GWAS of pod morphological and color characters in common bean

Authors: GARCIA, CARMEN - Agriculture Research And Development Service (SERIDA); CAMPA, ANA - Agriculture Research And Development Service (SERIDA); SOLER-GARZON, ALVARO - Washington State University; Miklas, Phillip - Phil; FERREIRA, JUAN JOSE - Agriculture Research And Development Service (SERIDA)

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/3/2021
Publication Date: 4/17/2021
Citation: Garcia, C., Campa, A., Soler-Garzon, A., Miklas, P.N., Ferreira, J. 2021. GWAS of pod morphological and color characters in common bean. Biomed Central (BMC) Plant Biology. 21. Article 184. https://doi.org/10.1186/s12870-021-02967-x.
DOI: https://doi.org/10.1186/s12870-021-02967-x

Interpretive Summary: Common bean is consumed as a grain (dry bean) or fresh pod (green bean, snap bean). The shape and color of seeds and pods influence consumer acceptance. This specific study investigated the genetics underlying the extensive variability for pod size and pod color traits in a diversity panel of 300 Spanish common bean accessions. Seventeen pod traits were measured ranging from pod length to pod width, and qualitative to quantitative color assessments. New genes were discovered and existing genes validated. Overall a better understanding of the genetics of pod size and color traits was gained, which will assist breeders in making more informed decisions about gene combinations to use while developing culitvars with improved pod qualities desired by consumers.

Technical Abstract: Many bean genotypes are cultivated for green pod production. We sought to investigate the genomic regions conditioning pod morphological and color characters. Single (SL) and multi-locus (ML) genome wide association analysis (GWAS) was used to investigate pod traits for a set of 301 bean lines of the Spanish Diversity Panel (SDP). The SDP was genotyped with 32,812 SNPs obtained from Genotyping by Sequencing. The panel was grown in two environments and phenotypic data were recorded for 17 fresh pods traits grouped in four pod characters: pod length, pod cross-section, pod color, and number of seeds per pod. In all, 23 QTL for pod length, 6 for cross-section, 18 for pod color, 6 for number of seeds per pod and 9 associated to two or more pod characters were detected. Most QTL were located in the telomeric region of chromosomes Pv01, Pv02, Pv04, Pv08, Pv09 and Pv10. Eighteen detected QTL co-localized with previously reported QTL. Twenty-two candidate genes involving developmental processes were detected underlying 11 QTL for pod morphological characters, four of them homologous to A. thaliana genes FIS2, SPL10, TTG2 and AML2 affecting silique size. Nine candidate genes involved in pigment synthesis, were found underlying five QTL for pod color. Overall new QTL identified and existing QTL validated as meta-QTL contribute to a better understanding of the complex inheritance of pod size and color traits in common bean.