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Special Issue "Advances in Genetics and Breeding of Grain Crops"

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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: 31 October 2023 | Viewed by 22183

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Special Issue Editors

Dr. Rajib Roychowdhury

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Guest Editor

Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO) – The Volcani Center, Rishon Lezion, Israel
Interests: crop genetics and genomics; marker-assisted breeding; disease resistance in plants; abiotic stress tolerance
Special Issues, Collections and Topics in MDPI journals

Dr. Francisco Fuentes

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Guest Editor

Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul. Casilla 306-22, Santiago, Chile
Interests: plant genetic improvement; plant genetic resources; integrated crop production systems; bioprospecting of natural products; nutrigenomic
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

All the human inhabitants and domesticated animals of our planet depend on grain crops for food and feed. Grain crops are field crops, and are categorized into major cereals (wheat, rice, maize, and rye), minor cereals (barley and oat), small grains (sorghum, teff, and millets), pseudocereals (quinoa and buckwheat), legumes (groundnut, soybean, pea, chickpea, cowpea, bean, lentil and grams), and others (e.g., sesame). These grain crops are used as major carbohydrate sources, protein sources, and edible oils. However, the ongoing changing climate negatively impacts grain crops by reducing the yield and quality attributes. Breeding these crops is a means of sustainable agriculture, in order to produce climate-smart grain with higher productivity and nutritive quality. Grain researchers are attempting to apply various approaches to improve grains, some of which follow: manipulating agronomical practices, assessing the interaction of the crops with multiple environments, breeding strategies involving the incorporation of beneficial traits, utilizing ever losing ancient genetic resources in breeding, high-throughput in-field phenotyping by using unmanned aerial vehicles (UAVs) and spectral platforms, finding the responsible genes and their mechanism of action for particular traits of interest, genetic analysis and QTLs for abiotic stress (drought, salinity, heat, cold, heavy metals and UV), tolerance and resistance to various diseases caused by fungal, bacterial and viral pathogens, mutagenesis and gene editing technologies to validate gene functionality, etc. As we are unable to manipulate the climate at the macroscale, scientific research on grain crops, using modern breeding technologies, can delimit the barrier to improve grains for the world's inhabitants.

Dr. Rajib Roychowdhury
Dr. Francisco Fuentes
Guest Editors

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Keywords

grain genetic resources
domestication traits
quality improvement
yield (grain number and weight) improvement
abiotic stress tolerance
heavy metal stress
disease resistance
Genotype–environment interaction (GxE)
genomic-assisted breeding
UAV and spectral analysis
marker-assisted selection and breeding
genomics strategies to understand beneficial traits
QTL mapping
mutagenesis
gene editing

Published Papers (18 papers)

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Research

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Open AccessArticle

Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum

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Plants 2023, 12(18), 3321; https://doi.org/10.3390/plants12183321 - 20 Sep 2023

Viewed by 218

Abstract

Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei’s expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice

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Plants 2023, 12(16), 2959; https://doi.org/10.3390/plants12162959 - 16 Aug 2023

Viewed by 420

Abstract

The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop yield, we conducted genome-wide transcriptomic analysis. By integrating our RNA sequencing data with public rice anatomical expression data, we identified 657 CRPGs. Verification involved testing six randomly selected CRPGs, all of which exhibited collar-preferential expression. The functional significance of CRPGs was assessed via Gene Ontology enrichment analysis, utilizing MapMan and KEGG, and literature analysis provided additional information for characterized CRPGs. Our findings revealed links between manipulating leaf angle and phytohormone-related pathways and stress responses. Moreover, based on the CRPGs, five transcription factors downstream of the liguleless 1 (LG1) gene were identified. Overall, the identified CRPGs provide potential targets for further research and breeding applications aimed at improving crop productivity by manipulating leaf architecture. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Construction of High-Density Genetic Map and QTL Mapping for Grain Shape in the Rice RIL Population

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Plants 2023, 12(16), 2911; https://doi.org/10.3390/plants12162911 - 10 Aug 2023

Viewed by 378

Abstract

Grain shape is an important agronomic trait directly associated with yield in rice. In order to explore new genes related to rice grain shape, a high-density genetic map containing 2193 Bin markers (526957 SNP) was constructed by whole-genome resequencing of 208 recombinant inbred (RILs) derived from a cross between ZP37 and R8605, with a total genetic distance of 1542.27 cM. The average genetic distance between markers was 0.76 cM, and the physical distance was 201.29 kb. Quantitative trait locus (QTL) mapping was performed for six agronomic traits related to rice grain length, grain width, length-to-width ratio, thousand-grain weight, grain cross-sectional area, and grain perimeter under three different environments. A total of 39 QTLs were identified, with mapping intervals ranging from 8.1 kb to 1781.6 kb and an average physical distance of 517.5 kb. Among them, 15 QTLs were repeatedly detected in multiple environments. Analysis of the genetic effects of the identified QTLs revealed 14 stable genetic loci, including three loci that overlapped with previously reported gene positions, and the remaining 11 loci were newly identified loci associated with two or more environments or traits. Locus 1, Locus 3, Locus 10, and Locus 14 were novel loci exhibiting pleiotropic effects on at least three traits and were detected in multiple environments. Locus 14, with a contribution rate greater than 10%, influenced grain width, length-to-width ratio, and grain cross-sectional area. Furthermore, pyramiding effects analysis of three stable genetic loci showed that increasing the number of QTL could effectively improve the phenotypic value of grain shape. Collectively, our findings provided a theoretical basis and genetic resources for the cloning, functional analysis, and molecular breeding of genes related to rice grain shape. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice

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Plants 2023, 12(11), 2206; https://doi.org/10.3390/plants12112206 - 03 Jun 2023

Cited by 1 | Viewed by 830

Abstract

Alkalinity stress is a major hindrance to enhancing rice production globally due to its damaging effect on plants’ growth and development compared with salinity stress. However, understanding of the physiological and molecular mechanisms of alkalinity tolerance is limited. Therefore, a panel of indica and japonica rice genotypes was evaluated for alkalinity tolerance at the seedling stage in a genome-wide association study to identify tolerant genotypes and candidate genes. Principal component analysis revealed that traits such as alkalinity tolerance score, shoot dry weight, and shoot fresh weight had the highest contribution to variations in tolerance, while shoot Na⁺ concentration, shoot Na⁺:K⁺ ratio, and root-to-shoot ratio had moderate contributions. Phenotypic clustering and population structure analysis grouped the genotypes into five subgroups. Several salt-susceptible genotypes such as IR29, Cocodrie, and Cheniere placed in the highly tolerant cluster suggesting different underlying tolerance mechanisms for salinity and alkalinity tolerance. Twenty-nine significant SNPs associated with alkalinity tolerance were identified. In addition to three alkalinity tolerance QTLs, qSNK4, qSNC9, and qSKC10, which co-localized with the earlier reported QTLs, a novel QTL, qSNC7, was identified. Six candidate genes that were differentially expressed between tolerant and susceptible genotypes were selected: LOC_Os04g50090 (Helix-loop-helix DNA-binding protein), LOC_Os08g23440 (amino acid permease family protein), LOC_Os09g32972 (MYB protein), LOC_Os08g25480 (Cytochrome P450), LOC_Os08g25390 (Bifunctional homoserine dehydrogenase), and LOC_Os09g38340 (C2H2 zinc finger protein). The genomic and genetic resources such as tolerant genotypes and candidate genes would be valuable for investigating the alkalinity tolerance mechanisms and for marker-assisted pyramiding of the favorable alleles for improving alkalinity tolerance at the seedling stage in rice. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Identification and Expression Analysis of the Isopentenyl Transferase (IPT) Gene Family under Lack of Nitrogen Stress in Oilseed (Brassica napus L.)

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Plants 2023, 12(11), 2166; https://doi.org/10.3390/plants12112166 - 30 May 2023

Cited by 1 | Viewed by 589

Abstract

BnIPT gene family members in Brassica napus and analyzing their expression under different exogenous hormones and abiotic stress treatments to provide a theoretical basis for clarifying their functions and molecular genetic mechanisms in nitrogen deficiency stress tolerance of B. napus. Using the Arabidopsis IPT protein as the seed sequence, combined with the IPT protein domain PF01715, 26 members of the BnIPT gene family were identified from the whole genome of the rape variety ZS11. Additionally, the physicochemical properties and structures, phylogenetic relationships, synteny relationships, protein–protein interaction network, and gene ontology enrichment were analyzed. Based on transcriptome data, the expression patterns of the BnIPT gene under different exogenous hormone and abiotic stress treatments were analyzed. We used the qPCR method to identify the relative expression level of BnIPT genes that may be related to the stress resistance of rapeseed in transcriptome analysis under normal nitrogen (N: 6 mmol·L⁻¹) and nitrogen deficiency (N: 0) conditions and analyzed its effect on rapeseed under nitrogen deficiency stress role in tolerance. In response to nitrogen deficiency signals, the BnIPT gene showed a trend of up-regulation in shoots and down-regulation in roots, indicating that it may affect the process of nitrogen transport and redistribution to enhance the stress resistance of rapeseed to respond to the nitrogen deficiency stress. This study provides a theoretical basis for clarifying the function and molecular genetic mechanism of the BnIPT gene family in nitrogen deficiency stress tolerance in rape. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Integrating BLUP, AMMI, and GGE Models to Explore GE Interactions for Adaptability and Stability of Winter Lentils (Lens culinaris Medik.)

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Plants 2023, 12(11), 2079; https://doi.org/10.3390/plants12112079 - 23 May 2023

Viewed by 1380

Abstract

Lentil yield is a complicated quantitative trait; it is significantly influenced by the environment. It is crucial for improving human health and nutritional security in the country as well as for a sustainable agricultural system. The study was laid out to determine the stable genotype through the collaboration of G × E by AMMI and GGE biplot and to identify the superior genotypes using 33 parametric and non-parametric stability statistics of 10 genotypes across four different conditions. The total G × E effect was divided into two primary components by the AMMI model. For days to flowering, days to maturity, plant height, pods per plant, and hundred seed weight, IPCA1 was significant and accounted for 83%, 75%, 100%, and 62%, respectively. Both IPCA1 and IPCA2 were non-significant for yield per plant and accounted for 62% of the overall G × E interaction. An estimated set of eight stability parameters showed strong positive correlations with mean seed yield, and these measurements can be utilized to choose stable genotypes. The productivity of lentils has varied greatly in the environment, ranging from 786 kg per ha in the MYM environment to 1658 kg per ha in the ISD environment, according to the AMMI biplot. Three genotypes (G8, G7, and G2) were shown to be the most stable based on non-parametric stability scores for grain yield. G8, G7, G2, and G5 were determined as the top lentil genotypes based on grain production using numerical stability metrics such as Francis’s coefficient of variation, Shukla stability value (σi²), and Wrick’s ecovalence (Wi). Genotypes G7, G10, and G4 were the most stable with the highest yield, according to BLUP-based simultaneous selection stability characteristics. The findings of graphic stability methods such as AMMI and GGE for identifying the high-yielding and stable lentil genotypes were very similar. While the GGE biplot indicated G2, G10, and G7 as the most stable and high-producing genotypes, AMMI analysis identified G2, G9, G10, and G7. These selected genotypes would be used to release a new variety. Considering all the stability models, such as Eberhart and Russell’s regression and deviation from regression, additive main effects, multiplicative interactions (AMMI) analysis, and GGE, the genotypes G2, G9, and G7 could be used as well-adapted genotypes with moderate grain yield in all tested environments. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Genetic Analyses of Mungbean [Vigna radiata (L.) Wilczek] Breeding Traits for Selecting Superior Genotype(s) Using Multivariate and Multi-Traits Indexing Approaches

Mohammad Golam Azam

Mohammad Amir Hossain

Umakanta Sarker

A. K. M. Mahabubul Alam

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Plants 2023, 12(10), 1984; https://doi.org/10.3390/plants12101984 - 15 May 2023

Cited by 2 | Viewed by 1510

Abstract

Mungbean [Vigna radiata (L.) Wilczek] is an important food, feed, and cash crop in rice-based agricultural ecosystems in Southeast Asia and other continents. It has the potential to enhance livelihoods due to its palatability, nutritional content, and digestibility. We evaluated 166 diverse mungbean genotypes in two seasons using multivariate and multi-traits index approaches to identify superior genotypes. The total Shannon diversity index (SDI) for qualitative traits ranged from moderate for terminal leaflet shape (0.592) to high for seed colour (1.279). The analysis of variances (ANOVA) indicated a highly significant difference across the genotypes for most of the studied traits. Descriptive analyses showed high diversity among genotypes for all morphological traits. Six components with eigen values larger than one contributed 76.50% of the variability in the principal component analysis (PCA). The first three PCs accounted for the maximum 29.90%, 15.70%, and 11.20% of the total variances, respectively. Yield per plant, pod weight, hundred seed weight, pod length, days to maturity, pods per plant, harvest index, biological yield per plant, and pod per cluster contributed more to PC1 and PC2 and showed a positive association and positive direct effect on seed yield. The genotypes were grouped into seven clusters with the maximum in cluster II (34) and the minimum in cluster VII (10) along with a range of intra-cluster and inter-cluster distances of 5.15 (cluster II) to 3.60 (cluster VII) and 9.53 (between clusters II and VI) to 4.88 (clusters I and VII), suggesting extreme divergence and the possibility for use in hybridization and selection. Cluster III showed the highest yield and yield-related traits. Yield per plant positively and significantly correlated with pod traits and hundred seed weight. Depending on the multi-trait stability index (MTSI), clusters I, III, and VII might be utilized as parents in the hybridization program to generate high-yielding, disease-resistant, and small-seeded mungbean. Based on all multivariate-approaches, G45, G5, G22, G55, G143, G144, G87, G138, G110, G133, and G120 may be considered as the best parents for further breeding programs. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Marker-Assisted Improvement for Durable Bacterial Blight Resistance in Aromatic Rice Cultivar HUR 917 Popular in Eastern Parts of India

Panduranga Bhagwan Arsode

Madhu Choudhary

Prakash Singh

Suman Chahar

Sanghamitra Samantaray

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Plants 2023, 12(6), 1363; https://doi.org/10.3390/plants12061363 - 18 Mar 2023

Viewed by 1247

Abstract

Bacterial blight (BB) is a devastating disease of rice in the tropics of Indian sub-continent, where the presence of Xoo races with varying levels of genetic diversity and virulence renders disease management extremely challenging. In this context, marker-assisted improvement of plant resistance has been proven as one of the most promising approaches for the development of sustainable rice cultivars. The present study demonstrates the marker-assisted introgression of the three BB resistant genes (Xa21 + xa13 + xa5) into the background of HUR 917, a popular aromatic short grain (ASG) rice cultivar in India. The performance of the resulting improved products (near isogenic lines (NILs), HR 23-5-37-83-5, HR 23-5-37-121-10, HR 23-5-37-121-14, HR 23-65-6-191-13, HR 23-65-6-237-2, HR 23-65-6-258-10 and HR 23-65-6-258-21) establishes the utility of marker-assisted selection (MAS) approach for accelerated trait introgression in rice. The MAS-bred lines carrying three introgressed genes showed broad spectrum BB resistance (lesion length, LL of 1.06 ± 1.35 cm to 4.61 ± 0.87 cm). Besides, these improved lines showed the complete product profile of recurrent parent HUR 917 along with the enhanced level of durable BB resistance. The improved introgression lines with durable BB resistance would contribute to sustainable rice production in India, particularly in the Indo-Gangetic plane that has substantial acreage under HUR 917. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Marker-Assisted Pyramiding of Blast-Resistance Genes in a japonica Elite Rice Cultivar through Forward and Background Selection

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Plants 2023, 12(4), 757; https://doi.org/10.3390/plants12040757 - 08 Feb 2023

Viewed by 1204

Abstract

Rice blast, caused by Pyricularia oryzae, is one of the main rice diseases worldwide. The pyramiding of blast-resistance (Pi) genes, coupled to Marker-Assisted BackCrossing (MABC), provides broad-spectrum and potentially durable resistance while limiting the donor genome in the background of an elite cultivar. In this work, MABC coupled to foreground and background selections based on KASP marker assays has been applied to introgress four Pi genes (Piz, Pib, Pita, and Pik) in a renowned japonica Italian rice variety, highly susceptible to blast. Molecular analyses on the backcross (BC) lines highlighted the presence of an additional blast-resistance gene, the Pita-linked Pita2/Ptr gene, therefore increasing the number of blast-resistance introgressed genes to five. The recurrent genome was recovered up to 95.65%. Several lines carrying four (including Pita2) Pi genes with high recovery percentage levels were also obtained. Phenotypic evaluations confirmed the effectiveness of the pyramided lines against multivirulent strains, which also had broad patterns of resistance in comparison to those expected based on the pyramided Pi genes. The developed blast-resistant japonica lines represent useful donors of multiple blast-resistance genes for future rice-breeding programs related to the japonica group. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Analysis of Domestication Loci in Wild Rice Populations

Sharmin Hasan

Agnelo Furtado

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Robert Henry

Plants 2023, 12(3), 489; https://doi.org/10.3390/plants12030489 - 20 Jan 2023

Viewed by 1236

Abstract

The domestication syndrome is defined as a collection of domestication-related traits that have undergone permanent genetic changes during the domestication of cereals. Australian wild rice populations have not been exposed to gene flow from domesticated rice populations. A high level of natural variation of the sequences at domestication loci (e.g., seed shattering, awn development, and grain size) was found in Australian AA genome wild rice from the primary gene pool of rice. This natural variation is much higher than that found in Asian cultivated rice and wild Asian rice populations. The Australian Oryza meridionalis populations exhibit a high level of homozygous polymorphisms relative to domesticated rice, inferring the fixation of distinct wild and domesticated alleles. Alleles of the seed shattering genes (SH4/SHA1 and OsSh1/SH1) present in the shattering-prone O. meridionalis populations are likely to be functional, while the dysfunctional alleles of these seed shattering genes are found in domesticated rice. This confirms that unlike Asian wild rice populations, Australian wild rice populations have remained genetically isolated from domesticated rice, retaining pre-domestication alleles in their wild populations that uniquely allow the impact of domestication on the rice genome to be characterized. This study also provides key information about the domestication loci in Australian wild rice populations that will be valuable in the utilization of these genetic resources in crop improvement and de novo domestication. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Novel Single-Nucleotide Variants for Morpho-Physiological Traits Involved in Enhancing Drought Stress Tolerance in Barley

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Plants 2022, 11(22), 3072; https://doi.org/10.3390/plants11223072 - 13 Nov 2022

Cited by 1 | Viewed by 951

Abstract

Barley (Hordeum vulgare L.) thrives in the arid and semi-arid regions of the world; nevertheless, it suffers large grain yield losses due to drought stress. A panel of 426 lines of barley was evaluated in Egypt under deficit (DI) and full irrigation (FI) during the 2019 and 2020 growing seasons. Observations were recorded on the number of days to flowering (NDF), total chlorophyll content (CH), canopy temperature (CAN), grain filling duration (GFD), plant height (PH), and grain yield (Yield) under DI and FI. The lines were genotyped using the 9K Infinium iSelect single nucleotide polymorphisms (SNP) genotyping platform, which resulted in 6913 high-quality SNPs. In conjunction with the SNP markers, the phenotypic data were subjected to a genome-wide association scan (GWAS) using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK). The GWAS results indicated that 36 SNPs were significantly associated with the studied traits under DI and FI. Furthermore, eight markers were significant and common across DI and FI water regimes, while 14 markers were uniquely associated with the studied traits under DI. Under DI and FI, three (11_10326, 11_20042, and 11_20170) and five (11_20099, 11_10326, 11_20840, 12_30298, and 11_20605) markers, respectively, had pleiotropic effect on at least two traits. Among the significant markers, 24 were annotated to known barley genes. Most of these genes were involved in plant responses to environmental stimuli such as drought. Overall, nine of the significant markers were previously reported, and 27 markers might be considered novel. Several markers identified in this study could enable the prediction of barley accessions with optimal agronomic performance under DI and FI. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Genetic Variability, Character Association, and Path Coefficient Analysis in Transplant Aman Rice Genotypes

Abu Salah Muhammad Faysal

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Plants 2022, 11(21), 2952; https://doi.org/10.3390/plants11212952 - 02 Nov 2022

Cited by 9 | Viewed by 1410

Abstract

A field experiment was carried out with 20 genotypes of Transplant Aman (T. Aman) rice at the Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur-1706, Bangladesh. The study was performed to evaluate the genetic deviation, trait association, and path coefficient (PC) based on grain yield (GY) and different yield-contributing agronomic characters. Variance analysis displayed extensive traits-wise variations across accessions, indicating variability and the opportunity for genetic selection for desirable traits. The high mean, range, and genotypic variances observed for most of the characters indicated a wide range of variation for these traits. All the characters indicated the minimum influence of environment on the expression of the trait and genetic factors had a significant role in the expressivity of these characters. High heritability in broad sense (h²_b) and high to moderate genetic advance in percent of the mean (GAPM) were recorded for all the characters except for panicle length (PL). Based on mean, range, and all genetic parameters, the selection of all the traits except for PL would contribute to the development of T. Aman rice genotypes. A correlation study revealed that selection based on plant height (PH), number of effective tillers per hill (NET), PL, number of filled spikelets per panicle (NFS), flag leaf length (FLL), spikelet sterility (SS) percentage, and harvest index (HI) would be effective for increasing the GY of rice. Genotypic correction with grain yield (GCGY), PC and principal component analysis (PCA) revealed that direct selection of NFS, HI, SS%, and FLL would be effective for improving the GY of rice in future breeding programs. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Assessment of GGE, AMMI, Regression, and Its Deviation Model to Identify Stable Rice Hybrids in Bangladesh

M Jamil Hasan

M Umma Kulsum

Umakanta Sarker

M Quamrul Islam Matin

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Plants 2022, 11(18), 2336; https://doi.org/10.3390/plants11182336 - 07 Sep 2022

Cited by 10 | Viewed by 1215

Abstract

Twenty-six rice hybrids were evaluated at three locations. Data were normally distributed after running the Shapiro–Wilk test. Plant height and effective tillers/hills showed leptokurtic distribution, indicating these traits were controlled by fewer genes, whereas the rest of the attributes had platykurtic distribution, indicating these traits were controlled by many genes. Most of the traits were significant for variety, locations, and variety × locations. For yield stability, the data were analyzed using additive main effect and multiplicative interaction (AMMI), genotype and genotype–environment interaction (GGE), and Eberhart and Russell’s model. Among 26 hybrids, BRRI99A × BRRI38R and BRRI hybrid dhan5 exhibited high yields at three locations. BRRI99A × BRRI45R, BRRI99A × BRRI31R, IR79156A × BRRI38R, and BRRI hybrid dhan3 were selected for mega-environments: Gazipur and Ishwardi. Among the tested locations, Gazipur (E2) and Ishwardi (E3) were identified as mega-environments for the hybrid combinations, including BRRI99A × BRRI36R, BRRI99A × BRRI49R, IR79156A × BRRI31R, IR79156A × BRRI38R, BRRI hybrid dhan5, BRRI99A × BRRI38R, BRRI99A × BRRI45R, and BRRI99A × BRRI31R based on their average action and fixity. Gazipur and Ishwardi were the best environments because their discriminative and representative ability was remarkable. The hybrid assessment, as well as area selection for hybrid rice breeding in Bangladesh, were revealed in this study. The hybrid BRRI99A × BRRI38R, BRRI99A × BRRI36R, and IR79156A × Rline7 belonged to medium-to-long slender grain types. Nowadays, the citizens of Bangladesh prefer fine-grain rice. Therefore, these fine-grain hybrids can be cultivated as preferable commercial varieties at three locations, such as Barisal, Gazipur, and Ishwardi in Bangladesh. The stable hybrids identified in the current study can be recommended for cultivation throughout the whole country without compromising the loss of grain yield of rice. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Genetic Analysis in Grain Legumes [Vigna radiata (L.) Wilczek] for Yield Improvement and Identifying Heterotic Hybrids

Arwa Abdulkreem AL-Huqail

Hanan R. H. Mohamed

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Ilaria Peluso

Plants 2022, 11(13), 1774; https://doi.org/10.3390/plants11131774 - 04 Jul 2022

Cited by 7 | Viewed by 1511

Abstract

Six mungbean parental lines and their fifteen F₁s produced from half-diallel mating design were investigated for combining ability and heterosis in terms of a yield and its components. Results showed highly significant variations among the parents and F₁s, suggesting a wide genetic variability for the studied characters. Analysis of variance indicated that genotypes mean square values, general combining ability (GCA) and specific combining ability (SCA) were highly significant (p ≤ 0.001) for all measured traits except for days to flowering, days to maturity, and pod length indicating genetic diversity of parents and both additive and non-additive gene effects in the inheritance of the measured traits. A higher effect of SCA than GCA for plant height and seeds per pod suggests the preponderance of non-additive gene effects in the expression of characters. Based on per se performance and GCA, BARI Mung-1, PS-7, and BMXK1-14004 were the best general combiners for yield per plant. In the context of SCA, hybrids BMXK1-14004 × Sonali mung, BMXK1-14004 × PS-7, BMXK1-14004 × BINA Mung-8, Sukumar × PS-7, and BARI Mung-1 × BINA Mung-8 were good specific combiners. BMXK1-14004 × Sonali mung and BMXK1-14004 × PS-7 were the best heterotic hybrids for yield and yield-contributing traits. These parents and crosses could be utilized for further use in breeding programs to improve yields in mungbean crops. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Detection of Genomic Regions Controlling the Antioxidant Enzymes, Phenolic Content, and Antioxidant Activities in Rice Grain through Association Mapping

Priyadarsini Sanghamitra

Saumya Ranjan Barik

Ramakrushna Bastia

Shakti Prakash Mohanty

and

Plants 2022, 11(11), 1463; https://doi.org/10.3390/plants11111463 - 30 May 2022

Cited by 7 | Viewed by 1330

Abstract

Because it is rich in antioxidant compounds, the staple food of rice provides many health benefits. Four antioxidant traits in rice grain, viz., catalase, CUPRAC, DPPH, FRAP and peroxidase, were mapped in a representative panel population containing 117 germplasm lines using 131 SSR markers through association mapping. Donor lines rich in multiple antioxidant properties were identified from the mapping population. The population was classified into three genetic groups and each group showed reasonable correspondence with the antioxidant traits. The presence of linkage disequilibrium in the population was confirmed from the estimated Fst values. A strong positive correlation of DPPH was established with TPC, FRAP and CUPRAC. A moderate to high mean gene diversity was observed in the panel population. Eleven significant marker-trait associations for antioxidant traits were mapped, namely, qACD2.1, qACD11.1 and qACD12.2 for DPPH; qCAT8.1 and qCAT11.1 for catalase; qFRAP11.1, qFRAP12.1 and qFRAP12.2 for FRAP; and qCUPRAC3.1, qCUPRAC11.1 and qCUPRA12.1 regulating CUPRAC. Co-localization of the QTLs for qACD11.1, qFRAP11.1 and qCUPRAC11.1 were detected, which may act as antioxidant hotspots regulating DPPH, FRAP and CUPRAC activities, respectively, while qACD12.2 and qFRAP12.1 remained close on the chromosome 12. These detected QTLs will be useful in antioxidant improvement programs in rice. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Emmer Wheat Eco-Geographic and Genomic Congruence Shapes Phenotypic Performance under Mediterranean Climate

Carolina Paola Sansaloni

Sariel Hübner

and

Roi Ben-David

Plants 2022, 11(11), 1460; https://doi.org/10.3390/plants11111460 - 30 May 2022

Cited by 3 | Viewed by 1640

Abstract

Emmer wheat (Triticum turgidum ssp. dicoccum) is one of the world’s oldest domesticated crops, and it harbors a potentially rich reservoir of agronomic and nutritional quality trait variations. The growing global demand for plant-based health-food niche markets has promoted new commercial interest in ancient grains, including Emmer wheat. Although T. dicoccum can also perform well under harsh environments, its cultivation along the Mediterranean agro-ecosystems is sparse. Here, we analyze a unique tetraploid wheat collection (n = 121) representing a wide geographic range of Emmer accessions, using 9897 DArTseq markers and on-field phenotypic characterization to quantify the extent of diversity among populations and the interactions between eco-geographic, genetic, and phenotypic attributes. Population genomic inferences based on the DArTseq data indicated that the collection could be split into four distinguished clusters in accordance with their eco-geographic origin although significant phenotypic variation was observed within clusters. Superior early vegetative vigor, shorter plant height, and early phenology were observed among emmer wheat accessions from Ethiopia compared to accessions from northern regions. This adaptive advantage highlights the potential of emmer wheat as an exotic germplasm for wheat improvement through breeding. The direct integration of such germplasm into conventional or organic farming agro-systems under the Mediterranean basin climate is also discussed. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Open AccessArticle

Comparative Mutagenic Effectiveness and Efficiency of Gamma Rays and Sodium Azide in Inducing Chlorophyll and Morphological Mutants of Cowpea

and

Plants 2022, 11(10), 1322; https://doi.org/10.3390/plants11101322 - 16 May 2022

Cited by 8 | Viewed by 2652

Abstract

Mutagenic effectiveness and efficiency are the most important factors determining the success of mutation breeding, a coherent tool for quickly enhancing genetic diversity in crops. However, conclusive evidence of using an effective and efficient dose of gamma (γ) rays and sodium azide (SA) for genetic improvement is scant. The present study assesses genetic diversity in M₂ mutants of cowpea and evaluates mutagenic effectiveness and efficiency of the single and combination doses of γ rays and SA. In M₀ generation, 7200 M₁ seeds obtained by SA treatment (0.01—0.1%) and γ irradiation (100—1000 Gy) at a dose rate of 11.58 Gy/min were sown to raise M₁ generation. A total of 57,620 M₂ seeds were generated from the M₁ generation of two varieties—Gomati VU-89 and Pusa-578, from which 47,650 seeds germinated. Moreover, plants (38,749) that survived were screened for chlorophyll and morphological mutations. Among the mutagens, SA followed by γ rays + SA and γ rays was most effective in inducing higher frequency and a broader spectrum of chlorophyll mutants. A wide range of morphological mutants affecting every growth stage was recorded with the highest frequency in 400 Gy γ rays + 0.04% SA treatment. These morphological mutants with desirable agronomic traits represent a valuable genetic resource for future breeding programs. This study revealed the potency of γ rays and SA in increasing genetic diversity and demonstrated the successful conduct of induced mutagenesis in the cowpea. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Review

Jump to: Research

Open AccessReview

CRISPR/Cas Technology Revolutionizes Crop Breeding

and

Plants 2023, 12(17), 3119; https://doi.org/10.3390/plants12173119 - 30 Aug 2023

Viewed by 451

Abstract

Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Producing haploid inducible lines by CRISPR-Cas9-mediated editing of OsMATL
Authors: Xiongxia Jin1; Jianhua Wang1; Tong Sun1; Silan Chen1; Chao Ouyang1; Yiting Mai1; Jin Yang2; Chuanying Fang3; Baoguang An1*
Affiliation: 1Hainan Bolian Rice Gene Technology Co., Ltd. 2 Nanchang University 3 Hainan University
Abstract: Traditional breeding requires multiple generations of selfing or backcrossing to obtain homozygous lines with excellent genes, but double-haploid breeding methods generally only need 2 generations, which greatly accelerates the breeding process. Double-haploid breeding process in maize has been applied for many years, and the corresponding haploid-inducing gene MATL has also been cloned. In this study, OsMATL was edited by in an elite indica rice CRISPR/Cas technology. It was found that the mutation of OsMATL leading to low seed setting rate. Two different mutation alleles (9311HI-2-5/21) were selected as male parents to pollinate with five receptors to investigate the haploid induction rate. The results showed that the haploid induction rates from different mutation alleles of the OsMATL gene varied with the highest induction rate reaching 10.34%. And the induction rates were not the same among different female parents. Overall, the haploid inducible line 9311HI-2-5 created in this study can be used in rice breeding to produce homozygous genetic resources, which would be beneficial to improve breeding efficiency.

Title: Genetic Analysis in Grain Legume (Vigna radiata L. Wilczek) for Yield Improvement and Identifying Heterotic Hybrids.
Authors: Umakanta Sarker
Affiliation: Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706, Bangladesh
Abstract: The selected mungbean genotypes were investigated for combining ability and heterosis based on their yield and yield contributing characteristics. Fifteen F1 populations generated by half-diallel mating and six parental lines were planted in three replications in a randomized complete block design at the Pulse Research Center, Bangladesh Agricultural Research Institute, Ishurdi, Pabna. Results showed highly significant variations within parents and F1s and demonstrated a wide genetic variability for the studied characters. Thus, the chance of hereditary improvement utilizing the selected genetic pools of mungbean is possible. Analysis of variance indicated that genotypes, general combining ability (GCA) and specific combining ability (SCA) mean square values were highly significant (p ≤ 0.001) for all measured traits except mean square for days to flowering, days to maturity, and pod length which indicated the genetic diversity of the parents and the importance of both additive and non-additive gene effects in the inheritance of the measured traits respectively. A higher effect of SCA than GCA was observed for plant height and seeds per pod pointed out to be the preponderance of non-additive gene effects in the expression of these characters. Based on per se performance and GCA of the parents, BARI Mung-1, PS-7 and BMXK1-14004 were found as the best general combiners for yield per plant. In the context of SCA, five hybrids viz. BMXK1-14004 × Sonali mung, BMXK1-14004 × PS-7, BMXK1-14004 × BINA Mung-8, Sukumar × PS-7, and BARI Mung-1 × BINA Mung-8 were professed as promising hybrid and good specific combiners. The most significant heterosis was observed at 26.09% over standard variety and 20.20% over better parent for seed yield per plant in the cross BMXK1-14004 × Sonali mung and BMXK1-14004 × PS-7 respectively which indicated a higher heterosis rate for yield and yield contributing traits. These parents and crosses could be utilized for further use in breeding programs to improve in yield of mungbean.

Title: Identification of Stable Rice Hybrids in Different Locations of Bangladesh
Authors: Umakanta Sarker
Affiliation: Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706, Bangladesh.
Abstract: Twenty-six (26) rice hybrids were evaluated at three locations. Data were normally distributed after running the Shapiro-Wilk test. Plant height and effective tillers/hill showed leptokurtic distribution, while the rest of the attributes had platykurtic distribution. Most of the traits were significant for variety, locations, and variety × locations. For yield stability, the data were analyzed using Additive Main Effect and Multiplicative Interaction (AMMI) and Genotype and Genotype Environment Interaction (GGE). Among the 26 hybrid combinations BRRI99A × BRRI38R, BRRI hybrid dhan5 exhibited high yielding at three locations following BRRI99A × BRRI45R, BRRI99A × BRRI31R, IR79156A × BRRI38R, BRRI hybrid dhan3 were selected for mega environments: - Gaipur and Ishwardi. Among the tested location Gazipur (E2) and Ishwardi (E3) were identified as mega environments for the hybrid combination BRRI99A × BRRI36R, BRRI99A × BRRI49R, IR79156A × BRRI31R, IR79156A × BRRI38R, BRRI hybrid dhan5, BRRI99A × BRRI38R, BRRI99A × BRRI45R, BRRI99A × BRRI31R based on mean performance and stability. Gazipur and Ishwardi was the best environment because their discriminative and representative ability was remarkable. The hybrid evaluation, as well as area identification for hybrid rice breeding in Bangladesh, were revealed in this study. The hybrid BRRI99A × BRRI38R, BRRI99A × BRRI36R, and IR79156A × Rline7 belonged to the medium to long slender grain type. Nowadays, citizens of Bangladesh prefer fine-grain rice. So, these hybrids were used for commercial cultivation over locations.

Title: Genetic Variability, Character Association, and Path Coefficient Analysis in T. Aman Rice Genotypes
Authors: Umakanta Sarker
Affiliation: Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706, Bangladesh.
Abstract: A field experiment was carried out with 20 genotypes of T. Aman rice at the Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur-1706. The study was performed to evaluate the genetic variability, character association, and path coefficient based on yield and different yield contributing agronomic characters. Significant variations were observed among the genotypes for all the characters studied. The high mean, range, and genotypic variances observed for most of the characters indicated a wide range of variation for these traits. All the characters indicated the minimum influence of environment on the expression of the trait and genetic factors had a significant role in the expressivity of these characters. High heritability and high to moderate genetic advance in percent of mean were recorded for all the characters except panicle length. Based on mean, range and all genetic parameters, selection of all the traits except panicle length would be effective for the improvement of T. Aman rice genotypes. A correlation study revealed that selection based on plant height, number of effective tillers per hill, panicle length, number of filled spikelets per panicle, flag leaf length, spikelet sterility percentage, and harvest index would be effective for increasing the grain yield of rice. Path coefficient analysis revealed that direct selection of the number of filled spikelets per panicle, spikelet sterility%, and harvest index would be effective for improving the grain yield of rice.

Title: Variability in Intraspecies population for the Seed Coat attributes in Amaranth grains
Authors: Jagatam Patayam Tahadam Dhadayam
Affiliation: Cytogenetics and Plant Breeding Section, Botany Department (UGC-CAS), The University of Burdwan, Burdwan-713104, West Bengal, India
Abstract: Seed character is an important part of any crop plant. The seeds of Amaranthus hybridus (Family-Amaranthaceae) are small in size and not possible to differentiate easily with naked eyes. A little work has been focused on seed morphology of Amaranthus hybridus but no specific work on seed micromorphology has yet been documented. Keeping all these views in mind, we have undertaken the venture for observing possible microfeatures under Scanning Electron Microscope (SEM). The micro-morphological typology of seed surfaces was investigated in eight accessions of Amaranthus hybridus using scanning electron microscopy. Morphological studies showed that seeds were either pyriform or sub-pyriform or sub-spherical in shape. Pleurogram was found on the seed surface in some accessions. The ornamentations of exo-testa were found to be either polygonal or reticular or crosslinked type or spindle shaped or scalariform or undulated lump with tertiary depositions or slits. The aim of this present study was to explore the seed characters which are useful as a tool for identifying crop species and variations among those accessions too. The micromorphological characteristics of the seed coats may provide valuable information for identification of seeds

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