple Pathotypes of Plasmodiophora brassicae from Turnip (Brassica rapa ssp. rapifera) into Spring B. napus Canola

by Kawalpreet Kaur, Yingyi Liu and Habibur Rahman

Agronomy 2022, 12(5), 1225; https://doi.org/10.3390/agronomy12051225 - 19 May 2022

Cited by 2 | Viewed by 2950

Abstract

Clubroot disease resistance has been introgressed from Brassica rapa into canola following different approaches including a B. napus × B. rapa interspecific cross; however, the details of this cross are not available. To extend our knowledge of this cross for the introgression of [...] Read more.

Clubroot disease resistance has been introgressed from Brassica rapa into canola following different approaches including a B. napus × B. rapa interspecific cross; however, the details of this cross are not available. To extend our knowledge of this cross for the introgression of resistance to multiple pathotypes, we crossed a clubroot-resistant turnip with a susceptible canola and backcrossed the F₁′s to canola. The backcross population was subjected to pedigree breeding with selection for clubroot resistance and canola-quality traits; selection for resistance to pathotype 3H and 3A was performed in the early and advanced generations, respectively. The advanced generation lines were also evaluated for resistance to 3H, 3A, 2B, and 5x, and for field resistance to clubroot, and agronomic and seed quality traits. Following this, we developed canola lines carrying resistance to multiple pathotypes and nuclear DNA content similar to B. napus. Resistance to 3H showed a weak correlation with other pathotypes whereas resistance to 3A showed a strong positive correlation with 5x indicating that resistance to these pathotypes was under a similar genetic control. Thus, the results demonstrate that resistance to multiple pathotypes can be introgressed from a turnip into a canola even when selection for resistance to single pathotype is performed in early generations. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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28 pages, 3697 KiB

Open AccessArticle

Characterisation of the Complete Chloroplast Genomes of Seven Hyacinthus orientalis L. Cultivars: Insights into Cultivar Phylogeny

by Kwan-Ho Wong, Hoi-Yan Wu, Bobby Lim-Ho Kong, Grace Wing-Chiu But, Tin-Yan Siu, Jerome Ho-Lam Hui, Pang-Chui Shaw and David Tai-Wai Lau

Horticulturae 2022, 8(5), 453; https://doi.org/10.3390/horticulturae8050453 - 18 May 2022

Cited by 4 | Viewed by 4458

Abstract

To improve agricultural performance and obtain potential economic benefits, an understanding of phylogenetic relationships of Hyacinthus cultivars is needed. This study aims to revisit the phylogenetic relationships of Hyacinthus cultivars using complete chloroplast genomes. Nine chloroplast genomes were de novo sequenced, assembled and [...] Read more.

To improve agricultural performance and obtain potential economic benefits, an understanding of phylogenetic relationships of Hyacinthus cultivars is needed. This study aims to revisit the phylogenetic relationships of Hyacinthus cultivars using complete chloroplast genomes. Nine chloroplast genomes were de novo sequenced, assembled and annotated from seven cultivars of Hyacinthus orientalis and two Scilloideae species including Bellevalia paradoxa and Scilla siberica. The chloroplast genomes of Hyacinthus cultivars ranged from 154,458 bp to 154,641 bp, while those of Bellevalia paradoxa and Scilla siberica were 154,020 bp and 154,943 bp, respectively. Each chloroplast genome was annotated with 133 genes, including 87 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Simple sequence repeats AAGC/CTTG and ACTAT/AGTAT were identified only in ‘Eros’, while AAATC/ATTTG were identified in all cultivars except ‘Eros’. Five haplotypes were identified based on 460 variable sites. Combined with six other previously published chloroplast genomes of Scilloideae, a sliding window analysis and a phylogenetic analysis were performed. Divergence hotspots ndhA and trnG-UGC were identified with a nucleotide diversity threshold at 0.04. The phylogenetic positions of Hyacinthus cultivars were different from the previous study using ISSR. Complete chloroplast genomes serve as new evidence in Hyacinthus cultivar phylogeny, contributing to cultivar identification, preservation and breeding. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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17 pages, 2031 KiB

Open AccessArticle

Phenotypic and Genotypic Characterization and Correlation Analysis of Pea (Pisum sativum L.) Diversity Panel

by Ana Uhlarik, Marina Ćeran, Dalibor Živanov, Radu Grumeza, Leif Skøt, Ellen Sizer-Coverdale and David Lloyd

Plants 2022, 11(10), 1321; https://doi.org/10.3390/plants11101321 - 16 May 2022

Cited by 19 | Viewed by 4309

Abstract

Phenotypic and genotypic characterization were performed to assess heritability, variability, and seed yield stability of pea genotypes used in breeding to increase the pea production area. A European pea diversity panel, including genotypes from North America, Asia, and Australia consisting of varieties, breeding [...] Read more.

Phenotypic and genotypic characterization were performed to assess heritability, variability, and seed yield stability of pea genotypes used in breeding to increase the pea production area. A European pea diversity panel, including genotypes from North America, Asia, and Australia consisting of varieties, breeding lines, pea, and landraces was examined in 2019 and 2020 in Serbia and Belgium using augmented block design. The highest heritability was for thousand seed weight; the highest coefficient of variation was for seed yield. The highest positive correlation was between number of seeds per plant and number of pods per plant; the highest negative correlation was between seed yield and protein content. Hierarchical clustering separated pea germplasm based on use and type. Different Principal component analysis grouping of landraces, breeding lines, and varieties, as well as forage types and garden and dry peas, confirms that there was an apparent decrease in similarity between the genotypes, which can be explained by their different purposes. Pea breeding should be focused on traits with consistent heritability and a positive effect on seed yield when selecting high-yielding genotypes, and on allowing for more widespread use of pea in various agricultural production systems. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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12 pages, 9419 KiB

Open AccessArticle

Extensive Sampling Provides New Insights into Phylogenetic Relationships between Wild and Domesticated Zanthoxylum Species in China

by Xue Chen, Lu Tian, Jieyun Tian, Gang Wang, Xia Gong, Shijing Feng and Anzhi Wei

Horticulturae 2022, 8(5), 440; https://doi.org/10.3390/horticulturae8050440 - 14 May 2022

Cited by 5 | Viewed by 3063

Abstract

Zanthoxylum, belonging to the Rutaceae family, is widely distributed in tropical and subtropical regions. The genus has high economic value as spices, oils, medicinal plants, and culinary applications. Zanthoxylum has a long history of domestication and cultivation in China. However, the phylogenetic [...] Read more.

Zanthoxylum, belonging to the Rutaceae family, is widely distributed in tropical and subtropical regions. The genus has high economic value as spices, oils, medicinal plants, and culinary applications. Zanthoxylum has a long history of domestication and cultivation in China. However, the phylogenetic relationships and origin of wild and cultivated Zanthoxylum species in China remain largely unknown. Moreover, there is still no clear molecular phylogenetic system for Zanthoxylum species. Herein, 373 Zanthoxylum samples were collected from all presently known provenances of Zanthoxylum in China. In this study, four chloroplast DNA (cpDNA) markers (matK, ndhH, psbB, rbcL) were used to comprehensively analyze the genetic diversity, relatedness, and geographical origin of Chinese Zanthoxylum species. The results were as follows: (1) The aligned length of the four pairs of cpDNA sequences was 3836 bp, and 68 haplotypes were identified according to 219 variable polymorphic sites, including 90 singleton variable sites, 129 parsimony informative sites, 3 Indels (insertions and deletions). (2) Phylogenetic tree and haplotype network strongly supported the division of Zanthoxylum species consistent with the taxonomic recognition of five species: Z. bungeanum, Z. piasezkii, Z. piperitum, Z. armatum, and Z. micranthum. (3) Divergence time estimation suggested that Zanthoxylum genus originated from the Late Eocene, and most Zanthoxylum species diverged after the Middle Miocene. (4) Haplotype 16 (H16) was at the bottom of the phylogenetic tree, had higher haplotype diversity (Hd) and nucleotide polymorphism (Pi) than other haplotypes, and was located in the center of the network figure. Therefore, we deduced that the cultivated Zanthoxylum species may originate in Zhouqu County, Gansu Province, China. Meanwhile, our research provided a scientific basis for the identification and breeding programs of Chinese Zanthoxylum species. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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19 pages, 1492 KiB

Open AccessArticle

Identification, Characterization and Comparison of the Genome-Scale UTR Introns from Six Citrus Species

by Chunzhen Cheng, Xiaobao Shi, Yongyan Zhang, Bin Wang, Junwei Wu, Shizao Yang and Shaohua Wang

Horticulturae 2022, 8(5), 434; https://doi.org/10.3390/horticulturae8050434 - 13 May 2022

Cited by 2 | Viewed by 2450

Abstract

Ever since their discovery, introns within the coding sequence (CDS) of transcripts have been paid great attention. However, the introns located in the untranslated regions (UTRs) are often ignored. Here, we identified, characterized and compared the UTR introns (UIs) from six citrus species. [...] Read more.

Ever since their discovery, introns within the coding sequence (CDS) of transcripts have been paid great attention. However, the introns located in the untranslated regions (UTRs) are often ignored. Here, we identified, characterized and compared the UTR introns (UIs) from six citrus species. Results showed that the average intron number of UTRs is greatly lower than that of CDSs. Among all six citrus species, the number and density of 5′UTR introns (5UIs) are higher than those of 3′UTR introns (3UIs). The UI densities varied greatly among different citrus species. There are 11 and 9 types of splice site (SS) pairs for the UIs of C. sinensis and C. medica, respectively. However, the UIs of the other four citrus species all own only three kinds of SS pairs. The ‘GT-AG’, accounting for more than 95% of both 5UIs and 3UIs SS pairs for all the six species, is the most popular type. Moreover, 81 5UIs and 26 3UIs were identified as common UIs among the six citrus species, and the transcripts containing these common UIs were mostly involved in gene expression or gene expression regulation. Our study revealed that the UIs’ length, abundance, density and SS pair types varied among different citrus species and that many UI-containing genes play important roles in gene expression regulation. Our findings have great implications for future citrus UI function research. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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21 pages, 9607 KiB

Open AccessArticle

Overexpression of CgbHLH001, a Positive Regulator to Adversity, Enhances the Photosynthetic Capacity of Maize Seedlings under Drought Stress

by Haiju Zhao, Ailiman Abulaizi, Changhai Wang and Haiyan Lan

Agronomy 2022, 12(5), 1149; https://doi.org/10.3390/agronomy12051149 - 10 May 2022

Cited by 6 | Viewed by 2563

Abstract

Drought is a major environmental factor limiting crop productivity. Photosynthesis is very sensitive to drought. Basic helix-loop-helix (bHLH) transcription factors (TFs) are important in response to abiotic stress. However, their functions remain unclear. Herein, we generated CgbHLH001 (a TF gene from halophyte Chenopodium [...] Read more.

Drought is a major environmental factor limiting crop productivity. Photosynthesis is very sensitive to drought. Basic helix-loop-helix (bHLH) transcription factors (TFs) are important in response to abiotic stress. However, their functions remain unclear. Herein, we generated CgbHLH001 (a TF gene from halophyte Chenopodium glaucum)-overexpressed (OE) and ZmbHLH-RNA interference (Ri) maize lines to investigate their photosynthesis-associated indexes under drought conditions. The photosynthetic capacity was increased in OE lines under drought stress compared with that in non-transgenic (NT) and Ri plants. A greater root biomass, higher root/shoot ratio, and a relatively lower leaf area reduction ratio was also observed in OE plants. Compared to NT and Ri plants, OE lines showed a higher chlorophyll content and net photosynthetic rate and better chlorophyll fluorescence parameters under drought conditions. Fructose and glucose contents were also significantly elevated in OE lines. Moreover, under stressful conditions, CgbHLH001 overexpression increased the expression of genes related to photosynthesis. Transcriptomic data showed that many differentially expressed genes were enriched in the photosynthetic system in OE and Ri plants under drought conditions and were prone to being upregulated under drought stress in OE plants. Therefore, our results suggest that CgbHLH001 improves photosynthetic efficiency under drought stress and confers drought tolerance in maize seedlings. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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14 pages, 1433 KiB

Open AccessEditor’s ChoiceArticle

High-Density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Flowering Dogwood (Cornus florida)

by Erin Pfarr Moreau, Josh A. Honig and Thomas J. Molnar

Horticulturae 2022, 8(5), 405; https://doi.org/10.3390/horticulturae8050405 - 5 May 2022

Cited by 2 | Viewed by 2512

Abstract

Flowering dogwood (Cornus florida L.) is a popular, spring-blooming ornamental tree native to the eastern United States. The species is in general very susceptible to powdery mildew caused by Erysiphe pulchra, which disfigures leaves, decreases growth, and negatively affects flowering. Breeding [...] Read more.

Flowering dogwood (Cornus florida L.) is a popular, spring-blooming ornamental tree native to the eastern United States. The species is in general very susceptible to powdery mildew caused by Erysiphe pulchra, which disfigures leaves, decreases growth, and negatively affects flowering. Breeding for resistance has been recognized as an ideal strategy for controlling the disease in C. florida, but efforts have been hindered by the rarity of PM resistance in available germplasm and knowledge of its genetic control. In this study, we mapped quantitative trait loci (QTL) associated with PM resistance/tolerance in two full sibling populations segregating for PM response: Rutgers H4AR15P25 (P25) × Rutgers H4AR15R28 (P28) (n = 195) and Rutgers H4AR15R25 × Rutgers H4AR15P35 (P35) (n = 83). High-density genetic linkage maps were constructed for the mapping populations using double digest restriction-site associated DNA sequencing-derived single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). The P25 × P28 map consisted of 2265 markers, spanning 1520 cM and 11 linkage groups (LGs) with an average marker spacing of 0.69 cM. The P25 × P35 map was constructed with 1788 markers, spanning 1256 cM and 11 LGs, with an average marker spacing of 0.72 cM. The maps had 604 markers in common and exhibited excellent collinearity. Through multiple QTL model mapping, one major QTL (LOD = 11.36 and R² = 58.9%) was identified in P25 × P35. Furthermore, a minor QTL (LOD = 3.30 and R² = 7.8%) was detected in P25 × P28. Due to their proximity onLG3, these QTL may be designating the same locus or tightly linked loci. The negative additive effects of both QTL signify that the PM susceptible male parents were contributing susceptibility alleles to the progeny. This is the first report of QTL associated with PM response on LG3 in C. florida and lays the groundwork for the development of marker-assisted selection for PM resistance in C. florida breeding programs. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 1514 KiB

Open AccessArticle

Utilization of Intra-Cultivar Variation for Grain Yield and Protein Content within Durum Wheat Cultivars

by Elissavet Ninou, Ioannis Mylonas, Ioulia Karagianni, Sonia Michailidou, Athanasios Tsivelikas, Iosif Sistanis, Ilias Avdikos, Evangelos Korpetis and Fokion Papathanasiou

Agriculture 2022, 12(5), 661; https://doi.org/10.3390/agriculture12050661 - 3 May 2022

Cited by 4 | Viewed by 2576

Abstract

This study assessed the variations in grain yield (GY) and protein content (PC) within two commercial durum wheat cultivars (Svevo and Maestrale) and evaluated their responses to intra-cultivar selection for both traits. We investigated whether the variations are exploitable and could result in [...] Read more.

This study assessed the variations in grain yield (GY) and protein content (PC) within two commercial durum wheat cultivars (Svevo and Maestrale) and evaluated their responses to intra-cultivar selection for both traits. We investigated whether the variations are exploitable and could result in concurrent GY and PC upgrading. The experiments were conducted in the IPBGR, Thessaloniki, Greece (2018–2020). The first year included two identical honeycomb design trials under ultra-low plant density (ULD) where the divergent selection was applied based on single plant yield and protein content. In the second year, progeny evaluation under typical crop density (TCD) for GY and PC occurred in a randomized complete block (RCB) and with three replications for each cultivar selected line. This revealed considerable variation within already improved commercial cultivars. Single-plant selection for GY and PC simultaneously resulted in: (a) one high-yielding line that significantly outperformed the original cultivar Svevo while maintaining high PC, and (b) two high-grain PC lines that outperformed the original cultivar Maestrale significantly while maintaining high GY. ULD allowed efficient selection for GY and PC simultaneously within narrow gene pools by maximizing phenotypic expression and differentiation among individual plants. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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16 pages, 567 KiB

Open AccessArticle

Accelerated Genetic Gains in Early-Maturing Maize Hybrids following Three Periods of Genetic Enhancement for Grain Yield under Low and High Soil-Nitrogen Environments

by Baffour Badu-Apraku, Morakinyo Abiodun Bamidele Fakorede and Adamu Masari Abubakar

Plants 2022, 11(9), 1208; https://doi.org/10.3390/plants11091208 - 29 Apr 2022

Cited by 4 | Viewed by 2221

Abstract

Maize (Zea mays L.) is an important staple, as well as cash crop, in sub-Saharan Africa (SSA). However, its production is severely constrained by low soil nitrogen (low N). Fifty-four early-maturing hybrids developed during three breeding periods, (2008–2010, 2011–2013 and 2014–2016) were [...] Read more.

Maize (Zea mays L.) is an important staple, as well as cash crop, in sub-Saharan Africa (SSA). However, its production is severely constrained by low soil nitrogen (low N). Fifty-four early-maturing hybrids developed during three breeding periods, (2008–2010, 2011–2013 and 2014–2016) were evaluated under low (30 kg ha⁻¹) and high (120 kg ha⁻¹) soil nitrogen (N) in Ile-Ife and Mokwa, Nigeria, from 2017 to 2019. The study was designed to (i) determine the genetic gains in grain yield of the early-maturing maize hybrids developed during the three breeding periods, (ii) determine the relationship between grain yield and other agronomic traits and (iii) identify the highest-yielding and most stable hybrids under low- and high-N environments. The 54 hybrids were evaluated using a 6 × 9 lattice design with three replications. Mean squares for hybrids were significant for measured traits under low- and high-N environments, except the mean squares for stalk lodging and EPP under low N. Annual genetic gains in grain yield were 75 kg ha⁻¹ year⁻¹ (2.91%) and 55 kg ha⁻¹ year⁻¹ (1.33%) under low- and high-N environments, respectively, indicating that substantial gains were achieved in the genetic enhancement of the early-maturing hybrids. The hybrids TZdEI 314 × TZdEI 105, TZdEI 378 × TZdEI 173, ENT 12 × TZEI 48 and TZdEI 352 × TZdEI 315 were identified as the highest-yielding and most stable across test environments and should be tested extensively on farms and commercialized in SSA. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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23 pages, 6599 KiB

Open AccessArticle

Comparative Analyses of Chloroplast Genomes Provide Comprehensive Insights into the Adaptive Evolution of Paphiopedilum (Orchidaceae)

by Hengzhao Liu, Hang Ye, Naiyu Zhang, Jiayu Ma, Jiangtao Wang, Guojia Hu, Mengdi Li and Peng Zhao

Horticulturae 2022, 8(5), 391; https://doi.org/10.3390/horticulturae8050391 - 28 Apr 2022

Cited by 22 | Viewed by 3704

Abstract

An elucidation of how the selection pressures caused by habitat environments affect plant plastid genomes and lead to the adaptive evolution of plants, is a very intense area of research in evolutionary biology. The genus Paphiopedilum is a predominant group of orchids that [...] Read more.

An elucidation of how the selection pressures caused by habitat environments affect plant plastid genomes and lead to the adaptive evolution of plants, is a very intense area of research in evolutionary biology. The genus Paphiopedilum is a predominant group of orchids that includes over 66 species with high horticultural and ornamental value. However, owing to the destructive exploitation and habitat deterioration of wild germplasm resources of Paphiopedilum, it needs more molecular genetic resources and studies on this genus. The chloroplast is cytoplasmically inherited and often used in evolutionary studies. Thus, for this study, we newly sequenced, assembled and annotated five chloroplast genomes of the Paphiopedilum species. The size of these genomes ranged from 155,886 bp (P. henryanum) to 160,503 bp (P. ‘GZSLKY’ Youyou) and they contained 121–122 genes, which consisted of 76 protein coding genes, eight ribosomal RNAs, and 37–38 transfer RNAs. Combined with the other 14 Paphiopedilum species, the characteristics of the repeat sequences, divergent hotspot regions, and the condo usage bias were evaluated and identified, respectively. The gene transfer analysis showed that some fragments of the ndh and ycf gene families were shared by both the chloroplast and nucleus. Although the genomic structure and gene content was conserved, there was a significant boundary shift caused by the inverted repeat (IR) expansion and small single copy (SSC) contraction. The lower GC content and loss of ndh genes could be the result of adaptive evolutionary responses to its unique habitats. The genes under positive selection, including accD, matK, psbM, rpl20, rps12, ycf1, and ycf2 might be regarded as potential candidate genes for further study, which significantly contribute to the adaptive evolution of Paphiopedilum. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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14 pages, 2545 KiB

Open AccessArticle

Morphoanatomy and Histochemistry of Septal Nectaries Related to Female Fertility in Banana Plants of the ‘Cavendish’ Subgroup

by Manassés dos Santos Silva, Adriele Nascimento Santana, Janay Almeida dos Santos-Serejo, Claudia Fortes Ferreira and Edson Perito Amorim

Plants 2022, 11(9), 1177; https://doi.org/10.3390/plants11091177 - 27 Apr 2022

Cited by 3 | Viewed by 2640

Abstract

The objective of this study was to gain a deeper understanding of the morphoanatomical and histochemical structures that compose the nectary of pistillate flowers (female), which are involved in the female fertility of banana plants belonging to the ‘Cavendish’ subgroup. The diploid Calcutta [...] Read more.

The objective of this study was to gain a deeper understanding of the morphoanatomical and histochemical structures that compose the nectary of pistillate flowers (female), which are involved in the female fertility of banana plants belonging to the ‘Cavendish’ subgroup. The diploid Calcutta 4 and the Grand Naine cultivar were used for the assessment. Five stages of floral development were proposed. Pistillate flower nectaries were subjected to morphological characterization, morphoanatomy, and histochemical tests (phenolic compounds, proteins, and lipids). Morphoanatomical analysis revealed a greater presence of narrow nectariferous ducts and more developed pluristratified papillae in Calcutta 4. In contrast, Grand Naine displayed cell disintegration in nectariferous ducts and pluristratified papillae, absent transmitting tissue, and greater amounts of vascular bundles at anthesis. However, Calcutta 4 displayed no changes in the nectariferous duct at any of the stages. An association was found between phenolic compounds and lipids in vacuoles adjacent to the vascular bundles, with greater amounts found in Grand Naine. The localization of phenolic compounds may suggest that these compounds play a role in nectar secretion or the oxidation of the nectary region, ultimately limiting the growth and passage of the pollen tube and preventing ovule fertilization. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 3265 KiB

Open AccessArticle

Marker-Assisted Improvement of Bread Wheat Variety HD2967 for Leaf and Stripe Rust Resistance

by Niharika Mallick, Shailendra K. Jha, Priyanka Agarwal, Anchal Mall, Niranjana M., Sachin Kumar, Manish K. Choudhary, Shreshtha Bansal, M. S. Saharan, J. B. Sharma and Vinod

Plants 2022, 11(9), 1152; https://doi.org/10.3390/plants11091152 - 24 Apr 2022

Cited by 12 | Viewed by 4832

Abstract

The mega wheat variety HD2967 was improved for leaf and stripe rust resistance by marker-assisted backcross breeding. After its release in 2011, HD2967 became susceptible to stripe rust and moderately susceptible to leaf rust. The leaf rust resistance gene LrTrk was transferred into [...] Read more.

The mega wheat variety HD2967 was improved for leaf and stripe rust resistance by marker-assisted backcross breeding. After its release in 2011, HD2967 became susceptible to stripe rust and moderately susceptible to leaf rust. The leaf rust resistance gene LrTrk was transferred into HD2967 from the durum wheat genotype Trinakria. Then, HD2967 was crossed with Trinakria to produce F₁ plant foreground selection for LrTrk and background selection for the recurrent parent genotype was carried out in BC₁F₁, BC₂F₁ and BC₂F₂ generations. Foreground selection was carried out with the linked marker Xgwm234, while polymorphic SSR markers between parents were used for background selection. Background selection resulted in the rapid recovery of the recurrent parent genome. A morphological evaluation of 6 near isogenic lines (NILs)—2 resistant to leaf and stripe rust, and 4 resistant to leaf rust only—showed no significant differences in yields among NILs and the recurrent parent HD2967. All of the 6 NILs showed the presence of 2NS/2AS translocation, carrying the linked genes Lr37/Sr38/Yr17 present in HD2967 and the targeted leaf rust resistance gene LrTrk. Two NILs also showed additional resistance to stripe rust. Therefore, these NILs with rust resistance and an at par yielding ability of H2967 can replace the susceptible cultivar HD2967 to reduce yield losses due to disease. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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14 pages, 2230 KiB

Open AccessArticle

PpMYB39 Activates PpDFR to Modulate Anthocyanin Biosynthesis during Peach Fruit Maturation

by Irshad Ahmad Khan, Masood Ur Rahman, Shazia Sakhi, Ghazala Nawaz, Aftab Ahmad Khan, Tanveer Ahmad, Mohammad Adnan and Shah Masaud Khan

Horticulturae 2022, 8(4), 332; https://doi.org/10.3390/horticulturae8040332 - 14 Apr 2022

Cited by 12 | Viewed by 3588

Abstract

Anthocyanins are a class of water-soluble flavonoids widely present in fruits and vegetables responsible for the red flesh formation of peach fruit. Previously, several genes of the MYB family have been reported as transcriptional regulators of the anthocyanin biosynthetic pathway of structural genes [...] Read more.

Anthocyanins are a class of water-soluble flavonoids widely present in fruits and vegetables responsible for the red flesh formation of peach fruit. Previously, several genes of the MYB family have been reported as transcriptional regulators of the anthocyanin biosynthetic pathway of structural genes in plants. In this study, through comparative transcriptome analysis of the white and red flesh peach cultivars of Harrow Blood and Asama Hakuto, a predicted transcription factor of the R2R3MYB family, PpMYB39, was identified to be associated with anthocyanin biosynthesis in peach fruit. In red-fleshed peach cultivars, the maximum amount of anthocyanin accumulated 95 days after full bloom (DAFB), at full maturity near ripening. Our results showed that, at this stage, PpMYB39 had the highest expression level among the 13 differentially expressed genes (DEGs) found in both red- and white-fleshed fruits, as well as a high correlation with total anthocyanin content throughout fruit development. Moreover, the expression analysis of the structural genes of the anthocyanin biosynthetic pathway in peach fruit revealed that Prunus persica Dihydroflavonol-4-reductase (PpDFR) was co-expressed and up-regulated with PpMYB39 at 95 DAFB, suggesting its possible role as a transcriptional activator of MYB39. This was further confirmed by a yeast one-hybrid assay and a dual luciferase reporter assay. Our results will be helpful in the breeding of peach cultivars and the identification and significance of color in peaches and related fruit species, in addition to providing an understanding of color formation in peach fruit for future research. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 3053 KiB

Open AccessArticle

Evolutionary History and Functional Diversification of the JmjC Domain-Containing Histone Demethylase Gene Family in Plants

by Shifeng Ma, Zhiqiang Zhang, Yingqiang Long, Wenqi Huo, Yuzhi Zhang, Xiaoqing Yang, Jie Zhang, Xinyang Li, Qiying Du, Wei Liu, Daigang Yang and Xiongfeng Ma

Plants 2022, 11(8), 1041; https://doi.org/10.3390/plants11081041 - 12 Apr 2022

Cited by 7 | Viewed by 3504

Abstract

Histone demethylases containing JumonjiC (JmjC) domains regulate gene transcription and chromatin structure by changing the methylation status of lysine residues and play an important role in plant growth and development. In this study, a total of 332 JmjC family genes were [...] Read more.

Histone demethylases containing JumonjiC (JmjC) domains regulate gene transcription and chromatin structure by changing the methylation status of lysine residues and play an important role in plant growth and development. In this study, a total of 332 JmjC family genes were identified from 21 different plant species. The evolutionary analysis results showed that the JmjC gene was detected in each species, that is, the gene has already appeared in algae. The phylogenetic analysis showed that the KDM3/JHDM2 subfamily genes may have appeared when plants transitioned from water to land, but were lost in lycophytes (Selaginella moellendorffii). During the evolutionary process, some subfamily genes may have been lost in individual species. According to the analysis of the conserved domains, all of the plant JmjC genes contained a typical JmjC domain, which was highly conserved during plant evolution. The analysis of cis-acting elements showed that the promoter region of the JmjC gene was rich in phytohormones and biotic and abiotic stress-related elements. The transcriptome data analysis and protein interaction analyses showed that JmjC genes play an important role in plant growth and development. The results clarified the evolutionary history of JmjC family genes in plants and lay the foundation for the analysis of the biological functions of JmjC family genes. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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18 pages, 1715 KiB

Open AccessArticle

Enhancing Genomic Prediction Models for Forecasting Days to Maturity in Soybean Genotypes Using Site-Specific and Cumulative Photoperiod Data

by Reyna Persa, George L. Graef, James E. Specht, Esteban Rios, Charlie D. Messina and Diego Jarquin

Agriculture 2022, 12(4), 545; https://doi.org/10.3390/agriculture12040545 - 11 Apr 2022

Cited by 3 | Viewed by 2855

Abstract

Genomic selection (GS) has revolutionized breeding strategies by predicting the rank performance of post-harvest traits via implementing genomic prediction (GP) models. However, predicting pre-harvest traits in unobserved environments might produce serious biases. In soybean, days to maturity (DTM) represents a crucial stage with [...] Read more.

Genomic selection (GS) has revolutionized breeding strategies by predicting the rank performance of post-harvest traits via implementing genomic prediction (GP) models. However, predicting pre-harvest traits in unobserved environments might produce serious biases. In soybean, days to maturity (DTM) represents a crucial stage with a significant impact on yield potential; thus, genotypes must be carefully selected to ensure latitudinal adaptation in this photoperiod-sensitive crop species. This research assessed the use of daylength for predicting DTM in unobserved environments (CV00). A soybean dataset comprising 367 genotypes spanning nine families of the Soybean Nested Association Mapping Panel (SoyNAM) and tested in 11 environments (year-by-location combinations) was considered in this study. The proposed method (CB) returned a root-mean-square error (RMSE) of 5.2 days, a Pearson correlation (PC) of 0.66, and the predicted vs. observed difference in the environmental means (PODEM) ranged from −3.3 to 4.5 days; however, in the absence of daylength data, the conventional GP implementation produced an RMSE of 9 days, a PC of 0.66, and a PODEM range from −14.7 to 7.9 days. These results highlight the importance of dissecting phenotypic variability (G × E) based on photoperiod data and non-predictable environmental stimuli for improving the predictive ability and accuracy of DTM in soybeans. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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19 pages, 3400 KiB

Open AccessArticle

Genetic Variation in Flowering Traits of Tasmanian Leptospermum scoparium and Association with Provenance Home Site Climatic Factors

by Christopher N. Wellington, René E. Vaillancourt, Brad M. Potts, Dale Worledge and Anthony P. O’Grady

Plants 2022, 11(8), 1029; https://doi.org/10.3390/plants11081029 - 10 Apr 2022

Cited by 1 | Viewed by 2380

Abstract

Leptospermum scoparium is emerging as an economically important plant for the commercial production of mānuka honey and essential oils, both exhibiting unique antibacterial attributes. To support its domestication this is the first quantitative genetic study of variation for L. scoparium traits. It utilised [...] Read more.

Leptospermum scoparium is emerging as an economically important plant for the commercial production of mānuka honey and essential oils, both exhibiting unique antibacterial attributes. To support its domestication this is the first quantitative genetic study of variation for L. scoparium traits. It utilised plants from 200 open-pollinated families derived from 40 native populations, from across the species range in Tasmania, grown in a common garden field trial. The traits studied were survival, growth, and the flowering traits precocity, the timing of seasonal peak flowering, flowering duration, and flowering intensity. Significant genetic variation was evident at the population level for all traits studied and at the family level for three traits—growth, flowering precocity, and time to peak flowering. These three traits had moderate to high narrow-sense heritability estimates ranging from 0.27 to 0.69. For six of the traits studied, population differences were associated with climate attributes at the locations where seed was collected, suggesting adaptation to the local climate may have contributed to the observed population differentiation. Population level geographical trends suggest that genotypes to focus on for domestication originate from the eastern half of Tasmania for precociousness and the western half of Tasmania for earlier time to peak flowering and extended flowering duration. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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21 pages, 1212 KiB

Open AccessArticle

Detection of QTLs for Plant Height Architecture Traits in Rice (Oryza sativa L.) by Association Mapping and the RSTEP-LRT Method

by Hélder Manuel Sitoe, Yuanqing Zhang, Siqi Chen, Yulong Li, Mehtab Ali, Ognigamal Sowadan, Benjamin Karikari, Erbao Liu, Xiaojing Dang, Hujun Qian and Delin Hong

Plants 2022, 11(7), 999; https://doi.org/10.3390/plants11070999 - 6 Apr 2022

Cited by 5 | Viewed by 2799

Abstract

Plant height (PH) and its component traits are critical determinants of lodging resistance and strongly influence yield in rice. The genetic architecture of PH and its component traits were mined in two mapping populations. In the natural population composed of 504 accessions, a [...] Read more.

Plant height (PH) and its component traits are critical determinants of lodging resistance and strongly influence yield in rice. The genetic architecture of PH and its component traits were mined in two mapping populations. In the natural population composed of 504 accessions, a total of forty simple sequence repeat (SSR) markers associated with PH and its component traits were detected across two environments via association mapping. Allele RM305-210 bp on chromosome 5 for PH had the largest phenotypic effect value (PEV) (−51.42 cm) with a reducing effect. Allele RM3533-220 bp on chromosome 9 for panicle length and allele RM264-120 bp on chromosome 8 for the length of upper first elongated internode (1IN) showed the highest positive PEV. Among the elongated internodes with negative effects being desirable, the allele RM348-130 bp showed the largest PEV (−7.48 cm) for the length of upper second elongated internode. In the chromosome segment substitution line population consisting of 53 lines, a total of nine QTLs were detected across two environments, with the phenotypic variance explained (PVE) ranging 10.07–28.42%. Among the detected QTLs, q1IN-7 explained the largest PVE (28.42%) for the 1IN, with an additive of 5.31 cm. The favorable allele RM257-125 bp on chromosome 9 for the 1IN increasing was detected in both populations. The favorable alleles provided here could be used to shape PH architecture against lodging. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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13 pages, 714 KiB

Open AccessArticle

Molecular Characterization of Prunus Cultivars from Romania by Microsatellite Markers

by Anca Butiuc-Keul, Ana Coste, Dragoș Postolache, Vasile Laslo, Adela Halmagyi, Victoria Cristea and Anca Farkas

Horticulturae 2022, 8(4), 291; https://doi.org/10.3390/horticulturae8040291 - 30 Mar 2022

Cited by 7 | Viewed by 2674

Abstract

In Romania, Prunus species have great economic and social importance. With the introduction of new cultivars arises the need to preserve and characterize the local Prunus germplasm. Thus, a set of 24 polymorphic SSRs were selected for the overall characterization, including 10 peach, [...] Read more.

In Romania, Prunus species have great economic and social importance. With the introduction of new cultivars arises the need to preserve and characterize the local Prunus germplasm. Thus, a set of 24 polymorphic SSRs were selected for the overall characterization, including 10 peach, 11 apricot and 5 nectarine cultivars. The average number of alleles per locus (Na = 1.958), in addition to overall observed (Ho = 0.299) and expected heterozygosity (He = 0.286) were lower or comparable to those reported in similar studies, probably explained by the smaller number of analyzed cultivars restricted to a smaller geographic area. Among 26 genotypes a total of 101 alleles were identified, of which 46 alleles were in peach, 55 in apricot and 40 in nectarine, respectively. Six alleles from six loci (CPPCT-030, Pchgms-003, Pchgms-004, Pchgms-010, UDP97-401, UDP98-405) were common to all taxonomic groups. The most informative loci were BPPCT-025, Pchgms-021 and UDP96-001 in peach; BPPCT-025, BPPCT-001 and UDP96-001 in nectarine; and BPPCT-002, BPPCT-025, Pchgms-004, Pchgms-020 and Pchgms-021 in apricot. Clustering and genetic similarity analysis indicated that the degree of interspecific divergence in peach and nectarine cultivars was less than that in peach and apricot. These results will be useful to prevent confusion between cultivars, to improve breeding strategies and to benefit the management of Prunus cultivars bred in Romania. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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17 pages, 4501 KiB

Open AccessArticle

Genome-Wide Association Analyses Reveal Candidate Genes Controlling Harvest Index and Related Agronomic Traits in Brassica napus L.

by Mengfan Qin, Jia Song, Na Guo, Miao Zhang, Yunlin Zhu, Zhen Huang and Aixia Xu

Agronomy 2022, 12(4), 814; https://doi.org/10.3390/agronomy12040814 - 27 Mar 2022

Cited by 4 | Viewed by 8110

Abstract

Harvest index (HI) is a complex and vital agronomic trait that is closely related to the economic benefits of rapeseed. In this study, we measured the HI and 13 HI-related agronomic traits of 104 core breeding lines of rapeseed during 3 years and [...] Read more.

Harvest index (HI) is a complex and vital agronomic trait that is closely related to the economic benefits of rapeseed. In this study, we measured the HI and 13 HI-related agronomic traits of 104 core breeding lines of rapeseed during 3 years and sequenced the populations using the Bnapus50K array. The phenotypic analyses showed the complex connections among HI and other traits. A total of 212 significant SNPs related to the traits and 22 stable SNPs were identified. Four SNPs, A01_1783685 (PH and SYP), C06_26638717 (PH and NSS), C03_4731660 (MIL and MINS), and C09_36899682 (PH and BYP), were identified as potential pleiotropic loci. Compared to previous reports, 49 consensus loci were obtained that were related to PH, TSW, NSP, BAI, NSS, SL, BN, MINS, SYP, and BYP. Twelve stable SNPs were detected as promising novel loci related to BN (A05_19368584 and A05_19764389), SL (A06_23598999, A06_23608274, and C07_38735522), PH (C04_47349279, C04_47585236, and C09_36899680), MINS (C05_6251826), NSS (C06_22559430 and C06_22570315), and HI (C05_6554451). In addition, 39 putative genes were identified in the candidate intervals. This study provides novel insights into the genetic mechanisms of HI and HI-related traits, and lays a foundation for molecular marker development and casual gene cloning to improve the harvest index of rapeseed. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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12 pages, 2542 KiB

Open AccessArticle

Stocky1, a Novel Gene Involved in Maize Seedling Development and Cuticle Integrity

by Angelo Gaiti, Stefano Sangiorgio, Franco Faoro, Carlo Massimo Pozzi, Giuseppe Gavazzi and Salvatore Roberto Pilu

Plants 2022, 11(7), 847; https://doi.org/10.3390/plants11070847 - 23 Mar 2022

Viewed by 2409

Abstract

The cuticle is the plant’s outermost layer that covers the surfaces of aerial parts. This structure is composed of a variety of aliphatic molecules and is well-known for its protective role against biotic and abiotic stresses in plants. Mutants with a permeable cuticle [...] Read more.

The cuticle is the plant’s outermost layer that covers the surfaces of aerial parts. This structure is composed of a variety of aliphatic molecules and is well-known for its protective role against biotic and abiotic stresses in plants. Mutants with a permeable cuticle show developmental defects such as organ fusions and altered seed germination and viability. In this study, we identified a novel maize mutant, stocky1, with unique features: lethal at the seedling stage, and showing a severely dwarfed phenotype, due to a defective cuticle. For the first time, the mutant was tentatively mapped to chromosome 5, bin 5.04. The mutant phenotype investigated in this work has the potential to contribute to the elucidation of the role of the cuticle during plant development. The possibility of controlling this trait is of relevance in the context of climate change, as it may contribute to tolerance to abiotic stresses. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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22 pages, 4537 KiB

Open AccessArticle

Thaumatin-like Protein (TLP) Genes in Garlic (Allium sativum L.): Genome-Wide Identification, Characterization, and Expression in Response to Fusarium proliferatum Infection

by Olga K. Anisimova, Elena Z. Kochieva, Anna V. Shchennikova and Mikhail A. Filyushin

Plants 2022, 11(6), 748; https://doi.org/10.3390/plants11060748 - 11 Mar 2022

Cited by 13 | Viewed by 3532

Abstract

Plant antifungal proteins include the pathogenesis-related (PR)-5 family of fungi- and other stress-responsive thaumatin-like proteins (TLPs). However, the information on the TLPs of garlic (Allium sativum L.), which is often infected with soil Fusarium fungi, is very limited. In the present study, [...] Read more.

Plant antifungal proteins include the pathogenesis-related (PR)-5 family of fungi- and other stress-responsive thaumatin-like proteins (TLPs). However, the information on the TLPs of garlic (Allium sativum L.), which is often infected with soil Fusarium fungi, is very limited. In the present study, we identified 32 TLP homologs in the A. sativum cv. Ershuizao genome, which may function in the defense against Fusarium attack. The promoters of A. sativumTLP (AsTLP) genes contained cis-acting elements associated with hormone signaling and response to various types of stress, including those caused by fungal pathogens and their elicitors. The expression of AsTLP genes in Fusarium-resistant and -susceptible garlic cultivars was differently regulated by F. proliferatum infection. Thus, in the roots the mRNA levels of AsTLP7–9 and 21 genes were increased in resistant and decreased in susceptible A. sativum cultivars, suggesting the involvement of these genes in the garlic response to F. proliferatum attack. Our results provide insights into the role of TLPs in garlic and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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21 pages, 1911 KiB

Open AccessReview

Interactions of Gibberellins with Phytohormones and Their Role in Stress Responses

by Ricardo Castro-Camba, Conchi Sánchez, Nieves Vidal and Jesús Mª Vielba

Horticulturae 2022, 8(3), 241; https://doi.org/10.3390/horticulturae8030241 - 10 Mar 2022

Cited by 41 | Viewed by 9612

Abstract

Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, [...] Read more.

Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, the current knowledge on gibberellins’ homeostasis and modes of action is outlined. Besides this, the complex interrelations between gibberellins and other plant growth regulators are also described, providing an intricate network of interactions that ultimately drives towards precise and specific gene expression. Thus, genes and proteins identified as being involved in gibberellin responses in model and non-model species are highlighted. Furthermore, the molecular mechanisms governing the gibberellins’ relation to stress responses are also depicted. This review aims to provide a comprehensive picture of the state-of-the-art of the current perceptions of the interactions of gibberellins with other phytohormones, and their responses to plant stresses, thus allowing for the identification of the specific mechanisms involved. This knowledge will help us to improve our understanding of gibberellins’ biology, and might help increase the biotechnological toolbox needed to refine plant resilience, particularly under a climate change scenario. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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11 pages, 7108 KiB

Open AccessArticle

Comparison between Germinated Seed and Isolated Microspore EMS Mutagenesis in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

by Yue Gao, Gaoyang Qu, Shengnan Huang, Zhiyong Liu, Meidi Zhang, Wei Fu, Jie Ren and Hui Feng

Horticulturae 2022, 8(3), 232; https://doi.org/10.3390/horticulturae8030232 - 8 Mar 2022

Cited by 20 | Viewed by 4422

Abstract

Mutagenesis is an important tool for breeding and genomic research. In this study, the germinated seeds and isolated microspores of a double haploid line ‘FT’ were treated with EMS, respectively, with the aim of comparing the effects of the two approaches on generating [...] Read more.

Mutagenesis is an important tool for breeding and genomic research. In this study, the germinated seeds and isolated microspores of a double haploid line ‘FT’ were treated with EMS, respectively, with the aim of comparing the effects of the two approaches on generating mutants in Chinese cabbage. For microspore EMS mutagenesis, the isolated microspores were treated with 0.12% EMS for 20 min, a total of 1268 plantlets were obtained, and 15 M₁ mutants were screened with a mutation frequency of 1.2%. For seed EMS mutagenesis, 7800 germinated seeds were treated with 0.8% EMS for 12 h, and a total of 701 M₂ mutants were screened, with a mutation frequency of 18.78%. In total, 716 mutants with heritable morphological variation including leaf color, leaf shape, leafy head, bolting, and fertility, were obtained from the EMS mutagenesis experiments. Homozygous mutant plants could be screened from M₁ lines by microspore mutagenesis, and M₂ lines by seed mutagenesis. The mutation frequency was higher in seed mutagenesis than in microspore mutagenesis. Based on these results, we propose that seed EMS mutagenesis is more suitable to generate a large-scale mutant library, and the microspore EMS mutagenesis is conducive to rapidly obtaining homozygous mutants. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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18 pages, 5156 KiB

Open AccessArticle

Metabolic Profiling of Sugars and Organic Acids, and Expression Analyses of Metabolism-Associated Genes in Two Yellow-Peel Pitaya Species

by Fangfang Xie, Canbin Chen, Jiaxuan Chen, Yuanju Yuan, Qingzhu Hua, Zhike Zhang, Jietang Zhao, Guibing Hu, Jianye Chen and Yonghua Qin

Plants 2022, 11(5), 694; https://doi.org/10.3390/plants11050694 - 4 Mar 2022

Cited by 10 | Viewed by 3810

Abstract

Sugar and organic acids are important factors determining pitaya fruit quality. However, changes in sugars and acids, and expressions of metabolism-associated genes during fruit maturation of yellow-peel pitayas are not well-documented. In this study, metabolic and expression analyses in pulps of different fruit [...] Read more.

Sugar and organic acids are important factors determining pitaya fruit quality. However, changes in sugars and acids, and expressions of metabolism-associated genes during fruit maturation of yellow-peel pitayas are not well-documented. In this study, metabolic and expression analyses in pulps of different fruit developmental stages of ‘Wucihuanglong’ (‘WCHL’, Hylocereus undatus) and ‘Youcihuanglong’ pitaya (‘YCHL’, Hylocereus megalanthus) were used to explore the sugar and organic acid metabolic process. Total phenols and flavonoids were mainly accumulated at S1 in pitaya pulps. Ascorbic acid contents of ‘WCHL’ pitaya were higher than that of ‘YCHL’ pitaya during fruit maturation. Starch was mainly accumulated at early fruit development stages while soluble sugars were rich in late stages. Sucrose, fructose, and glucose were the main sugar components of ‘YCHL’ pitaya while glucose was dominant in ‘WCHL’ pitaya. Malic and citric acids were the main organic acids in ‘WCHL’ and ‘YCHL’ pitayas, respectively. Based on the transcriptome analyses, 118 genes involved in pitaya sugar and organic acid metabolism were obtained. Results from the correlation analyses between the expression profiling of candidate genes and the contents of sugar and organic acid showed that 51 genes had a significant correlation relationship and probably perform key role in pitaya sugar and organic acid metabolism processes. The finding of the present study provides new information for quality regulation of pitayas. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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12 pages, 2017 KiB

Open AccessArticle

Development and Cross-Species Transferability of Novel Genomic-SSR Markers and Their Utility in Hybrid Identification and Trait Association Analysis in Chinese Cherry

by Zhenshan Liu, Jing Zhang, Yan Wang, Hao Wang, Lei Wang, Lu Zhang, Muran Xiong, Wen He, Shaofeng Yang, Qing Chen, Tao Chen, Ya Luo, Yong Zhang, Haoru Tang and Xiaorong Wang

Horticulturae 2022, 8(3), 222; https://doi.org/10.3390/horticulturae8030222 - 3 Mar 2022

Cited by 15 | Viewed by 3011

Abstract

Chinese cherry (Cerasus pseudocerasus (Lindl.) G.Don) is an economically important tetraploid fruiting cherry species native to China. Simple sequence repeats (SSRs)—due to their codominance, polymorphism, and stability—have been widely applied in genetic identification and trait-association analysis. In this study, using comparative genomics [...] Read more.

Chinese cherry (Cerasus pseudocerasus (Lindl.) G.Don) is an economically important tetraploid fruiting cherry species native to China. Simple sequence repeats (SSRs)—due to their codominance, polymorphism, and stability—have been widely applied in genetic identification and trait-association analysis. In this study, using comparative genomics strategy and the data of one high-quality whole genome and seven preliminarily assembled genome sequences, we constructed a database containing 25,779 polymorphic SSR loci to efficiently develop novel markers. Sixty-four SSR loci covering eight linkage groups were selected to design primer pairs. Sixty (93.75%) primer pairs yielded specific bands and 32 (50.00%) exhibited moderate-to-high levels of informativeness (PIC ranging from 0.264 to 0.728) in 94 Chinese cherry accessions. A total of 38 primer pairs exhibited high transferability across 13 Cerasus taxa. The marker SAUCps203 was species-specific in C. pseudocerasus by checking with 114 accessions from Cerasus and 16 relatives, suggesting its potential application in accurate identification of Chinese cherry or its interspecific hybrid. Moreover, 1081 out of 1122 individuals from three cross F₁ populations of Chinese cherry were identified as true hybrid offspring by using only five SSR markers. Trait association analysis suggested that 20 SSR loci were significantly associated with soluble solids and fruit size, with explained phenotypic variance ranging from 9.02% to 26.35%. This study will provide a basis for SSR-based germplasm identification and further marker-assisted selection (MAS) of Chinese cherry. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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16 pages, 2360 KiB

Open AccessArticle

In Silico Genome-Wide Characterisation of the Lipid Transfer Protein Multigenic Family in Sunflower (H. annuus L.)

by Alberto Vangelisti, Samuel Simoni, Gabriele Usai, Flavia Mascagni, Maria Ventimiglia, Lucia Natali, Andrea Cavallini and Tommaso Giordani

Plants 2022, 11(5), 664; https://doi.org/10.3390/plants11050664 - 28 Feb 2022

Cited by 6 | Viewed by 3138

Abstract

The sunflower (Helianthus annuus L.) is among the most widely cultivated crops in the world due to the oilseed production. Lipid transfer proteins (LTPs) are low molecular mass proteins encoded by a broad multigenic family in higher plants, showing a vast range [...] Read more.

The sunflower (Helianthus annuus L.) is among the most widely cultivated crops in the world due to the oilseed production. Lipid transfer proteins (LTPs) are low molecular mass proteins encoded by a broad multigenic family in higher plants, showing a vast range of functions; these proteins have not been characterised in sunflower at the genomic level. In this work, we exploited the reliable genome sequence of sunflower to identify and characterise the LTP multigenic family in H. annuus. Overall, 101 sunflower putative LTP genes were identified using a homology search and the HMM algorithm. The selected sequences were characterised through phylogenetic analysis, exon–intron organisation, and protein structural motifs. Sunflower LTPs were subdivided into four clades, reflecting their genomic and structural organisation. This gene family was further investigated by analysing the possible duplication origin of genes, which showed the prevalence of tandem and whole genome duplication events, a result that is in line with polyploidisation events that occurred during sunflower genome evolution. Furthermore, LTP gene expression was evaluated on cDNA libraries constructed on six sunflower tissues (leaf, root, ligule, seed, stamen, and pistil) and from roots treated with stimuli mimicking biotic and abiotic stress. Genes encoding LTPs belonging to three out of four clades responded specifically to external stimuli, especially to abscisic acid, auxin, and the saline environment. Interestingly, genes encoding proteins belonging to one clade were expressed exclusively in sunflower seeds. This work is a first attempt of genome-wide identification and characterisation of the LTP multigenic family in a plant species. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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14 pages, 3123 KiB

Open AccessArticle

EuPIP1;2, a Plasma Membrane Aquaporin Gene from Eucommia ulmoides, Enhances Drought and Salt Tolerance in Transgenic Tobacco

by Jiajia Chen, Jianrong Li, Yanhui Huang, Yan Li, Changfeng Su and Xiaofang Zeng

Agronomy 2022, 12(3), 615; https://doi.org/10.3390/agronomy12030615 - 28 Feb 2022

Cited by 7 | Viewed by 2907

Abstract

Aquaporins are a specific type of membrane channel proteins that efficiently transport water molecules and other small molecular substrates in plants. In this study, we isolated the plasma membrane aquaporin gene EuPIP1;2 from Eucommia ulmoides, an important medicinal plant in China. The [...] Read more.

Aquaporins are a specific type of membrane channel proteins that efficiently transport water molecules and other small molecular substrates in plants. In this study, we isolated the plasma membrane aquaporin gene EuPIP1;2 from Eucommia ulmoides, an important medicinal plant in China. The EuPIP1;2 protein was localized on the plasma membrane. Quantitative RT-PCR analysis revealed that EuPIP1;2 was constitutively expressed in all analyzed tissues, with the highest expression levels detected in the fruit and root. Overexpression of EuPIP1;2 in transgenic tobacco enhanced plant tolerance of drought and salinity. Under drought and salt stress, the transgenic lines exhibited higher percentage germination, longer roots, and enhanced percentage survival compared with wild-type plants. The contents of malonaldehyde and proline suggested that EuPIP1;2 improved drought and salt tolerance in transgenic lines by reducing damage to membranes and improving osmotic adjustment. We predict that EuPIP1;2 could be applied to improve drought and salt tolerance in transgenic plants. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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12 pages, 1397 KiB

Open AccessArticle

Grain Quality Affected by Introducing Photorespiratory Bypasses into Rice

by Chuanling Zhang, Xiaofen Zhong, Dagen Lin, Kaixin Wu, Zhan Wu, Zhisheng Zhang and Xinxiang Peng

Agronomy 2022, 12(3), 566; https://doi.org/10.3390/agronomy12030566 - 24 Feb 2022

Cited by 9 | Viewed by 3032

Abstract

Grain quality is a critical component of high-yielding varieties to ensure acceptance by an ever-increasing population and living standards. During the past years, several photorespiration bypasses have been introduced into C3 plants, among which our GOC and GCGT bypasses exhibit increased photosynthesis and [...] Read more.

Grain quality is a critical component of high-yielding varieties to ensure acceptance by an ever-increasing population and living standards. During the past years, several photorespiration bypasses have been introduced into C3 plants, among which our GOC and GCGT bypasses exhibit increased photosynthesis and yield in rice. However, to the best of our knowledge, there are still no reports referring to effects of the bypasses on grain quality. Thus, the objective of this study is to determine the effect of GOC and GCGT bypasses on grain quality, and the mechanism of how photorespiratory bypasses affect grain quality was also investigated. Compared with the WT of Zhonghua 11, GOC4 and GCGT20 plants had higher nutritional quality and cooking quality as grain protein content was significantly increased by 11.27% and 14.97%, and alkali spreading value was significantly increased by 7.6% and 4.63%, respectively, whereas appearance quality appears to be negatively affected since the chalky rice rate was increased by 32.6% and 68%, respectively. Analyses also demonstrated that the changes in grain quality may result from the increased total nitrogen and constrained carbohydrate transport in the transgenic plants. Altogether, the results not only suggest that the increased photosynthesis and yield by introducing the photorespiratory bypasses can significantly affect grain quality parameters for rice, either positively or negatively, but also imply that the coordination of source–sink transport may play important roles in grain quality formation for high-yielding crops via increased photosynthetic efficiency. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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13 pages, 1357 KiB

Open AccessArticle

Pomological Traits and Genome Size of Prunus armeniaca L. Considering to Geographical Origin

by Eliška Rampáčková, Martina Mrázová, Jana Čížková and Tomáš Nečas

Horticulturae 2022, 8(3), 199; https://doi.org/10.3390/horticulturae8030199 - 24 Feb 2022

Cited by 8 | Viewed by 2432

Abstract

Apricot (Prunus armeniaca L.) is an important fruit crop and member of the Prunus genus of the Rosaceae family that is planted in many temperate regions worldwide. The quality of fruit is assessed by many pomological parameters which can serve as a [...] Read more.

Apricot (Prunus armeniaca L.) is an important fruit crop and member of the Prunus genus of the Rosaceae family that is planted in many temperate regions worldwide. The quality of fruit is assessed by many pomological parameters which can serve as a decisive factor in apricot breeding, because the introduction of new cultivars is required. These parameters can differ with climate conditions, geographical location or geographic ecological origin. Similarly, another biological characteristic can be measured depending on these terms. The present study was conducted with the aim of estimating pomological traits together with the nuclear DNA content of 35 apricot cultivars with different geographical origins. Only CV values lower than 5% were considered in flow cytometry analysis. All analyzed cultivars were diploid and the genome size value ranged from 0.587 to 0.644 pg/2C, where Turkish apricots reached the highest value (on average 0.628 pg/2C) followed by the European group (on average 0.625 pg/2C). A Spearman-rank correlation was used and the different correlation was found for specific geographical groups of apricot cultivars. The genome size values of apricots and related botanical species P. mume, P. sibirica and P. ansu showed to be very similar values. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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13 pages, 4454 KiB

Open AccessArticle

Evaluation of Germplasm and Development of Markers for Resistance to Plasmodiophora brassicae in Radish (Raphanussativus L.)

by Qingbiao Wang, Yanping Wang, Huihui Qian, Ziye Zhang and Li Zhang

Agronomy 2022, 12(3), 554; https://doi.org/10.3390/agronomy12030554 - 23 Feb 2022

Cited by 3 | Viewed by 2945

Abstract

The rapid spread of clubroot disease caused by Plasmodiophora brassicae threatens radish (Raphanus sativus) production in China because some cultivation types lack clubroot-resistant (CR) genes. However, few molecular markers for clubroot resistance have been developed and used in hybrid breeding programs. [...] Read more.

The rapid spread of clubroot disease caused by Plasmodiophora brassicae threatens radish (Raphanus sativus) production in China because some cultivation types lack clubroot-resistant (CR) genes. However, few molecular markers for clubroot resistance have been developed and used in hybrid breeding programs. In this study, 27 immune and 6 highly resistant accessions were identified among 95 radish inbred lines. The genes Rsa10003637 and Rsa10025569/Rsa10025571 were respectively identified from an XYB36-2 reference genome as the homologs of Crr1 and CRa from Brassica rapa by means of homology and synteny analysis. The association between the degree of clubroot resistance and the genotype of these CR genes suggested that Rsa10025569-H3 can be used as a clubroot-resistant haplotype. The sequence identity of Rsa10025569 in clubroot-resistant lines (CR-60 and CR-88) and clubroot-susceptible lines (CR-10 and CR-35) was 92.47%, and there was a 699 bp insertion at the end of the fourth exon in the clubroot-susceptible line. Association analysis of a BC₁F₁ population derived from the cross CR-88 (resistance) × CR-10 (susceptible) revealed an apparent correlation between polymorphisms at the Rsa10025569 locus and degree of clubroot resistance. On the basis of the results, molecular marker-assisted selection was used to transfer disease resistance genes to susceptible varieties and a new CR germplasm of Xinlimei was obtained. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 50051 KiB

Open AccessArticle

Comparisons of Anatomical Characteristics and Transcriptomic Differences between Heterografts and Homografts in Pyrus L.

by Piyu Ji, Chenglin Liang, Yingjie Yang, Ran Wang, Yue Wang, Meitong Yuan, Zhiyun Qiu, Yuanyuan Cheng, Jianlong Liu and Dingli Li

Plants 2022, 11(5), 580; https://doi.org/10.3390/plants11050580 - 22 Feb 2022

Cited by 9 | Viewed by 2485

Abstract

Pear (Pyrus L.) is an important temperate fruit worldwide, and grafting is widely used in pear vegetative propagation. However, the mechanisms of graft healing or incompatibility remain poorly understood in Pyrus. To study the differences in graft healing in Pyrus, [...] Read more.

Pear (Pyrus L.) is an important temperate fruit worldwide, and grafting is widely used in pear vegetative propagation. However, the mechanisms of graft healing or incompatibility remain poorly understood in Pyrus. To study the differences in graft healing in Pyrus, the homograft “Qingzhen D1/Qingzhen D1” and the heterograft “QAUP-1/Qingzhen D1” as compatibility and incompatibility combinations were compared. Anatomical differences indicated the healing process was faster in homografts than in heterografts. During the healing process, four critical stages in graft union formation were identified in the two types of grafts. The expression of the genes associated with hormone signaling (auxin and cytokinins), and lignin biosynthesis was delayed in the healing process of heterografts. In addition, the PbBglu13 gene, encoded β-glucosidase, was more highly up-regulated in heterografts than in homografts to promote healing. Meanwhile, the most of DEGs related starch and sucrose metabolism were found to be up-regulated in heterografts; those results indicated that cellulose and sugar signals were also involved in graft healing. The results of this study improved the understanding of the differences in the mechanisms of graft healing between homografts and heterografts. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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11 pages, 2281 KiB

Open AccessArticle

Molecular Characterization and Genetic Structure Evaluation of Breeding Populations of Fennel (Foeniculum vulgare Mill.)

by Francesco Scariolo, Fabio Palumbo and Gianni Barcaccia

Agronomy 2022, 12(3), 542; https://doi.org/10.3390/agronomy12030542 - 22 Feb 2022

Cited by 4 | Viewed by 2888

Abstract

Fennel, or Foeniculum vulgare Mill., is an important horticultural crop belonging to the Apiaceae family that is cultivated worldwide and used in the agri-food sector and for pharmaceutical preparations. Breeding strategies in this species usually involve three parental lines, including two maternal lines [...] Read more.

Fennel, or Foeniculum vulgare Mill., is an important horticultural crop belonging to the Apiaceae family that is cultivated worldwide and used in the agri-food sector and for pharmaceutical preparations. Breeding strategies in this species usually involve three parental lines, including two maternal lines (one cytoplasmic male-sterile line and an ideotype representative maintainer line) that are crossed to obtain an ideotype representative of the cytoplasmic male-sterile line and one paternal line, used as a pollinator in crosses with the progeny of the derived maternal lines. From this cross, F1 hybrid progenies are obtained, which are characterized by high levels of heterozygosity and hybrid vigor. In this study, over 450 plants, representing 8 breeding populations and their respective 3 parental and 1 progeny line, were genotyped by means of codominant molecular markers. The 12 highly polymorphic microsatellites enabled the analyses of the genetic variability, distinctiveness and stability of each breeding line. Moreover, the genetic structure of the core collection was investigated, which, together with the homozygosity, gene flow and genetic similarity results, allowed the identification of unsuitable lines to be used in breeding plans due to their low homozygosity (10.4% in the pollinator line of population 7). Moreover, the Bayesian reconstruction of the core collection’s genetic structure, based on the codominant markers used, allowed us to confirm the distinctiveness results obtained from the genetic similarity investigation and the computed gene flow estimates. Among these, a trend in hybrid heterozygosity was also observed, that increased when the genetic similarity between the respective parental lines decreased. Thus, this research proposes a suitable method for genotyping fennel populations in pre- and post-breeding approaches, such as marker-assisted breeding or breeding line distinctiveness and stability verifications. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 3028 KiB

Open AccessArticle

Electrophysiological, Morphologic, and Transcriptomic Profiling of the Ogura-CMS, DGMS and Maintainer Broccoli Lines

by Zhansheng Li, Lixiao Song, Yumei Liu, Fengqing Han and Wei Liu

Plants 2022, 11(4), 561; https://doi.org/10.3390/plants11040561 - 21 Feb 2022

Cited by 6 | Viewed by 2752

Abstract

To better serve breeding of broccoli, the electrophysiological, morphological and transcriptomic profiling of the isogenic Ogura-CMS, DGMS and their maintainer fertile lines, were carried out by scanning electron microscopy, investigation of agronomic traits and RNA-sequencing analysis. The agronomic traits of plant height, length [...] Read more.

To better serve breeding of broccoli, the electrophysiological, morphological and transcriptomic profiling of the isogenic Ogura-CMS, DGMS and their maintainer fertile lines, were carried out by scanning electron microscopy, investigation of agronomic traits and RNA-sequencing analysis. The agronomic traits of plant height, length of the largest leaf, plant spread angle, single head weight, head width and stem diameter showed stronger performance in Ogura-CMS broccoli than in DGMS line or maintainer fertile line. However, the Ogura-CMS broccoli was poorer in the seed yield and seed germination than in the DGMS line and maintainer fertile line. Additionally, the DGMS broccoli had longer maturation and flowering periods than the Ogura-CMS and maintainer fertile lines. There were obvious differences in the honey gland, happening in the male sterility and fertile lines of broccoli. Additionally, the mechanism regulating Ogura-CMS and DGMS in broccoli was investigated using florets transcriptome analyses of the Ogura-CMS, DGMS and maintainer fertile lines. As a result, a total of 2670 differentially expressed genes (DEGs) were detected, including 1054 up- and 1616 downregulated genes in the Ogura-CMS and DGMS lines compared to the maintainer fertile line. A number of functionally known genes involved in plant hormones (auxin, salicylic acid and brassinosteroid), five Mitochondrial Oxidative Phosphorylation (OXPHOS) genes of atp8, LOC106319879, LOC106324734, LOC106314622 and LOC106298585, and three upregulated genes (Lhcb1, Lhcb3 and Lhcb5) associated with the photosynthesis-antenna protein pathway, were obviously detected to be highly associated with reproductive development including flowering time, maturity and reproductive period in the Ogura-CMS and DGMS broccoli comparing to their maintainer fertile line. Our research would provide a comprehensive foundation for understanding the differences of electrophysiological, morphological and transcriptomic profiles in the Ogura-CMS, DGMS and maintainer broccoli, and as well as being beneficial to exploring the mechanism of male sterility in Brassica crops. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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15 pages, 2751 KiB

Open AccessArticle

Combination of Marker-Assisted Backcross Selection of Yr59 and Phenotypic Selection to Improve Stripe Rust Resistance and Agronomic Performance in Four Elite Wheat Cultivars

by Min Zhang, Taohong Fang, Xinli Zhou, Xianming Chen, Xin Li, Junyan Feng, Suizhuang Yang and Zhensheng Kang

Agronomy 2022, 12(2), 497; https://doi.org/10.3390/agronomy12020497 - 17 Feb 2022

Cited by 7 | Viewed by 3687

Abstract

In this study, we successfully introgressed and validated Yr59 into four elite wheat cultivars, Jimai 22, Chuanmai 42, Zhengmai 9023 and Xinmai 26 through marker-assisted backcross selection. Used as female parents, these four cultivars were crossed with wheat line PI 660061 (Yr59 [...] Read more.

In this study, we successfully introgressed and validated Yr59 into four elite wheat cultivars, Jimai 22, Chuanmai 42, Zhengmai 9023 and Xinmai 26 through marker-assisted backcross selection. Used as female parents, these four cultivars were crossed with wheat line PI 660061 (Yr59). After two backcrosses and marker-assisted selection, the progenies were selfed and advanced to the BC₂F₄ generation. A total of 123 BC₂F₄ lines were selected based on agronomic traits and stripe rust resistance, and their BC₂F₅ and BC₂F₆ progenies were further evaluated for stripe rust resistance and agronomic traits. Seven markers linked with relevant genes, including Xbarc32, Xwgp5175, Xwmc557 and Xcfa2040 linked with Yr59; Xwmc658 with YrJ22; WE173 and Xbarc181 with Yr26, were used to genotype the breeding lines. A total of 109 introgression lines with positive markers for Yr59 were identified for further stripe rust and agronomic trait evaluation. Finally, 16 lines had higher levels resistance to stripe rust, and similar or superior agronomic traits compared to their parents were obtained. These lines can be released as new cultivars for various regions after regional tests and also can be used as resistance stocks for regional breeding programs to develop new cultivars with adequate and durable resistance to stripe rust. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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18 pages, 3958 KiB

Open AccessArticle

Discovery of Major Quantitative Trait Loci and Candidate Genes for Fresh Seed Dormancy in Groundnut

by Deekshitha Bomireddy, Sunil S. Gangurde, Murali T. Variath, Pasupuleti Janila, Surendra S. Manohar, Vinay Sharma, Sejal Parmar, Dnyaneshwar Deshmukh, Mangala Reddisekhar, Devarapalli Mohan Reddy, Palagiri Sudhakar, Bommu Veera Bhaskara Reddy, Rajeev K. Varshney, Baozhu Guo and Manish K. Pandey

Agronomy 2022, 12(2), 404; https://doi.org/10.3390/agronomy12020404 - 6 Feb 2022

Cited by 13 | Viewed by 3484

Abstract

Spanish bunch groundnut varieties occupy most of the cultivated area in Asia and Africa, and these varieties lack required 2-3 weeks of fresh seed dormancy (FSD) hampering kernel quality. Genomic breeding can help to improve commercial groundnut cultivars for FSD in a shorter [...] Read more.

Spanish bunch groundnut varieties occupy most of the cultivated area in Asia and Africa, and these varieties lack required 2-3 weeks of fresh seed dormancy (FSD) hampering kernel quality. Genomic breeding can help to improve commercial groundnut cultivars for FSD in a shorter time with greater precision. In this regard, a recombinant inbred line (RIL) population from the cross ICGV 02266 (non-dormant) × ICGV 97045 (dormant) was developed and genotyped with a 5 K mid-density genotyping assay. A linkage map was constructed with 325 SNP loci spanning a total map length of 2335.3 cM and five major QTLs were identified on chromosomes Ah01, Ah11, Ah06, Ah16 and Ah17. Based on differential gene expression using transcriptomic information from dormant (Tifrunner) and non-dormant (ICGV 91114) genotypes, histone deacetylases, histone-lysine N-methyltransferase, cytochrome P450, protein kinases, and ethylene-responsive transcription factor were identified as key regulators involved in the hormonal regulation of dormancy. Six Kompetitive Allele Specific PCR (KASP) markers were successfully validated in the diverse panel including selected RILs of the same population and germplasm lines. These validated KASP markers could facilitate faster breeding of new varieties with desired dormancy using marker-assisted early generation selection. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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16 pages, 4231 KiB

Open AccessArticle

Detection of Chromosomal Segments Introgressed from Wild Species of Carrot into Cultivars: Quantitative Trait Loci Mapping for Morphological Features in Backcross Inbred Lines

by Chenggang Ou, Tingting Sun, Xing Liu, Chengjiang Li, Min Li, Xuewei Wang, Huaifu Ren, Zhiwei Zhao and Feiyun Zhuang

Plants 2022, 11(3), 391; https://doi.org/10.3390/plants11030391 - 30 Jan 2022

Cited by 5 | Viewed by 2963

Abstract

Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although [...] Read more.

Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although several studies have focused on identifying genetic loci that contribute to the morphology of storage roots. A backcross inbred line (BIL) population derived from a cross between the wild species Daucus carota ssp. carota “Songzi” and the orange cultivar “Amsterdam forcing” was developed. The morphological features in the BIL population became more diverse after several generations of selfing BC₂F₁ plants. Only few lines retained features of wild parent. Genomic resequencing of the two parental lines and the BILs resulted in 3,223,651 single nucleotide polymorphisms (SNPs), and 13,445 bin markers were generated using a sliding window approach. We constructed a genetic map with 2027 bins containing 154,776 SNPs; the total genetic distance was 1436.43 cM and the average interval between the bins was 0.71 cm. Five stable QTLs related to root length, root shoulder width, dry material content of root, and ratio of root shoulder width to root middle width were consistently detected on chromosome 2 in both years and explained 23.4–66.9% of the phenotypic variance. The effects of introgressed genomic segments from the wild species on the storage root are reported and will enable the identification of functional genes that control root morphological traits in carrot. Full article

(This article belongs to the Topic Plant Breeding, Genetics and Genomics)

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