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.

Reyazul Rouf Mir,Vanya Bawa,Neeraj Choudhary,Sofora Jan,Mahendar Thudi,Bikram Singh,Annapurna Chitikineni,Rajneesh Paliwal,Rajeev Kumar Varshney,Ajay Kumar,Mohd Ashraf Bhat

doi:10.3389/fgene.2020.609603

Abstract

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.

Highlights

Common bean (Phaseolus vulgaris L.) is one of the most important diploid grain legume crops (2n = 2x = 22) with a small genome size of 587 Mbp (Broughton et al, 2003)
Yield-contributing traits, such as the number of pods/plant, the number of seeds/pod, 100-seed weight, and grain yield/plant, are important target traits in common bean breeding programs worldwide. The analysis of these four important traits in a core set of 96 lines revealed a broad spectrum of variation as indicated by the wide range and high phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) values
GCV values were lower than PCV values for all traits indicating a significant influence of environment on these traits, underlining the need to test the stability of performance across a range of environments (Table 1)

Summary

Introduction

Common bean (Phaseolus vulgaris L.) is one of the most important diploid grain legume crops (2n = 2x = 22) with a small genome size of 587 Mbp (Broughton et al, 2003). It is the major source of calories and proteins for the people in developing countries of the world (FAO1). Common bean is one of the most ancient crops of the Americas (Broughton et al, 2003; McClean et al, 2004) and possesses two important already diverged gene pool species: the Mesoamerican and Andean gene pool species. The characterized crop germplasm forms the basis of crop improvement programs and the development of genetic resources, such as mapping populations and core collections, for the genetic dissection of important traits through quantitative trait locus (QTL) mapping and genome-wide association mapping approaches (McClean et al, 2012)

Methods

Results

Conclusion