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16 pages, 1323 KiB

Open AccessArticle

Genome-Wide Association Study (GWAS) for Resistance to Sclerotinia sclerotiorum in Common Bean

by Ana Campa, Carmen García-Fernández and Juan José Ferreira

Genes 2020, 11(12), 1496; https://doi.org/10.3390/genes11121496 - 12 Dec 2020

Cited by 11 | Viewed by 2733

White mold (WM) is a devastating fungal disease affecting common bean (Phaseolus vulgaris L.). In this research, a genome-wide association study (GWAS) for WM resistance was conducted using 294 lines of the Spanish diversity panel. One single-locus method and six multi-locus methods [...] Read more.

White mold (WM) is a devastating fungal disease affecting common bean (Phaseolus vulgaris L.). In this research, a genome-wide association study (GWAS) for WM resistance was conducted using 294 lines of the Spanish diversity panel. One single-locus method and six multi-locus methods were used in the GWAS. Response to this fungus showed a continuous distribution, and 28 lines were identified as potential resistance sources, including lines of Andean and Mesoamerican origin, as well as intermediate lines between the two gene pools. Twenty-two significant associations were identified, which were organized into 15 quantitative trait intervals (QTIs) located on chromosomes Pv01, Pv02, Pv03, Pv04, Pv08, and Pv09. Seven of these QTIs were identified for the first time, whereas eight corresponded to chromosome regions previously identified in the WM resistance. In all, 468 genes were annotated in these regions, 61 of which were proposed potential candidate genes for WM resistance, based on their function related to the three main defense stages on the host: recognition (22), signal transduction (8), and defense response (31). Results obtained from this work will contribute to a better understanding of the complex quantitative resistance to WM in common bean and reveal information of significance for future breeding programs. Full article

(This article belongs to the Special Issue Food Legume Genomics)

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21 pages, 5458 KiB

Open AccessArticle

Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.)

by Mounirou Hachim Alyr, Justine Pallu, Aissatou Sambou, Joel Romaric Nguepjop, Maguette Seye, Hodo-Abalo Tossim, Yvette Rachelle Djiboune, Djibril Sane, Jean-François Rami and Daniel Fonceka

Genes 2020, 11(12), 1402; https://doi.org/10.3390/genes11121402 - 25 Nov 2020

Cited by 21 | Viewed by 3461

Abstract

Fruit and seed size are important yield component traits that have been selected during crop domestication. In previous studies, Advanced Backcross Quantitative Trait Loci (AB-QTL) and Chromosome Segment Substitution Line (CSSL) populations were developed in peanut by crossing the cultivated variety Fleur11 and [...] Read more.

Fruit and seed size are important yield component traits that have been selected during crop domestication. In previous studies, Advanced Backcross Quantitative Trait Loci (AB-QTL) and Chromosome Segment Substitution Line (CSSL) populations were developed in peanut by crossing the cultivated variety Fleur11 and a synthetic wild allotetraploid (Arachis ipaensis × Arachis duranensis)^4x. In the AB-QTL population, a major QTL for pod and seed size was detected in a ~5 Mb interval in the proximal region of chromosome A07. In the CSSL population, the line 12CS_091, which carries the QTL region and that produces smaller pods and seeds than Fleur11, was identified. In this study, we used a two-step strategy to fine-map the seed size QTL region on chromosome A07. We developed new SSR and SNP markers, as well as near-isogenic lines (NILs) in the target QTL region. We first located the QTL in ~1 Mb region between two SSR markers, thanks to the genotyping of a large F₂ population of 2172 individuals and a single marker analysis approach. We then used nine new SNP markers evenly distributed in the refined QTL region to genotype 490 F₃ plants derived from 88 F₂, and we selected 10 NILs. The phenotyping of the NILs and marker/trait association allowed us to narrowing down the QTL region to a 168.37 kb chromosome segment, between the SNPs Aradu_A07_1148327 and Aradu_A07_1316694. This region contains 22 predicted genes. Among these genes, Aradu.DN3DB and Aradu.RLZ61, which encode a transcriptional regulator STERILE APETALA-like (SAP) and an F-box SNEEZY (SNE), respectively, were of particular interest. The function of these genes in regulating the variation of fruit and seed size is discussed. This study will contribute to a better knowledge of genes that have been targeted during peanut domestication. Full article

(This article belongs to the Special Issue Food Legume Genomics)

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22 pages, 3577 KiB

Open AccessArticle

Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

by Caléo Panhoca de Almeida, Jean Fausto de Carvalho Paulino, Sérgio Augusto Morais Carbonell, Alisson Fernando Chiorato, Qijian Song, Valerio Di Vittori, Monica Rodriguez, Roberto Papa and Luciana Lasry Benchimol-Reis

Genes 2020, 11(11), 1298; https://doi.org/10.3390/genes11111298 - 30 Oct 2020

Cited by 23 | Viewed by 4747

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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18 pages, 2442 KiB

Open AccessArticle

Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes

by Roshan Kulkarni, Ratan Chopra, Jennifer Chagoya, Charles E. Simpson, Michael R. Baring, Andrew Hillhouse, Naveen Puppala, Kelly Chamberlin and Mark D. Burow

Genes 2020, 11(10), 1220; https://doi.org/10.3390/genes11101220 - 18 Oct 2020

Cited by 2 | Viewed by 2937

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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14 pages, 2479 KiB

Open AccessArticle

High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover

by Mustafa M. H. Abd El-Wahab, Maha Aljabri, Mohamed S. Sarhan, Gamal Osman, Shichen Wang, Mahmoud Mabrouk, Hattem M. El-Shabrawi, Ahmed M. M. Gabr, Ahmed M. Abd El-Haliem, Donal M. O'Sullivan and Mohamed El-Soda

Genes 2020, 11(8), 893; https://doi.org/10.3390/genes11080893 - 05 Aug 2020

Cited by 6 | Viewed by 4355

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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11 pages, 989 KiB

Open AccessArticle

A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.)

by Caleb Manamik Breria, Ching-Hsiang Hsieh, Tsair-Bor Yen, Jo-Yi Yen, Thomas J. Noble and Roland Schafleitner

Genes 2020, 11(7), 759; https://doi.org/10.3390/genes11070759 - 07 Jul 2020

Cited by 20 | Viewed by 3898

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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16 pages, 346 KiB

Open AccessArticle

Identification of Regulatory SNPs Associated with Vicine and Convicine Content of Vicia faba Based on Genotyping by Sequencing Data Using Deep Learning

by Felix Heinrich, Martin Wutke, Pronaya Prosun Das, Miriam Kamp, Mehmet Gültas, Wolfgang Link and Armin Otto Schmitt

Genes 2020, 11(6), 614; https://doi.org/10.3390/genes11060614 - 05 Jun 2020

Cited by 15 | Viewed by 4824

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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12 pages, 1963 KiB

Open AccessArticle

Narrowing Down a Major QTL Region Conferring Pod Fiber Contents in Yardlong Bean (Vigna unguiculata), a Vegetable Cowpea

by Phurisorn Watcharatpong, Akito Kaga, Xin Chen and Prakit Somta

Genes 2020, 11(4), 363; https://doi.org/10.3390/genes11040363 - 27 Mar 2020

Cited by 20 | Viewed by 3432

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 F_2:3 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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