Genome-wide association study identifies candidate loci with major contributions to the genetic control of pod morphological traits in snap bean

Authors: SABALLOS, ANA - Oak Ridge Institute For Science And Education (ORISE); Williams, Martin

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2023
Publication Date: 12/20/2023
Citation: Saballos, A., Williams, M. 2023. Genome-wide association study identifies candidate loci with major contributions to the genetic control of pod morphological traits in snap bean. Journal of the American Society for Horticultural Science. 146(1):1-14. https://doi.org/10.21273/JASHS05318-23.
DOI: https://doi.org/10.21273/JASHS05318-23

Interpretive Summary: Snap bean refers to a group of crop cultivars with a range of vegetable pod types that are popular among American consumers, including Romano (flat) beans, wax (yellow) beans, and green beans. Snap bean pod appearance is primarily the result of plant genetics; however, the genes underlying pod traits is poorly known. This research used a collection of 377 snap bean lines, representing diversity of the crop grown in the U.S. over the last century, to investigate the genetic basis of pod morphological traits. Genetic control of snap bean pod traits is complex and we found several regions of the crop's genome associated with pod appearance. The impact of this research is that it provides plant breeders with tools to improve the crop to meet consumer expectations.

Technical Abstract: Snap beans are cultivars of common bean (Phaseolus vulgaris) that are cultivated for their fleshy immature pods that exhibit a wide diversity of pod shapes and sizes. The genetic basis of the snap bean pod shape is complex and involves the interaction of multiple genes. This study used a snap bean diversity panel composed of heirloom and improved cultivars used in North America and genome-wide association studies (GWAS) to investigate the genetic basis of pod morphological characteristics, including length, width, height, width/height ratio, and coefficients of variation (CVs). The GWAS detected multiple genomic regions associated with each pod trait, with a total of 20 quantitative trait loci (QTLs) for pod length, 9 for pod width, 14 for pod height, and 10 for pod width/height ratio. Regarding the CV of each pod trait, genome-wide association analyses detected six QTL for length CVs, five for width CVs, 15 for height CVs, and six for width/height ratio CVs. Thirteen regions in seven chromosomes were associated with two or more pod traits. Eighteen QTLs for pod traits in this study colocated with previously reported QTLs for pod and seed traits. The QTL intervals encompass gene models with homologues in other species that are involved in the control of developmental processes. These results capture the complex nature of the genetic control of snap bean pod traits and confirm the significance of genomic regions harboring overlapping QTLs identified in this and other studies. The phenotypic expression of pod traits in snap bean appears to be under the control of a few genomic regions with a strong effect with additional contributions of multiple small-effect regions. Validation of the function of the candidate genes identified in associated regions will contribute to our understanding of legume pod development.