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Genetic Diversity of Germplasm Resources in Cereals and Legumes
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Genetic Diversity of Germplasm Resources in Cereals and Legumes

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetic Resources".

Deadline for manuscript submissions: closed (10 August 2024) | Viewed by 7053

Special Issue Editors

Prof. Dr. Zdenka Gálová

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Guest Editor
Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, 94976 Nitra, Slovakia
Interests: genetic diversity; molecular markers; plant biotechnology; genotyping
Dr. Tomáš Vyhnánek

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Guest Editor
Department of Plant Biology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
Interests: plant genetics; molecular genetics; DNA markers; plant biotechnologies; plant breeding
Dr. Želmí­ra Balážová

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Guest Editor
Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, 94976 Nitra, Slovakia
Interests: DNA markers; plant biotechnology; genetic diversity; genotyping

Special Issue Information

Dear Colleagues,

Plant samples stored in the form of genetic resources in gene banks belong to the cultural wealth and heritage of every nation and the entire humanity at the same time. Their collection and preservation in a viable state is a basic prerequisite for the preservation of genetic diversity in the plant kingdom on our planet for future generations. Biological diversity is and will be the starting point for the creation of new, improved plant genotypes, which is closely related to the production of sufficient quality food for the rapidly increasing human population. Omic approaches (genomics, transcriptomics, proteomics, metabolomics, etc.) and biotechnological methods play an important role in the characterization of plant genetic resources, which, together with phenotyping, provide breeders with significant information about the variety.

Cereals, pseudocereals, and legumes are among the most important groups of crops providing nutrition for a large part of the human population and animals in the world. Systematic documentation and evaluation of the plant genome based on molecular markers that capture variability at the level of DNA or its protein products is essential for the management of plant genetic resources. The technology of molecular markers makes it possible to make the breeding process more efficient by using a large number of new techniques with the aim of improving selection strategies in plant breeding. Molecular markers are also suitable tools for further studies related to the analysis of plant genomes, their mapping, construction of the genetic and linkage maps, detection of the genetic homogeneity and use in molecular breeding, diagnostics, taxonomy, etc. This Special Issue of Plants is dedicated to these very interesting and inspiring topics. The aim of this Special Issue of Plants is to provide a better understanding of the genetic diversity, germplasm resources, and new biotechnologies of sustained cereals, pseudocereals, and legumes improvement.

Prof. Dr. Zdenka Gálová
Dr. Tomáš Vyhnánek
Dr. Želmí­ra Balážová
Guest Editors

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Keywords

  • genetic diversity
  • polymorphism
  • genetic resources
  • cereals and pseudocereals
  • legumes
  • molecular methods
  • genotyping

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Published Papers (6 papers)

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Research

12 pages, 1064 KiB  
Article
Identification of Insertion and Deletion (InDel) Markers for Chickpea (Cicer arietinum L.) Based on Double-Digest Restriction Site-Associated DNA Sequencing
by Duygu Sari
Plants 2024, 13(17), 2530; https://doi.org/10.3390/plants13172530 - 9 Sep 2024
Viewed by 642
Abstract
Enhancing the marker repository and the development of breeder-friendly markers in chickpeas is important in relation to chickpea genomics-assisted breeding applications. Insertion–deletion (InDel) markers are widely distributed across genomes and easily observed with specifically designed primers, leading to less time, cost, and labor [...] Read more.
Enhancing the marker repository and the development of breeder-friendly markers in chickpeas is important in relation to chickpea genomics-assisted breeding applications. Insertion–deletion (InDel) markers are widely distributed across genomes and easily observed with specifically designed primers, leading to less time, cost, and labor requirements. In light of this, the present study focused on the identification and development of InDel markers through the use of double-digest restriction site-associated DNA sequencing (ddRADSeq) data from 20 chickpea accessions. Bioinformatic analysis identified 20,700 InDel sites, including 15,031 (72.61%) deletions and 5669 (27.39%) insertions, among the chickpea accessions. The InDel markers ranged from 1 to 25 bp in length, while single-nucleotide-length InDel markers were found to represent the majority of the InDel sites and account for 79% of the total InDel markers. However, we focused on InDel markers wherein the length was greater than a single nucleotide to avoid any read or alignment errors. Among all of the InDel markers, 96.1% were less than 10 bp, 3.6% were between 10 and 20 bp, and 0.3% were more than 20 bp in length. We examined the InDel markers that were 10 bp and longer for the development of InDel markers based on a consideration of the genomic distribution and low-cost genotyping with agarose gels. A total of 29 InDel regions were selected, and primers were successfully designed to evaluate their efficiency. Annotation analysis of the InDel markers revealed them to be found with the highest frequency in the intergenic regions (82.76%), followed by the introns (6.90%), coding sequences (6.90%), and exons (3.45%). Genetic diversity analysis demonstrated that the polymorphic information content of the markers varied from 0.09 to 0.37, with an average of 0.20. Taken together, these results showed the efficiency of InDel marker development for chickpea genetic and genomic studies using the ddRADSeq method. The identified markers might prove valuable for chickpea breeders. Full article
(This article belongs to the Special Issue Genetic Diversity of Germplasm Resources in Cereals and Legumes)
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16 pages, 7388 KiB  
Article
Identification of Sources of Resistance to Aphanomyces Root Rot in Pisum
by Sara Rodriguez-Mena, Diego Rubiales and Mario González
Plants 2024, 13(17), 2454; https://doi.org/10.3390/plants13172454 - 2 Sep 2024
Viewed by 1073
Abstract
Aphanomyces root rot (ARR), caused by Aphanomyces euteiches, is one of the most devastating diseases that affect the production of peas. Several control strategies such as crop rotation, biocontrol, and fungicides have been proposed, but none provides a complete solution. Therefore, the [...] Read more.
Aphanomyces root rot (ARR), caused by Aphanomyces euteiches, is one of the most devastating diseases that affect the production of peas. Several control strategies such as crop rotation, biocontrol, and fungicides have been proposed, but none provides a complete solution. Therefore, the deployment of resistant cultivars is fundamental. ARR resistance breeding is hampered by the moderate levels of resistance identified so far. The available screening protocols require post-inoculation root assessment, which is destructive, time-consuming, and tedious. In an attempt to address these limitations, we developed a non-destructive screening protocol based on foliar symptoms and used it to identify new sources of resistance in a Pisum spp. germplasm collection. Accessions were root inoculated separately with two A. euteiches isolates, and leaf symptoms were assessed at 5, 10, 14, 17, and 20 days after inoculation (DAI). Although the majority of accessions exhibited high levels of susceptibility, thirty of them exhibited moderate resistance. These thirty accessions were selected for a second experiment, in which they were inoculated with both A. euteiches isolates at two inoculum doses. The objective of this second trial was to confirm the resistance of these accessions by evaluating root and biomass loss, as well as foliar symptoms, and to compare root and foliar evaluations. As a result, a high correlation (R2 = 0.75) between foliar and root evaluations was observed, validating the foliar evaluation method. Notably, accessions from P.s. subsp. humile exhibited the lowest symptomatology across all evaluation methods, representing valuable genetic resources for breeding programs aimed at developing pea varieties resistant to ARR. Full article
(This article belongs to the Special Issue Genetic Diversity of Germplasm Resources in Cereals and Legumes)
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14 pages, 1027 KiB  
Article
Genetic Control of Effective Seedling Leaf Rust Resistance in Aegilops biuncialis Vis. Accessions from the VIR Collection
by Maria A. Kolesova and Lev G. Tyryshkin
Plants 2024, 13(16), 2199; https://doi.org/10.3390/plants13162199 - 8 Aug 2024
Viewed by 846
Abstract
Leaf rust (caused by Puccinia triticina Erikss., Pt) is a severe foliar disease of cultivated wheat worldwide. Severe development of the disease results in significant losses in seed yield and quality. Growing immune varieties is the most rational method for Pt control [...] Read more.
Leaf rust (caused by Puccinia triticina Erikss., Pt) is a severe foliar disease of cultivated wheat worldwide. Severe development of the disease results in significant losses in seed yield and quality. Growing immune varieties is the most rational method for Pt control in terms of effectiveness and ecological safety. However, the gene pool of cultivated wheat is very narrow for seedling Pt effective resistance genes, which hampers breeding for this trait. One of the well-known methods to broaden genetic diversity for resistance is the introgression of highly effective genes from wild relatives into the genomes of cultivated wheat. The Aegilops L. species have been proven to be perfectly suited for this purpose. No gene for Pt resistance has been transferred to wheat from Aegilops biuncialis Vis. (Lorent’s goatgrass) up to now. Previously, we selected eight accessions of the species from the VIR (N.I. Vavilov All-Russian Institute of Plant Genetic Resources) genebank that showed a perfect level of resistance to leaf rust. In this research, we studied the genetic control of resistance using hybridological, phytopathological, and molecular analyses. According to the F1–F3 hybrid evaluation results, each accession possesses one dominant gene for Pt resistance, and genes in different accessions are allelic or very tightly linked. Phytopathological test clone analysis showed that this gene is not identical to Lr9, Lr19, Lr24, Lr39, and Lr47, which are effective against Pt populations in some areas of Russia. This conclusion was partially supported by the results of the identification of DNA markers specific to these genes in bread wheat. Thus, we identified one dominant gene (temporarily symbolized as LrBi1) for effective seedling Pt resistance; it is recommended for introgression to cultivated wheat via interspecific hybridization. Full article
(This article belongs to the Special Issue Genetic Diversity of Germplasm Resources in Cereals and Legumes)
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15 pages, 2264 KiB  
Article
Characterization of Genetic Variability of Common and Tartary Buckwheat Genotypes Using Microsatellite Markers
by Želmíra Balážová, Lucia Čišecká, Zdenka Gálová, Zuzana Hromadová, Milan Chňapek, Barbara Pipan and Vladimir Meglič
Plants 2024, 13(15), 2147; https://doi.org/10.3390/plants13152147 - 2 Aug 2024
Viewed by 727
Abstract
Buckwheat is a highly nutritional pseudocereal with antioxidant potential. The aim of this study was to analyze the genetic variability of 21 varieties of common buckwheat (Fagopyrum esculentum Moench.) and 14 varieties of Tartary buckwheat (Fagopyrum tataricum Gaertn.) using microsatellite markers. [...] Read more.
Buckwheat is a highly nutritional pseudocereal with antioxidant potential. The aim of this study was to analyze the genetic variability of 21 varieties of common buckwheat (Fagopyrum esculentum Moench.) and 14 varieties of Tartary buckwheat (Fagopyrum tataricum Gaertn.) using microsatellite markers. By analyzing 21 SSR markers, an average of 11.6 alleles per locus were amplified and an average PIC value of 0.711 was determined. We determined the heterozygous status of the individuals and variability in the set using the SSR analysis on the basis of expected heterozygosity (He, 0.477), observed heterozygosity (Ho, 0.675), Shannon’s index (I, 0.820), and fixation indices (FST, FIS, FIT). Based on the SSR analyses, the lower level of expected heterozygosity in the analyzed set of Tartary buckwheat genotypes was observed compared to common buckwheat. With the help of a hierarchical cluster analysis using the UPGMA algorithm, Structure analysis, and PCoA analysis for the SSR markers, we divided the buckwheat varieties in the dendrogram into two main clusters according to the species. The AMOVA analysis showed that genetic variability between the individuals prevails in the analyzed set. The SSR technique proved to be a suitable tool for the determination of intra- and inter-varietal genetic variability and for analysis of diversity. Full article
(This article belongs to the Special Issue Genetic Diversity of Germplasm Resources in Cereals and Legumes)
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21 pages, 20225 KiB  
Article
Genetic Dissection of Diverse Seed Coat Patterns in Cowpea through a Comprehensive GWAS Approach
by Haizheng Xiong, Yilin Chen, Waltram Ravelombola, Beiquan Mou, Xiaolun Sun, Qingyang Zhang, Yiting Xiao, Yang Tian, Qun Luo, Ibtisam Alatawi, Kenani Edward Chiwina, Hanan Mohammedsaeed Alkabkabi and Ainong Shi
Plants 2024, 13(9), 1275; https://doi.org/10.3390/plants13091275 - 5 May 2024
Cited by 1 | Viewed by 1887
Abstract
This study investigates the genetic determinants of seed coat color and pattern variations in cowpea (Vigna unguiculata), employing a genome-wide association approach. Analyzing a mapping panel of 296 cowpea varieties with 110,000 single nucleotide polymorphisms (SNPs), we focused on eight unique [...] Read more.
This study investigates the genetic determinants of seed coat color and pattern variations in cowpea (Vigna unguiculata), employing a genome-wide association approach. Analyzing a mapping panel of 296 cowpea varieties with 110,000 single nucleotide polymorphisms (SNPs), we focused on eight unique coat patterns: (1) Red and (2) Cream seed; (3) White and (4) Brown/Tan seed coat; (5) Pink, (6) Black, (7) Browneye and (8) Red/Brown Holstein. Across six GWAS models (GLM, SRM, MLM, MLMM, FarmCPU from GAPIT3, and TASSEL5), 13 significant SNP markers were identified and led to the discovery of 23 candidate genes. Among these, four specific genes may play a direct role in determining seed coat pigment. These findings lay a foundational basis for future breeding programs aimed at creating cowpea varieties aligned with consumer preferences and market requirements. Full article
(This article belongs to the Special Issue Genetic Diversity of Germplasm Resources in Cereals and Legumes)
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14 pages, 1100 KiB  
Article
Mining of QTLs for Spring Bread Wheat Spike Productivity by Comparing Spring Wheat Cultivars Released in Different Decades of the Last Century
by Natalia Shvachko, Maria Solovyeva, Irina Rozanova, Ilya Kibkalo, Maria Kolesova, Alla Brykova, Anna Andreeva, Evgeny Zuev, Andreas Börner and Elena Khlestkina
Plants 2024, 13(8), 1081; https://doi.org/10.3390/plants13081081 - 12 Apr 2024
Viewed by 1178
Abstract
Genome-wide association studies (GWAS) are among the genetic tools for the mining of genomic loci associated with useful agronomic traits. The study enabled us to find new genetic markers associated with grain yield as well as quality. The sample under study consisted of [...] Read more.
Genome-wide association studies (GWAS) are among the genetic tools for the mining of genomic loci associated with useful agronomic traits. The study enabled us to find new genetic markers associated with grain yield as well as quality. The sample under study consisted of spring wheat cultivars developed in different decades of the last century. A panel of 186 accessions was evaluated at VIR’s experiment station in Pushkin across a 3-year period of field trials. In total, 24 SNPs associated with six productivity characteristics were revealed. Along with detecting significant markers for each year of the field study, meta-analyses were conducted. Loci associated with useful yield-related agronomic characteristics were detected on chromosomes 4A, 5A, 6A, 6B, and 7B. In addition to previously described regions, novel loci associated with grain yield and quality were identified during the study. We presume that the utilization of contrast cultivars which originated in different breeding periods allowed us to identify new markers associated with useful agronomic characteristics. Full article
(This article belongs to the Special Issue Genetic Diversity of Germplasm Resources in Cereals and Legumes)
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