Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas

The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer’s selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity, He) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker–trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield.

Download Full-text

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

Genes ◽

10.3390/genes11121496 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1496

Author(s):

Ana Campa ◽

Carmen García-Fernández ◽

Juan José Ferreira

Keyword(s):

Association Study ◽

Common Bean ◽

Genome Wide Association Study ◽

Continuous Distribution ◽

Genome Wide Association ◽

Host Recognition ◽

Gene Pools ◽

Potential Candidate ◽

Genome Wide ◽

A Genome

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.

Download Full-text

Genome‐wide association analysis of drought resistance based on seed germination vigour and germination rate at the bud stage in common bean ( Phaseolus vulgaris L.)

Agronomy Journal ◽

10.1002/agj2.20683 ◽

2021 ◽

Author(s):

Lei Wu ◽

Yujie Chang ◽

Lanfen Wang ◽

Shumin Wang ◽

Jing Wu

Keyword(s):

Phaseolus Vulgaris ◽

Seed Germination ◽

Common Bean ◽

Association Analysis ◽

Drought Resistance ◽

Germination Rate ◽

Genome Wide Association ◽

Phaseolus Vulgaris L ◽

Genome Wide Association Analysis ◽

Genome Wide

Download Full-text

Genome-wide association and genomic prediction identifies soybean cyst nematode resistance in common bean including a syntenic region to soybean Rhg1 locus

Horticulture Research ◽

10.1038/s41438-018-0085-3 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 8

Author(s):

Liwei Wen ◽

Hao-Xun Chang ◽

Patrick J. Brown ◽

Leslie L. Domier ◽

Glen L. Hartman

Keyword(s):

Common Bean ◽

Genomic Prediction ◽

Soybean Cyst Nematode ◽

Nematode Resistance ◽

Cyst Nematode ◽

Syntenic Region ◽

Genome Wide Association ◽

Genome Wide ◽

Soybean Cyst Nematode Resistance

Download Full-text

Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.)

Genomics ◽

10.1016/j.ygeno.2020.03.030 ◽

2020 ◽

Vol 112 (6) ◽

pp. 4536-4546

Author(s):

Semih Erdogmus ◽

Duygu Ates ◽

Seda Nemli ◽

Bulent Yagmur ◽

Tansel Kaygisiz Asciogul ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Phaseolus Vulgaris L ◽

Genome Wide ◽

The Common

Download Full-text

European landrace diversity for common bean biofortification: a genome-wide association study

Scientific Reports ◽

10.1038/s41598-020-76417-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Leonardo Caproni ◽

Lorenzo Raggi ◽

Elise F. Talsma ◽

Peter Wenzl ◽

Valeria Negri

Keyword(s):

Common Bean ◽

Genome Wide Association Study ◽

Preliminary Evidence ◽

Snp Markers ◽

Genome Wide Association ◽

Future Research ◽

Balanced Diet ◽

Genome Wide ◽

Seed Content ◽

A Genome

AbstractMineral deficiencies represent a global challenge that needs to be urgently addressed. An adequate intake of iron and zinc results in a balanced diet that reduces chances of impairment of many metabolic processes that can lead to clinical consequences. In plants, bioavailability of such nutrients is reduced by presence of compounds such as phytic acid, that can chelate minerals and reduce their absorption. Biofortification of common bean (Phaseolus vulgaris L.) represents an important strategy to reduce mineral deficiencies, especially in areas of the world where this crop plays a key role in the diet. In this study, a panel of diversity encompassing 192 homozygous genotypes, was screened for iron, zinc and phytate seed content. Results indicate a broad variation of these traits and allowed the identification of accessions reasonably carrying favourable trait combinations. A significant association between zinc seed content and some molecular SNP markers co-located on the common bean Pv01 chromosome was detected by means of genome-wide association analysis. The gene Phvul001G233500, encoding for an E3 ubiquitin-protein ligase, is proposed to explain detected associations. This result represents a preliminary evidence that can foster future research aiming at understanding the genetic mechanisms behind zinc accumulation in beans.

Download Full-text

Genome-Wide Association Studies of Anthracnose and Angular Leaf Spot Resistance in Common Bean (Phaseolus vulgaris L.)

PLoS ONE ◽

10.1371/journal.pone.0150506 ◽

2016 ◽

Vol 11 (3) ◽

pp. e0150506 ◽

Cited By ~ 33

Author(s):

Juliana Morini Küpper Cardoso Perseguini ◽

Paula Rodrigues Oblessuc ◽

João Ricardo Bachega Feijó Rosa ◽

Kleber Alves Gomes ◽

Alisson Fernando Chiorato ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Leaf Spot ◽

Association Studies ◽

Angular Leaf Spot ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Phaseolus Vulgaris L ◽

Genome Wide

Download Full-text

Genome-Wide Association Study of Rice Core Set Related to Grain Weight

Plant Breeding and Biotechnology ◽

10.9787/pbb.2018.6.3.293 ◽

2018 ◽

Vol 6 (3) ◽

pp. 293-304 ◽

Cited By ~ 2

Author(s):

Buung Choi ◽

Ji-Min Yoo ◽

Sang-Beom Lee ◽

Gyeong-Jin Kim ◽

Kyu-Won Kim ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Grain Weight ◽

Genome Wide Association ◽

Genome Wide ◽

Core Set

Download Full-text

Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean (Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity

Frontiers in Plant Science ◽

10.3389/fpls.2021.628687 ◽

2021 ◽

Vol 12 ◽

Author(s):

Daniel Ambachew ◽

Matthew W. Blair

Keyword(s):

Common Bean ◽

Candidate Genes ◽

Aluminum Toxicity ◽

Root Traits ◽

Al Toxicity ◽

Genome Wide Association ◽

Soil Conditions ◽

Polygenic Inheritance ◽

Genome Wide ◽

Significant Difference

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed.

Download Full-text

Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean

Frontiers in Plant Science ◽

10.3389/fpls.2021.748829 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jessica Delfini ◽

Vânia Moda-Cirino ◽

José dos Santos Neto ◽

Douglas Mariani Zeffa ◽

Alison Fernando Nogueira ◽

...

Keyword(s):

Common Bean ◽

Quantitative Trait ◽

Seed Weight ◽

Genetic Improvement ◽

Agronomic Traits ◽

Genome Wide Association ◽

Multiple Methods ◽

Favorable Alleles ◽

Genome Wide ◽

Multiple Environments

The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.

Download Full-text