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Title: Genome-wide association study identifies candidate loci underlying seven agronomic traits in Middle American diversity panel in common bean (Phaseolus vulgaris L.)

Author
item MOGHADDAM, SAMIRA - North Dakota State University
item MAMIDI, S - Hudsonalpha Institute For Biotechnology
item OSORNO, JUAN - North Dakota State University
item LEE, RIAN - North Dakota State University
item BRICK, MARK - Colorado State University
item KELLY, JAMES - Michigan State University
item Miklas, Phillip - Phil
item URREA, CARLOS - University Of Nebraska
item Song, Qijian
item Cregan, Perry
item GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology
item SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology
item MCCLEAN, PHIL - North Dakota State University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2016
Publication Date: 10/6/2016
Citation: Moghaddam, S., Mamidi, S., Osorno, J., Lee, R., Brick, M., Kelly, J., Miklas, P.N., Urrea, C., Song, Q., Cregan, P.B., Grimwood, J., Schmutz, J., McClean, P. 2016. Genome-wide association study identifies candidate loci underlying seven agronomic traits in Middle American diversity panel in common bean (Phaseolus vulgaris L.). The Plant Genome. 9:1-21.

Interpretive Summary: A new genomic revolution in dry bean has provided tools to decipher the genetic code underlying important agronomic traits. This study describes the genotyping and phenotyping of a panel of approximately 275 accessions of dry bean representing the Middle American (Mexico) center of diversity. The agronomic performance of the accessions in different US production regions: North Dakota, Michigan, Nebraska, and Colorado was matched to genetic markers (SNPs) along the chromosomes to find specific chromosomal regions affecting certain traits like seed size and resistance to lodging. This study is a significant step forward toward identifying specific genes influencing agronomic traits in dry bean. A better understanding of these traits and the genes controlling them will assist breeders in developing cultivars with desired traits and enhanced performance.

Technical 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 associate 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 U.S. locations, and a GWAS using over 150,000 SNPs (minor allele frequency = 5%) was conducted for seven agronomic traits. The degree of inter- and intra-chromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. LD varied between chromosomes for the entire MDP and among race Mesoamerican and Durango/Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. GWAS 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 co-localized signals in a narrow genomic interval for three inter-related traits: growth habit, lodging, and canopy height. Overall, this study detected ~30 candidate genes based on a priori and a 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.