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Advances in Genetic Diversity and Population Structure of Plant Species

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (20 September 2023) | Viewed by 23810

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Special Issue Editors

Prof. Dr. Xiangdong Liu

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Guest Editor

College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Interests: plant breeding and genetics; cytogenetics; plant reproduction biology; polyploidy; rice; plant germplasm enhancement
Special Issues, Collections and Topics in MDPI journals

Dr. Muhammud Qasim Shahid

E-Mail Website
Guest Editor

College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Interests: molecular markers; plant breeding and genetics; agricultural biotechnology; plant genomics; polyploidy; rice; agronomy; plant reproduction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The world is currently being confronted with an increasing population, food insecurity, and climate change. As of April 2019, the world population was estimated at 7.7 billion, and it is forecast to grow to more than 9 billion by 2050. Because the world’s is growing population at unprecedented rate, feeding this population is becoming big challenge, and there is a need to increase the world’s food production by 60%–110%. Industrialization has brought economic prosperity; additionally, it has resulted in a larger population and urbanization. However, it has played a significant role in climate change as well. Climate change is resulting in a hazardous scenario for global food security through reducing food production by disturbing the cropping pattern and lowering the resistance of crops to biotic and biotic stress. Researchers have applied plant breeding as the most effective tool for dealing with these issues. However, the role of plant breeding in genetic erosion is also universally accepted. Therefore, our current food cultivars are not performing well under these unpresented climatic conditions because of a genetic bottleneck. To mitigate all of these problems, there is a need to harness plant diversity.

The collection, conservation, and characterization of genetic resources is a valid strategy in this regard because it helps to explore the genotypic and phenotypic variations that can be effectively utilized by the breeding community. The narrow genetic base of our food crops can be broadened by considering landraces, crop wild relatives, and underutilized and neglected plant species. The development of new crop varieties that are resistant to various biotic and abiotic stress with enhanced yield and nutritional quality can be accelerated by applying and combining new and old breeding technologies. A new generation of foods and ingredients with enhanced intrinsic nutritional quality and taste could be developed through the utilization of plant diversity to improve the dietary patterns and health of the population.

This Special Issue will focus on highlighting the importance of plant biodiversity and genetic resources for a sustainable agriculture production system. We welcome original research papers, reviews, perspectives, opinions, and modeling approaches regarding plant genetic diversity; breeding, omics, and biotechnological technologies; and the biodiversity conservation of plant species.

Prof. Dr. Xiangdong Liu
Dr. Muhammud Qasim Shahid
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

germplasm characterization
phenotypic evaluation
molecular characterization
molecular breeding
germplasm conservation
phenotypic markers
molecular markers
functional markers
molecular breeding
next generation sequencing
genotyping by sequencing
marker-assisted selection
genetic mapping
QTL mapping
GWAS
plants
cereals
legumes
oilseeds
medicinal plants
endangered species
horticultural crops
genetic erosion
biodiversity conservation and enhancement
valuing plant genetic diversity
plant wild relatives
genetic improvement of crops
DNA banking for plant breeding
climate change resilience
cultivar development
agricultural productivity
omics and biotechnological technologies

Related Special Issue

Advances in Genetic Diversity and Population Structure of Plant Species, 2nd Edition in Plants (1 article)

Published Papers (14 papers)

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Research

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17 pages, 12136 KiB

Open AccessArticle

Comprehensive Genome-Wide Identification of the RNA-Binding Glycine-Rich Gene Family and Expression Profiling under Abiotic Stress in Brassica oleracea

by Mengmeng Duan, Mei Zong, Ning Guo, Shuo Han, Guixiang Wang, Liming Miao and Fan Liu

Plants 2023, 12(21), 3706; https://doi.org/10.3390/plants12213706 - 27 Oct 2023

Cited by 1 | Viewed by 979

Abstract

The RNA-binding glycine-rich proteins (RBGs) of the glycine-rich protein family play vital roles in regulating gene expression both at the transcriptional and post-transcriptional levels. However, the members and functions in response to abiotic stresses of the RBG gene family remain unclear in Brassica oleracea. In this study, a total of 19 BoiRBG genes were identified through genome-wide analysis in broccoli. The characteristics of BoiRBG sequences and their evolution were examined. An analysis of synteny indicated that the expansion of the BoiRBG gene family was primarily driven by whole-genome duplication and tandem duplication events. The BoiRBG expression patterns revealed that these genes are involved in reaction to diverse abiotic stress conditions (i.e., simulated drought, salinity, heat, cold, and abscisic acid) and different organs. In the present research, the up-regulation of BoiRBGA13 expression was observed when subjected to both NaCl-induced and cold stress conditions in broccoli. Moreover, the overexpression of BoiRBGA13 resulted in a noteworthy reduction in taproot lengths under NaCl stress, as well as the inhibition of seed germination under cold stress in broccoli, indicating that RBGs play different roles under various stresses. This study provides insights into the evolution and functions of BoiRBG genes in Brassica oleracea and other Brassicaceae family plants. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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12 pages, 3144 KiB

Open AccessArticle

A Structure Variation in qPH8.2 Detrimentally Affects Plant Architecture and Yield in Rice

by Wenqiang Sun, Qiang Sun, Li Tian, Yongjian Sun and Sibin Yu

Plants 2023, 12(18), 3336; https://doi.org/10.3390/plants12183336 - 21 Sep 2023

Cited by 1 | Viewed by 936

Abstract

Plant height is an important agronomic trait associated with plant architecture and grain yield in rice (Oryza sativa L.). In this study, we report the identification of quantitative trait loci (QTL) for plant height using a chromosomal segment substitution line (CSSL) population with substituted segments from japonica variety Nipponbare (NIP) in the background of the indica variety 9311. Eight stable QTLs for plant height were identified in three environments. Among them, six loci were co-localized with known genes such as semidwarf-1 (sd1) and Grain Number per Panicle1 (GNP1) involved in gibberellin biosynthesis. A minor QTL qPH8.2 on chromosome 8 was verified and fine-mapped to a 74 kb region. Sequence comparison of the genomic region revealed the presence/absence of a 42 kb insertion between NIP and 9311. This insertion occurred predominantly in temperate japonica rice. Comparisons on the near-isogenic lines showed that the qPH8.2 allele from NIP exhibits pleiotropic effects on plant growth, including reduced plant height, leaf length, photosynthetic capacity, delayed heading date, decreased yield, and increased tiller angle. These results indicate that qPH8.2 from temperate japonica triggers adverse effects on plant growth and yield when introduced into the indica rice, highlighting the importance of the inter-subspecies crossing breeding programs. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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24 pages, 3820 KiB

Open AccessArticle

Phenotypic Variation Analysis and Excellent Clone Selection of Alnus cremastogyne from Different Provenances

by Yue Zheng, Maosong Feng, Xue Li, Xingyan Huang, Gang Chen, Wenyu Bai, Xueju Xu, Jiayi Li, Xiaohong Li, Bin Leng, Hao Sun, Chunyan He and Yunjie Chen

Plants 2023, 12(18), 3259; https://doi.org/10.3390/plants12183259 - 13 Sep 2023

Cited by 1 | Viewed by 968

Abstract

Alnus cremastogyne is a rapidly growing broad-leaved tree species that is widely distributed in southwest China. It has a significant economic and ecological value. However, with the expansion of the planting area, the influence of phenotypic variation and differentiation on Alnus cremastogyne has increased, resulting in a continuous decline in its genetic quality. Therefore, it is crucial to investigate the phenotypic variation of Alnus cremastogyne and select excellent breeding materials for genetic improvement. Herein, four growth-related phenotypic traits (diameter at breast height, the height of trees, volume, height under the branches) and twelve reproductive-related phenotypic traits (fresh weight of single cone, dry weight of single cone, seed weight per plant, thousand kernel weight, cone length, cone width, cone length × cone width, fruit shape index, seed rate, germination rate, germination potential, germination index) of 40 clones from four provenances were measured and analyzed. The phenotypic variation was comprehensively evaluated by correlation analysis, principal component analysis and cluster analysis, and excellent clones were selected as breeding materials. The results revealed that there were abundant phenotypic traits variations among and within provenances. Most of the phenotypic traits were highly significant differences (p < 0.01) among provenances. The phenotypic variation among provenances (26.36%) was greater than that of within provenances clones (24.80%). The average phenotypic differentiation coefficient was accounted for 52.61% among provenances, indicating that the phenotypic variation mainly came from among provenances. The coefficient of variation ranged from 9.41% (fruit shape index) to 97.19% (seed weight per plant), and the repeatability ranged from 0.36 (volume) to 0.77 (cone width). Correlation analysis revealed a significantly positive correlation among most phenotypic traits. In principal component analysis, the cumulative contribution rate of the first three principal components was 79.18%, representing the main information on the measured phenotypic traits. The cluster analysis revealed four groups for the 40 clones. Group I and group II exhibited better performance phenotypic traits as compared with group III and group IV. In addition, the four groups are not clearly clustered following the distance from the provenance. Employing the multi-trait comprehensive evaluation method, 12 excellent clones were selected, and the average genetic gain for each phenotypic trait ranged from 4.78% (diameter at breast height) to 32.05% (dry weight of single cone). These selected excellent clones can serve as candidate materials for the improvement and transformation of Alnus cremastogyne seed orchards. In addition, this study can also provide a theoretical foundation for the genetic improvement, breeding, and clone selection of Alnus cremastogyne. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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12 pages, 3826 KiB

Open AccessArticle

Identification and Genome-Wide Gene Expression Perturbation of a Trisomy in Chinese Kale (Brassica oleracea var. alboglabra)

by Qun Feng, Junxing Yu, Jie Yu, Mingyang Hu, Lei Gu, Hongcheng Wang, Xuye Du, Bin Zhu and Mengxian Cai

Plants 2023, 12(18), 3199; https://doi.org/10.3390/plants12183199 - 7 Sep 2023

Viewed by 1146

Abstract

Trisomy harbouring an extra copy of the chromosome generally causes a variety of physical and intellectual disabilities in mammals but is an extremely rare and important genetic stock in plants. In this study, a spontaneous trisomy plant in a Chinese kale accession (Brassica oleracea var. alboglabra, CC, 2n = 18) that showed significantly smaller plant architecture when compared to other normal plants was found and subsequently confirmed by cytological analysis in which the chromosome set of 2n = 19 and abnormal chromosome behaviour were observed. Then, based on the gene expression deviation determined by RNA-seq, the extra chromosome copy in this trisomy was identified as chromosome C2 (TC2). Compared to normal plants, TC2 not only showed generally upregulated differentially expressed genes (DEGs) on chromosome C2 (97.21% of 573 DEGs in chromosome C2) but also exhibited a whole-genome expression perturbation, in which 1329 DEGs (69.87% of total DEGs) were observed along two-copy chromosomes (trans-effect). The genes in the high (gene expression value > 100) and medium (100 > gene expression value > 10) groups were more prone to decreased gene expression, but the genes in the low group (10 > gene expression value > 0.1) showed upregulated expression deviation. In addition, GO (Gene ontology) annotation analysis revealed that the upregulated DEGs in the trans-effect group were overrepresented by the genes involved in the response to stress category, while the downregulated DEGs in the trans-effect group were mostly enriched in pathways related to DNA synthesis. In conclusion, we think our results can provide important resources for genetic analysis in B. oleracea and show some novel insights for understanding trisomy plant biology. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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12 pages, 5149 KiB

Open AccessArticle

Genome-Wide Identification, Phylogeny and Expression Analysis of Subtilisin (SBT) Gene Family under Wheat Biotic and Abiotic Stress

by Xiaotong Zhao, Farhan Goher, Lei Chen, Jiancheng Song and Jiqiang Zhao

Plants 2023, 12(17), 3065; https://doi.org/10.3390/plants12173065 - 25 Aug 2023

Cited by 1 | Viewed by 1282

Abstract

The subtilisin-like protease (SBT) family is widely known for its role in stress resistance to a number of stressors in different plant species, but is rarely studied in wheat. Subtilisin-like serine proteases (SBTs) are serine proteolytic enzymes that hydrolyze proteins into small peptides, which bind to receptors as signal molecules or ligands and participate in signal transduction. In this study, we identified 255 putative SBT genes from the wheat reference genome and then divided these into seven clades. Subsequently, we performed syntenic relation analysis, exon-intron organization, motif composition, and cis-element analysis. Further, expression analysis based on RNA-seq and tissue-specific expression patterns revealed that TaSBT gene family expression has multiple intrinsic functions during various abiotic and biotic stresses. Analysis of RNA-seq expression assays and further validation through qRT PCR suggested that some of the TaSBT genes have significant changes in expression levels during Pst interaction. TaSBT7, TaSBT26, TaSBT102, and TaSBT193 genes showed increasing expression levels during compatible and non-compatible interactions, while the expression levels of TaSBT111 and TaSBT213 showed a decreasing trend, indicating that these members of the wheat SBT gene family may have a role in wheat’s defense against pathogens. In conclusion, these results expand our understanding of the SBT gene family, and provide a valuable reference for future research on the stress resistance function and comprehensive data of wheat SBT members. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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12 pages, 1263 KiB

Open AccessArticle

Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers

by Rongju Li, Yinling Huang, Xinsen Yang, Meng Su, Huaiyang Xiong, Yang Dai, Wei Wu, Xinwu Pei and Qianhua Yuan

Plants 2023, 12(15), 2876; https://doi.org/10.3390/plants12152876 - 5 Aug 2023

Cited by 2 | Viewed by 1403

Abstract

Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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12 pages, 1334 KiB

Open AccessArticle

Population Structure of Modern Winter Wheat Accessions from Central Asia

by Akerke Amalova, Kanat Yermekbayev, Simon Griffiths, Mark Owen Winfield, Alexey Morgounov, Saule Abugalieva and Yerlan Turuspekov

Plants 2023, 12(12), 2233; https://doi.org/10.3390/plants12122233 - 6 Jun 2023

Cited by 1 | Viewed by 1065

Abstract

Despite the importance of winter wheat in Central Asian countries, there are limited reports describing their diversity within this region. In this study, the population structures of 115 modern winter wheat cultivars from four Central Asian countries were compared to germplasms from six other geographic origins using 10,746 polymorphic single-nucleotide polymorphism (SNP) markers. After applying the STRUCTURE package, we found that in terms of the most optimal K steps, samples from Kazakhstan and Kyrgyzstan were grouped together with samples from Russia, while samples from Tajikistan and Uzbekistan were grouped with samples from Afghanistan. The mean value of Nei’s genetic diversity index for the germplasm from four groups from Central Asia was 0.261, which is comparable to that of the six other groups studied: Europe, Australia, the USA, Afghanistan, Turkey, and Russia. The Principal Coordinate Analysis (PCoA) showed that samples from Kyrgyzstan, Tajikistan, and Uzbekistan were close to samples from Turkey, while Kazakh accessions were located near samples from Russia. The evaluation of 10,746 SNPs in Central Asian wheat suggested that 1006 markers had opposing allele frequencies. Further assessment of the physical positions of these 1006 SNPs in the Wheat Ensembl database indicated that most of these markers are constituents of genes associated with plant stress tolerance and adaptability. Therefore, the SNP markers identified can be effectively used in regional winter wheat breeding projects for facilitating plant adaptation and stress resistance. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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12 pages, 1981 KiB

Open AccessArticle

Identification, Characterization, and Cytological Analysis of Several Unexpected Hybrids Derived from Reciprocal Crosses between Raphanobrassica and Its Diploid Parents

by Jie Yu, Shaolin Lei, Shiting Fang, Niufang Tai, Wei Yu, Ziwei Yang, Lei Gu, Hongcheng Wang, Xuye Du, Bin Zhu and Mengxian Cai

Plants 2023, 12(9), 1875; https://doi.org/10.3390/plants12091875 - 4 May 2023

Cited by 1 | Viewed by 1545

Abstract

Interspecific hybridization and accompanying backcross between crops and relatives have been recognized as a powerful method to broaden genetic diversity and transfer desirable adaptive traits. Crosses between radish (Raphanus sativus, RR, 2n = 18) and Brassica oleracea (CC, 2n = 18), which formed allotetraploid Raphanobrassica (RRCC, 2n = 36), initiated the construction of resynthetic allopolyploids. However, these progenies from the backcrosses between Raphanobrassica and the two diploid parents have not been well deciphered. Herein, thousands of backcrosses using both Raphanobrassica and the two diploid parents as pollen donors were employed. Several hybrids with expected (2n = 27) and unexpected chromosome numbers (2n = 26 and 2n = 36) were obtained. Fluorescence in situ hybridization (FISH) analysis with R-genome-specific sequences as probes demonstrated that the genome structures of the two expected hybrids were RRC and CCR, and the genome structures of the three unexpected hybrids were RRRC, CCCR, and RRC’ (harbouring an incomplete C genome). The unexpected hybrids with extra R or C genomes showed similar phenotypic characteristics to their expected hybrids. FISH analysis with C-genome-specific sequences as probes demonstrated that the unexpected allotetraploid hybrids exhibited significantly more intergenomic chromosome pairings than the expected hybrids. The expected and unexpected hybrids provide not only novel germplasm resources for the breeding of radish and B. oleracea but also very important genetic material for genome dosage analysis. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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13 pages, 1921 KiB

Open AccessArticle

Population Genomics Study and Implications for the Conservation of Zabelia tyaihyonii Based on Genotyping-By-Sequencing

by Halam Kang, Sung-Mo An, Yoo-Jung Park, Yoo-Bin Lee, Jung-Hyun Lee, Kyeong-Sik Cheon and Kyung-Ah Kim

Plants 2023, 12(1), 171; https://doi.org/10.3390/plants12010171 - 30 Dec 2022

Cited by 3 | Viewed by 1834

Abstract

Zabelia tyaihyonii (Nakai) Hisauti and H. Hara is a perennial shrub endemic to Republic of Korea that grows naturally in only a very limited region of the dolomite areas of Gangwon-do and Chungcheongbuk-do Provinces in the Republic of Korea. Given its geographical characteristics, it is more vulnerable than more widely distributed species. Despite the need for comprehensive information to support conservation, population genetic information for this species is very scarce. In this study, we analyzed the genetic diversity and population structure of 94 individuals from six populations of Z. tyaihyonii using a genotyping-by-sequencing (GBS) approach to provide important information for proper conservation and management. Our results, based on 3088 single nucleotide polymorphisms (SNPs), showed a mean expected heterozygosity (He) of 0.233, no sign of within-population inbreeding (G_IS that was close to or even below zero in all populations), and a high level of genetic differentiation (F_ST = 0.170). Analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (84.5%) rather than among populations (17.0%). We suggested that six management units were proposed for conservation considering Bayesian structure analysis and phylogenetic analysis, and given the various current situations faced by Z. tyaihyonii, it is believed that not only the in situ conservation but also the ex situ conservation should be considered. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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17 pages, 5544 KiB

Open AccessArticle

Genomic and Morphological Differentiation of Spirit Producing Agave angustifolia Traditional Landraces Cultivated in Jalisco, Mexico

by Dánae Cabrera-Toledo, Eddy Mendoza-Galindo, Nerea Larranaga, Alfredo Herrera-Estrella, Marilyn Vásquez-Cruz and Tania Hernández-Hernández

Plants 2022, 11(17), 2274; https://doi.org/10.3390/plants11172274 - 31 Aug 2022

Cited by 6 | Viewed by 5224

Abstract

Traditional agave spirits such as mezcal or tequila are produced all over Mexico using different species of Agave. Amongst them, A. angustifolia is the most popular given its agricultural extension. A. angustifolia is a wild species extensively distributed from North to Central America, and previous studies show that it is highly related to the tequila agave A. tequilana. In different regions of Mexico, A. angustifolia is cultivated under different types and levels of management, and although traditional producers identify several landraces, for the non-trained eye there are no perceivable differences. After interviews with producers from different localities in Jalisco, Mexico, we sampled A. angustifolia plants classified as different landraces, measured several morphological traits, and characterized their genetic differentiation and diversity at the genome-wide level. We included additional samples identified as A. tequilana and A. rhodacantha to evaluate their relationship with A. angustifolia. In contrast with previous studies, our pool of ca 20K high quality unlinked SNPs provided more information and helped us to distinguish different genetic groups that are congruent with the ethnobotanical landraces. We found no evidence to genetically delimitate A. tequilana, A. rhodacantha and A. angustifolia. Our large genome level dataset allows a better understanding of the genetic identity of important A. angustifolia traditional and autochthonous landraces. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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11 pages, 1496 KiB

Open AccessArticle

Source Identification and Genome-Wide Association Analysis of Crown Rot Resistance in Wheat

by Lefan Pu, Farhan Goher, Mengke Zeng, Dongsheng Wu, Qingdong Zeng, Dejun Han and Chunlian Li

Plants 2022, 11(15), 1912; https://doi.org/10.3390/plants11151912 - 24 Jul 2022

Viewed by 1431

Abstract

Crown rot (CR) is a soil-borne disease of wheat in arid and semiarid areas of the world. The incidence rate and severity of CR are increasing with each passing year, which seriously threatens the safety of world wheat production. Here, 522 wheat varieties/lines representing genetic diversity were used to identify and evaluate the resistance source to CR disease. Six varieties, including Zimai 12, Xinong 509, Mazhamai, Sifangmai, and Dawson, were classified as resistant ® to CR. Seventy-nine varieties were classified as moderately resistant (MR) to CR, accounting for 15.13% of the tested varieties. The wheat 660 K SNP array was used to identify resistance loci by genome-wide association analysis (GWAS). A total of 33 SNPs, located on chromosomes 1A, 1B, 1D, 4A, and 4D, were significantly correlated with seedling resistance to CR in two years. Among them, one SNP on chromosome 1A and nine SNPs on chromosome 1B showed most significant resistance to disease, phenotypic variance explained (PVE) by these SNPs were more than 8.45%. Except that significant locus AX-110436287 and AX109621209 on chromosome 1B and AX-94692276 on 1D are close to the already reported QTL, other SNPs are newly discovered resistance loci. These results could lay a strong theoretical foundation for the genetic improvement and breeding for CR resistance in wheat. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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20 pages, 1609 KiB

Open AccessArticle

Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan

by Yuliya Genievskaya, Nicola Pecchioni, Giovanni Laidò, Shynar Anuarbek, Aralbek Rsaliyev, Vladimir Chudinov, Alibek Zatybekov, Yerlan Turuspekov and Saule Abugalieva

Plants 2022, 11(15), 1904; https://doi.org/10.3390/plants11151904 - 22 Jul 2022

Cited by 5 | Viewed by 1835

Abstract

Leaf rust (LR) and stem rust (SR) are diseases increasingly impacting wheat production worldwide. Fungal pathogens producing rust diseases in wheat may cause yield losses of up to 50–60%. One of the most effective methods for preventing such losses is the development of resistant cultivars with high yield potential. This goal can be achieved through complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. The objective of this study was to identify sources of tetraploid wheat resistance to LR and SR races, both at the seedling growth stage in the greenhouse and at the adult plant stage in field experiments, under the conditions of the North Kazakhstan region. A panel consisting of 193 tetraploid wheat accessions was used in a genome-wide association study (GWAS) for the identification of quantitative trait loci (QTLs) associated with LR and SR resistance, using 16,425 polymorphic single-nucleotide polymorphism (SNP) markers in the seedling and adult stages of plant development. The investigated panel consisted of seven tetraploid subspecies (Triticum turgidum ssp. durum, ssp. turanicum, ssp. turgidum, ssp. polonicum, ssp. carthlicum, ssp. dicoccum, and ssp. dicoccoides). The GWAS, based on the phenotypic evaluation of the tetraploid collection’s reaction to the two rust species at the seedling (in the greenhouse) and adult (in the field) stages, revealed 38 QTLs (p < 0.001), comprising 17 for LR resistance and 21 for SR resistance. Ten QTLs were associated with the reaction to LR at the seedling stage, while six QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. Eleven QTLs were associated with SR response at the seedling stage, while nine QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. A comparison of these results with previous LR and SR studies indicated that 11 of the 38 QTLs are presumably novel loci. The QTLs identified in this work can potentially be used for marker-assisted selection of tetraploid and hexaploid wheat for the breeding of new LR- and SR-resistant cultivars. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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11 pages, 4384 KiB

Open AccessBrief Report

Population Structure and Genetic Diversity of the 175 Soybean Breeding Lines and Varieties Cultivated in West Siberia and Other Regions of Russia

by Nadezhda A. Potapova, Alexander S. Zlobin, Roman N. Perfil’ev, Gennady V. Vasiliev, Elena A. Salina and Yakov A. Tsepilov

Plants 2023, 12(19), 3490; https://doi.org/10.3390/plants12193490 - 6 Oct 2023

Viewed by 1054

Abstract

Soybean is a leguminous plant cultivated in many countries and is considered important in the food industry due to the high levels of oil and protein content in the beans. The high demand for soybeans and its products in the industry requires the expansion of cultivation areas. Despite climatic restrictions, West Siberia is gradually expanding its area of soybean cultivation. In this study, we present the first analysis of the population structure and genetic diversity of the 175 soybean Glycine max breeding lines and varieties cultivated in West Siberia (103 accessions) and other regions of Russia (72 accessions), and we compare them with the cultivated soybean varieties from other geographical locations. Principal component analysis revealed several genetic clusters with different levels of genetic heterogeneity. Studied accessions are genetically similar to varieties from China, Japan, and the USA and are genetically distant to varieties from South Korea. Admixture analysis revealed four ancestry groups based on genetic ancestry and geographical origin, which are consistent with the regions of cultivation and origin of accessions and correspond to the principal component analysis result. Population statistics, including nucleotide diversity, Tajima’s D, and linkage disequilibrium, are comparatively similar to those observed for studied accessions of a different origin. This study provides essential population and genetic information about the unique collection of breeding lines and varieties cultivated in West Siberia and other Russian regions to foster further evolutionary, genome-wide associations and functional breeding studies. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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9 pages, 2430 KiB

Open AccessViewpoint

Unraveling Large and Polyploidy Genome of the Crucifer Orychophragmus violaceus in China, a Potential Oil Crop

by Qi Pan, Pan Zeng and Zaiyun Li

Plants 2023, 12(2), 374; https://doi.org/10.3390/plants12020374 - 13 Jan 2023

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Abstract

The genus Orychophragmus in the Brassicaceae family includes the types with 2n = 20, 22, 24, and 48. The species O. violaceus (L.) O. E. Schulz has 2n = 24 and is widely cultivated as an ornamental plant in China. This review summarizes the research progress of its genome structure and evolution in the context of cytogenetics and genome sequencing. This species has a large genome size of ~1 Gb and longer chromosomes than those of Brassica species, which is attributable to the burst of TE insertions. Even more, one tetraploidization event from about 600–800 million years ago is elucidated to occur during its genome evolution, which is consistent with the polyploidy nature of its genome revealed by the meiotic pairing patterns. Its chromosomes are still characterized by a larger size and deeper staining than those from Brassica species in their intergeneric hybrids, which is likely related to their inherent differences between genome structures and cytology. Its genome is dissected by the development of additional alien lines, and some traits are located on individual chromosomes. Due to the abundant dihydroxy fatty acids in its seed oil with superior lubricant properties and wide environmental adaptations, this plant promises to be utilized as one new oil crop in the future. Full article

(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species)

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