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Genetics and Breeding of Legume Crops

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 May 2024) | Viewed by 15289

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Special Issue Editors

Prof. Dr. Xingxing Yuan

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Guest Editor

Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
Interests: legumes; genetic resources; molecular breeding; QTL; gene mapping

Dr. Prakit Somta

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Guest Editor

Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
Interests: plant breeding; plant genetic resources; legumes; mung bean; Vigna; molecular breeding; QTL
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Dear Colleagues,

Legume crops are a source of proteins, amino acids, carbohydrates (starch), oils, vitamins and minerals, dietary fibers, and phytochemicals for a large proportion of the world population. Consuming high levels of legumes lowers the risk of some non-communicable diseases, such as diabetes, heart disease, and cancer. They are a part of every human civilization’s development. Legumes also play positive roles in cropping systems—principally in rotations with cereals and help replenish soil’s nitrogen supply. Legume root nodules harbor symbiotic bacteria Rhizobia and/or Bradyrhizobia that can bring nitrogen into the soils. At present, only a small portion of legume crops are utilized in industry, while a large number of the crops are still underutilized. Nonetheless, in recent years, legume crops have been in the spotlight as raw materials for plant-based meats—a future food. However, due to an increasing world population, climate changes, and changing in consumer behavior, there is an urgent need to develop new cultivars of legume crops that meet the needs of farmers, consumers and industries to cope with the rapidly changing world. Compared to cereals, several food legume crops, with exception to soybean, are “slow runners” in genetics and breeding research. Recent advances in DNA sequencing technology and plant phenotyping technology have led to rapid progress in the genetics and breeding research of legume crops.

This Special Issue on “Genetics and Breeding of Legume Crops” compiles papers on both theoretical and applied research highlighting all aspects of the genetics and breeding of legume crops, from Mendelian inheritance to advanced DNA marker technology, gene/QTL mapping, genetic engineering, genome editing, and new techniques and technologies related to genetics and breeding.

The aim of this collection of articles is to gain further valuable insights into the plant resilience to abiotic stresses by covering multidisciplinary studies ranging from physiological, biochemical, molecular, and modelling analyses. Multiplex omics approaches designed to study pathways of plant response to single and multiple types of abiotic stresses are encouraged.

Prof. Dr. Xingxing Yuan
Dr. Prakit Somta
Guest Editors

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Keywords

legumes
molecular breeding
conventional breeding
QTL
genomics
marker-assisted selection
genome editing
plant genetic resources

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Published Papers (9 papers)

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31 pages, 3267 KiB

Open AccessArticle

Identification and Candidate Gene Evaluation of a Large Fast Neutron-Induced Deletion Associated with a High-Oil Phenotype in Soybean Seeds

by William R. Serson, Mohammad Fazel Soltani Gishini, Robert M. Stupar, Adrian O. Stec, Paul R. Armstrong and David Hildebrand

Genes 2024, 15(7), 892; https://doi.org/10.3390/genes15070892 - 8 Jul 2024

Viewed by 1263

Abstract

Since the dawn of agriculture, crops have been genetically altered for desirable characteristics. This has included the selection of natural and induced mutants. Increasing the production of plant oils such as soybean (Glycine max) oil as a renewable resource for food and fuel is valuable. Successful breeding for higher oil levels in soybeans, however, usually results in reduced seed protein. A soybean fast neutron population was screened for oil content, and three high oil mutants with minimal reductions in protein levels were found. Three backcross F2 populations derived from these mutants exhibited segregation for seed oil content. DNA was pooled from the high-oil and normal-oil plants within each population and assessed by comparative genomic hybridization. A deletion encompassing 20 gene models on chromosome 14 was found to co-segregate with the high-oil trait in two of the three populations. Eighteen genes in the deleted region have known functions that appear unrelated to oil biosynthesis and accumulation pathways, while one of the unknown genes (Glyma.14G101900) may contribute to the regulation of lipid droplet formation. This high-oil trait can facilitate the breeding of high-oil soybeans without protein reduction, resulting in higher meal protein levels. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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13 pages, 2085 KiB

Open AccessFeature PaperArticle

Inheritance of Resistance to Chickpea Fusarium Wilt Disease (Fusarium oxysporum f. sp. ciceris Race 2) in a Wide-Cross Cicer arietinum × Cicer reticulatum Mapping Family

by Abdulkarim Lakmes, Abdullah Jhar, Ari Sadanandom, Adrian Christopher Brennan and Abdullah Kahriman

Genes 2024, 15(6), 819; https://doi.org/10.3390/genes15060819 - 20 Jun 2024

Cited by 1 | Viewed by 822

Abstract

Chickpea (Cicer arietinum) is a major food legume providing high quality nutrition, especially in developing regions. Chickpea wilt (Fusarium oxysporum f. sp. ciceris) causes significant annual losses. Integrated disease management of Fusarium wilt is supported by resistant varieties. Relatively few resistance genes are known so there is value in exploring genetic resources in chickpea wild relatives. This study investigates the inheritance of Fusarium wilt resistance (race 2) in recombinant inbred lines (RILs) from a cross between a cultivated susceptible chickpea variety (Gokce) and a wild resistant Cicer reticulatum line (Kayat-077). RILs, parents, resistant and susceptible tester lines were twice grown in the greenhouse with inoculation and disease symptoms scored. DNA was extracted from dried leaves and individuals were single nucleotide polymorphism (SNP) genotyped. SNPs were placed on the reference chickpea genome and quantitative trait locus (QTL) mapping was performed. Significant QTL regions were examined using PulseDB to identify candidate genes. The results showed the segregation of Fusarium wilt resistance conforming to a single gene inheritance. One significant QTL was found at the start of chromosome 8, containing 138 genes, three of which were disease-resistance candidates for chickpea breeding. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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11 pages, 1866 KiB

Open AccessArticle

Genetic Heterogeneity in Cowpea Genotypes (Vigna unguiculata L. Walp) Using DArTseq (GBS)-Derived Single Nucleotide Polymorphisms

by Goitsemang Mahlomola Hendry Dikane and Moosa Mahmood Sedibe

Genes 2024, 15(6), 764; https://doi.org/10.3390/genes15060764 - 11 Jun 2024

Viewed by 666

Abstract

Cowpeas (Vigna unguiculata L. Walp) have been credible constituents of nutritious food and forage in human and animal diets since the Neolithic era. The modern technique of Diversity Array Technology (DArTseq) is both cost-effective and rapid in producing thousands of high-throughputs, genotyped, single nucleotide polymorphisms (SNPs) in wide-genomic analyses of genetic diversity. The aim of this study was to assess the heterogeneity in cowpea genotypes using DArTseq-derived SNPs. A total of 92 cowpea genotypes were selected, and their fourteen-day-old leaves were freeze-dried for five days. DNA was extracted using the CTAB protocol, genotyped using DArTseq, and analysed using DArTsoft14. A total of 33,920 DArTseq-derived SNPs were recalled for filtering analysis, with a final total of 16,960 SNPs. The analyses were computed using vcfR, poppr, and ape in R Studio v1.2.5001-3 software. The heatmap revealed that the TVU 9596 (SB26), Orelu (SB72), 90K-284-2 (SB55), RV 403 (SB17), and RV 498 (SB16) genotypes were heterogenous. The mean values for polymorphic information content, observed heterozygosity, expected heterozygosity, major allele frequency, and the inbreeding coefficient were 0.345, 0.386, 0.345, 0.729, and 0.113, respectively. Moreover, they validated the diversity of the evaluated cowpea genotypes, which could be used for potential breeding programmes and management of cowpea germplasm. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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14 pages, 3506 KiB

Open AccessArticle

Dissecting the Genetic Diversity of USDA Cowpea Germplasm Collection Using Kompetitive Allele Specific PCR-Single Nucleotide Polymorphism Markers

by Jesse Potts, Vincent N. Michael, Geoffrey Meru, Xingbo Wu and Matthew W. Blair

Genes 2024, 15(3), 362; https://doi.org/10.3390/genes15030362 - 14 Mar 2024

Cited by 1 | Viewed by 1448

Abstract

Cowpea (Vigna unguiculata L. Walp) is an important grain legume crop of the subtropics, particularly in West Africa, where it contributes to the livelihoods of small-scale farmers. Despite being a drought-resilient crop, cowpea production is hampered by insect pests, diseases, parasitic weeds, and various abiotic stresses. Genetic improvement can help overcome these limitations, and exploring diverse cowpea genetic resources is crucial for cowpea breeding. This study evaluated the genetic diversity of 361 cowpea accessions from the USDA core collection for the species using 102 Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers. A total of 102 KASP-SNP was validated in the germplasm panel, and 72 showed polymorphism across the germplasm panel. The polymorphism information content (PIC) of all SNPs ranged from 0.1 to 0.37, with an average of 0.29, while the mean observed heterozygosity was 0.52. The population structure revealed three distinct populations that clustered into two major groups after phylogenetic analysis. Analysis of molecular variance (AMOVA) indicated greater genetic variation within populations than among populations. Although cowpea generally has a narrow genetic diversity, the accessions used in this study exhibited considerable variation across geographical regions, sub-species, and improvement status. These results indicated that the selected KASP genotyping assay can provide robust and accurate genotyping data for application in the selection and management of cowpea germplasm in breeding programs and genebanks. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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11 pages, 4790 KiB

Open AccessArticle

Mapping and Detection of Genes Related to Trichome Development in Black Gram (Vigna mungo (L.) Hepper)

by Dan Gong, Jianling Li, Suhua Wang, Aihua Sha and Lixia Wang

Genes 2024, 15(3), 308; https://doi.org/10.3390/genes15030308 - 27 Feb 2024

Viewed by 1300

Abstract

Black gram (Vigna mungo (L.) Hepper) is a pulses crop with good digestible protein and a high carbohydrate content, so it is widely consumed as human food and animal feed. Trichomes are large, specialized epidermal cells that confer advantages on plants under biotic and abiotic stresses. Genes regulating the development of trichomes are well characterized in Arabidopsis and tomato. However, little is known about trichome development in black gram. In this study, a high-density map with 5734 bin markers using an F₂ population derived from a trichome-bearing and a glabrous cultivar of black gram was constructed, and a major quantitative trait locus (QTL) related to trichomes was identified. Six candidate genes were located in the mapped interval region. Fourteen single-nucleotide polymorphisms (SNPs) or insertion/deletions (indels) were associated with those genes. One indel was located in the coding region of the gene designated as Scaffold_9372_HRSCAF_11447.164. Real-time quantitative PCR (qPCR) analysis demonstrated that only one candidate gene, Scaffold_9372_HRSCAF_11447.166, was differentially expressed in the stem between the two parental lines. These two candidate genes encoded the RNA polymerase-associated protein Rtf1 and Bromodomain adjacent to zinc finger domain protein 1A (BAZ1A). These results provide insights into the regulation of trichome development in black gram. The candidate genes may be useful for creating transgenic plants with improved stress resistance and for developing molecular markers for trichome selection in black gram breeding programs. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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18 pages, 3517 KiB

Open AccessArticle

Integration of GWAS and RNA-Seq Analysis to Identify SNPs and Candidate Genes Associated with Alkali Stress Tolerance at the Germination Stage in Mung Bean

by Ning Xu, Bingru Chen, Yuxin Cheng, Yufei Su, Mengyuan Song, Rongqiu Guo, Minghai Wang, Kunpeng Deng, Tianjiao Lan, Shuying Bao, Guifang Wang, Zhongxiao Guo and Lihe Yu

Genes 2023, 14(6), 1294; https://doi.org/10.3390/genes14061294 - 19 Jun 2023

Cited by 3 | Viewed by 2643

Abstract

Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association study (GWAS) was performed to detect alkali-tolerant genetic loci and candidate genes in 277 mung bean accessions during germination. Using the relative values of two germination traits, 19 QTLs containing 32 SNPs significantly associated with alkali tolerance on nine chromosomes were identified, and they explained 3.6 to 14.6% of the phenotypic variance. Moreover, 691 candidate genes were mined within the LD intervals containing significant trait-associated SNPs. Transcriptome sequencing of alkali-tolerant accession 132–346 under alkali and control conditions after 24 h of treatment was conducted, and 2565 DEGs were identified. An integrated analysis of the GWAS and DEGs revealed six hub genes involved in alkali tolerance responses. Moreover, the expression of hub genes was further validated by qRT-PCR. These findings improve our understanding of the molecular mechanism of alkali stress tolerance and provide potential resources (SNPs and genes) for the genetic improvement of alkali tolerance in mung bean. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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18 pages, 4320 KiB

Open AccessArticle

Identification and Functional Characterization of WRKY, PHD and MYB Three Salt Stress Responsive Gene Families in Mungbean (Vigna radiata L.)

by Shicong Li, Jinyang Liu, Chenchen Xue, Yun Lin, Qiang Yan, Jingbin Chen, Ranran Wu, Xin Chen and Xingxing Yuan

Genes 2023, 14(2), 463; https://doi.org/10.3390/genes14020463 - 10 Feb 2023

Cited by 1 | Viewed by 2253

Abstract

WRKY-, PHD-, and MYB-like proteins are three important types of transcription factors in mungbeans, and play an important role in development and stress resistance. The genes’ structures and characteristics were clearly reported and were shown to contain the conservative WRKYGQK heptapeptide sequence, Cys4-His-cys3 zinc binding motif, and HTH (helix) tryptophan cluster W structure, respectively. Knowledge on the response of these genes to salt stress is largely unknown. To address this issue, 83 VrWRKYs, 47 VrPHDs, and 149 VrMYBs were identified by using comparative genomics, transcriptomics, and molecular biology methods in mungbeans. An intraspecific synteny analysis revealed that the three gene families had strong co-linearity and an interspecies synteny analysis showed that mungbean and Arabidopsis were relatively close in genetic relationship. Moreover, 20, 10, and 20 genes showed significantly different expression levels after 15 days of salt treatment (p < 0.05; Log₂ FC > 0.5), respectively. Additionally, in the qRT-PCR analysis, VrPHD14 had varying degrees of response to NaCl and PEG treatments after 12 h. VrWRKY49 was upregulated by ABA treatment, especially in the beginning (within 24 h). VrMYB96 was significantly upregulated in the early stages of ABA, NaCl, and PEG stress treatments (during the first 4 h). VrWRKY38 was significantly upregulated by ABA and NaCl treatments, but downregulated by PEG treatment. We also constructed a gene network centered on the seven DEGs under NaCl treatment; the results showed that VrWRKY38 was in the center of the PPI network and most of the homologous Arabidopsis genes of the interacted genes were reported to have response to biological stress. Candidate genes identified in this study provide abundant gene resources for the study of salt tolerance in mungbeans. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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9 pages, 1479 KiB

Open AccessArticle

Mapping QTLs Controlling Soybean Rust Disease Resistance in Chiang Mai 5, an Induced Mutant Cultivar

by Thongchai Chanchu, Tarika Yimram, Sompong Chankaew, Akito Kaga and Prakit Somta

Genes 2023, 14(1), 19; https://doi.org/10.3390/genes14010019 - 21 Dec 2022

Cited by 5 | Viewed by 1594

Abstract

Soybean rust (SBR) caused by the fungus Phakopsora pachyrhizi is an important folia disease of soybean (Glycine max). In this study, we identified QTLs controlling SBR in Chiang Mai 5 (CM5), an SBR-resistant cultivar developed by induced mutation breeding. A recombinant inbred line (RIL) population of 108 lines developed from a cross between Sukhothai 2 (SKT2, a susceptible cultivar) and CM5 was evaluated for SBR resistance under field conditions in Thailand. QTL analysis for the resistance in the RIL population identified a single QTL, qSBR18.1, for resistance. qSBR18.1 was mapped to a 212-kb region on chromosome 18 between simple sequence repeat markers Satt288 and sc21_3420 and accounted for 21.31–35.09% depending on the traits evaluated for resistance. The qSBR18.1 interval overlapped with genomic regions containing resistance to P. pachyrhizi 4 (Rpp4), a locus for SBR resistance. Three tightly linked genes, Glyma.18G226250, Glyma.18G226300, and Glyma.18G226500, each encoding leucine-rich repeat-containing protein, were identified as candidate genes for SBR resistance at the qSRB18.1. The qSBR18.1 would be useful for breeding of SBR resistance. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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19 pages, 5024 KiB

Open AccessArticle

Genome-Wide Identification of Common Bean PvLTP Family Genes and Expression Profiling Analysis in Response to Drought Stress

by Xue Dong, Huijun Zhu, Xiaopeng Hao, Yan Wang, Xiaolei Ma, Jiandong Zhao and Jianwu Chang

Genes 2022, 13(12), 2394; https://doi.org/10.3390/genes13122394 - 16 Dec 2022

Cited by 2 | Viewed by 1869

Abstract

Common bean is one of the most important legume crops for human consumption. Its yield is adversely affected by environmental stress. Plant non-specific lipid transfer proteins (nsLTPs) are essential for plant growth, development, and resistance to abiotic stress, such as salt, drought, and alkali. However, changes in nsLTP family genes responding to drought stress are less known. The PvLTP gene family in the common bean was identified by a comprehensive genome-wide analysis. Molecular weights, theoretical isoelectric points, phylogenetic tree, conserved motifs, gene structures, gene duplications, chromosome localization, and expression profiles were analyzed by SignalP 5.0, ExPASy, ClustalX 2.1, MEGA 7.0, NCBI-CDD, MEME, Weblogo, and TBtools 1.09876, respectively. Heatmap and qRT-PCR analyses were performed to validate the expression profiles of PvLTP genes in different organs. In addition, the expression patterns of nine PvLTP genes in common beans treated with drought stress were investigated by qRT-PCR. We obtained 58 putative PvLTP genes in the common bean genome via genome-wide analyses. Based on the diversity of the eight-cysteine motif (ECM), these genes were categorized into five types (I, II, IV, V, and VIII). The signal peptides of the PvLTP precursors were predicted to be from 16 to 42 amino acid residues. PvLTPs had a predicated theoretical isoelectric point of 3.94–10.34 and a molecular weight of 7.15–12.17 kDa. The phylogenetic analysis showed that PvLTPs were closer to AtLTPs than OsLTPs. Conserved motif and gene structure analyses indicated that PvLTPs were randomly distributed on all chromosomes except chromosome 9. In addition, 23 tandem duplicates of PvLTP genes were arranged in 10 gene clusters on chromosomes 1 and 2. The heatmap and qRT-PCR showed that PvLTP expression significantly varied in different tissues. Moreover, 9 PvLTP genes were up-regulated under drought treatment. Our results reveal that PvLTPs play potentially vital roles in plants and provide a comprehensive reference for studies on PvLTP genes and a theoretical basis for further analysis of regulatory mechanisms influencing drought tolerance in the common bean. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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