Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean

Authors

Samira Mafi Moghaddam, North Dakota State UniversityFollow
Sujan Mamidi, North Dakota State University
Juan M. Osorno, North Dakota State UniversityFollow
Rian Lee, North Dakota State UniversityFollow
Mark A. Brick, Colorado State UniversityFollow
James Kelly, Michigan State University
Phillip N. Miklas, USDA-ARSFollow
Carlos A. Urrea, University of Nebraska-LincolnFollow
Qijian Song, USDA-ARSFollow
Perry B. Cregan, USDA-ARSFollow
Jane Grimwood, HudsonAlpha Institute of Biotechnology
Jeremy Schmutz, HudsonAlpha Institute of Biotechnology
Phillip E. McClean, North Dakota State UniversityFollow

Date of this Version

10-6-2016

Citation

The Plant Genome (November 2016), Vol. 9, No. 3, pp. 1-21, doi: 10.3835/plantgenome2016.02.0012.

Comments

Copyright © Crop Science Society of America. This is an open access article distributed under the CC BY-NC-ND license.

Abstract

Common bean (Phaseolus vulgaris L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter- and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango–Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome-wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ~30 candidate genes based on a priori and candidate gene search strategies centered on the 100-kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean.