Special Issue "Food Legume Genomics"

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

Deadline for manuscript submissions: 15 February 2021.

Special Issue Editors

Dr. Elena Bitocchi
Website
Guest Editor
Department of Agricultural, Food and Environmental Sciences (D3A) Polytechnic, University of Marche, Ancona, Italy.
Interests: Population Genomics; Evolution; Plant Genetic Resources; Plant Breeding
Dr. Monica Rodriguez
Website
Guest Editor
Department of Agriculture Sassari, University of Sassari, Sassari, Italy
Interests: Molecular Biology; Genetics; Evolution; Biotechnology; Plant Biology; Plant Breeding; Genomics; Sequencing; Genetic Analysis.

Special Issue Information

Dear Colleagues,

Recently, we assisted to an ever-increasing interest for food legumes due to the fact that they represent a valuable source of proteins, lipids, and fiber, and an alternative source of these compounds in human consumption. In particular, pulses, a crucial source of protein in less developed countries, are also becoming increasingly important in developed countries, where they can be used as alternative sources of food protein over animal products, and for their health benefits related to regular consumption.

A general lack of systematic breeding efforts to increase yield capacity, adaptation to different agro-ecosystems and quality of food legumes was the rule during the past decades. Thus, a breeding effort to broad the genetic bases of elite germplasm of these crops is required to improve agronomic performances, resistance to biotic and abiotic stresses, nutritional and technological quality of seeds. This Special Issue in Genes on “Food Legume Genomics” will contribute to increase the knowledge of food legume plant genetic resources by deep genomic and phenotypic characterization (e.g. omics technologies) of underutilized and underexploited genetic diversity present in available wild and domesticated germplasm, along with the parallel characterization of mapping populations to identify, by  applying the most recent population genomics, linkage and association mapping approaches, the genetic control of important phenotypic traits. The new results will be the starting point of breeding programs aimed to improve food legume varieties.

Dr. Elena Bitocchi
Dr. Monica Rodriguez
Guest Editors

Manuscript Submission Information

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Keywords

  • genomics
  • molecular phenotyping
  • phenomics
  • association mapping
  • population genomics
  • nutritional quality

Published Papers (6 papers)

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Research

Open AccessArticle
Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding
Genes 2020, 11(11), 1298; https://doi.org/10.3390/genes11111298 - 30 Oct 2020
Abstract
Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity [...] Read more.
Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements. Full article
(This article belongs to the Special Issue Food Legume Genomics)
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Open AccessArticle
Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes
Genes 2020, 11(10), 1220; https://doi.org/10.3390/genes11101220 - 18 Oct 2020
Abstract
The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of [...] Read more.
The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost. Full article
(This article belongs to the Special Issue Food Legume Genomics)
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Open AccessArticle
High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover
Genes 2020, 11(8), 893; https://doi.org/10.3390/genes11080893 - 05 Aug 2020
Abstract
Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this [...] Read more.
Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs. Full article
(This article belongs to the Special Issue Food Legume Genomics)
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Open AccessArticle
A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.)
Genes 2020, 11(7), 759; https://doi.org/10.3390/genes11070759 - 07 Jul 2020
Cited by 1
Abstract
Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a [...] Read more.
Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene Vradi07g01630, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes Vradi09g09510 and Vradi09g09600, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance. Full article
(This article belongs to the Special Issue Food Legume Genomics)
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Open AccessArticle
Identification of Regulatory SNPs Associated with Vicine and Convicine Content of Vicia faba Based on Genotyping by Sequencing Data Using Deep Learning
Genes 2020, 11(6), 614; https://doi.org/10.3390/genes11060614 - 05 Jun 2020
Cited by 1
Abstract
Faba bean (Vicia faba) is a grain legume, which is globally grown for both human consumption as well as feed for livestock. Despite its agro-ecological importance the usage of Vicia faba is severely hampered by its anti-nutritive seed-compounds vicine and convicine [...] Read more.
Faba bean (Vicia faba) is a grain legume, which is globally grown for both human consumption as well as feed for livestock. Despite its agro-ecological importance the usage of Vicia faba is severely hampered by its anti-nutritive seed-compounds vicine and convicine (V+C). The genes responsible for a low V+C content have not yet been identified. In this study, we aim to computationally identify regulatory SNPs (rSNPs), i.e., SNPs in promoter regions of genes that are deemed to govern the V+C content of Vicia faba. For this purpose we first trained a deep learning model with the gene annotations of seven related species of the Leguminosae family. Applying our model, we predicted putative promoters in a partial genome of Vicia faba that we assembled from genotyping-by-sequencing (GBS) data. Exploiting the synteny between Medicago truncatula and Vicia faba, we identified two rSNPs which are statistically significantly associated with V+C content. In particular, the allele substitutions regarding these rSNPs result in dramatic changes of the binding sites of the transcription factors (TFs) MYB4, MYB61, and SQUA. The knowledge about TFs and their rSNPs may enhance our understanding of the regulatory programs controlling V+C content of Vicia faba and could provide new hypotheses for future breeding programs. Full article
(This article belongs to the Special Issue Food Legume Genomics)
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Open AccessArticle
Narrowing Down a Major QTL Region Conferring Pod Fiber Contents in Yardlong Bean (Vigna unguiculata), a Vegetable Cowpea
Genes 2020, 11(4), 363; https://doi.org/10.3390/genes11040363 - 27 Mar 2020
Cited by 2
Abstract
Yardlong bean (Vigna unguiculata (L.) Walp. ssp. sesquipedalis), a subgroup of cowpea, is an important vegetable legume crop of Asia where its young pods are consumed in both fresh and cooked forms. Pod fiber contents (cellulose, hemicellulose and lignin) correlates with [...] Read more.
Yardlong bean (Vigna unguiculata (L.) Walp. ssp. sesquipedalis), a subgroup of cowpea, is an important vegetable legume crop of Asia where its young pods are consumed in both fresh and cooked forms. Pod fiber contents (cellulose, hemicellulose and lignin) correlates with pod tenderness (softness/hardness) and pod shattering. In a previous study using populations derived from crosses between yardlong bean and wild cowpea (V. unguiculata ssp. unguiculata var. spontanea), three major quantitative trait loci (QTLs), qCel7.1, qHem7.1 and qLig7.1, controlling these fibers were identified on linkage group 7 (cowpea chromosome 5) and are co-located with QTLs for pod tenderness and pod shattering. The objective of this study was to identify candidate gene(s) controlling the pod fiber contents. Fine mapping for qCel7.1, qHem7.1 and qLig7.1 was conducted using F2 and F2:3 populations of 309 and 334 individuals, respectively, from the same cross combination. New DNA markers were developed from cowpea reference genome sequence and used for fine mapping. A QTL analysis showed that in most cases, each pod fiber content was controlled by one major and one minor QTLs on the LG7. The major QTLs for cellulose, hemicellulose and lignin in pod were always mapped to the same regions or close to each other. In addition, a major QTL for pod shattering was also located in the region. Although there were several annotated genes relating to pod fiber contents in the region, two genes including Vigun05g266600 (VuBGLU12) encoding a beta glucosidase and Vigun05g273500 (VuMYB26b) encoding a transcription factor MYB26 were identified as candidate genes for the pod fiber contents and pod shattering. Function(s) of these genes in relation to pod wall fiber biosynthesis and pod shattering was discussed. Full article
(This article belongs to the Special Issue Food Legume Genomics)
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