Genome-Wide Association Study (GWAS) of White Mold Resistance in Snap Bean

Abstract

White mold can result in snap bean yield losses of 90 to 100% when field conditions favor the pathogen. A genome-wide association study (GWAS) was conducted to detect loci significantly associated with white mold resistance in a panel of snap bean (Phaseolus vulgaris L.) cultivars. Two populations of snap bean were used in this study. The first population was the BeanCAP (Coordinated Agriculture Project) Snap Bean Diversity Panel (SBDP) (n = 136), and the second population was the Snap Bean Association Panel (SnAP) (n = 378). SBDP was evaluated for white mold reaction in the field in 2012 and 2013, and SnAP was screened in a greenhouse only using the seedling straw test in 2016. Two reference genomes representing the Andean and Middle American centers of domestication were utilized to align the genotyping-by-sequencing (GBS) data. A GWAS was performed using FarmCPU with one principal component after comparing five models. Thirty-four single-nucleotide polymorphisms (SNPs) significantly associated with white mold resistance were detected. Eleven significant SNPs were identified by the seedling straw test, and 23 significant SNPs were identified by field data. Fifteen SNPs were identified within a 100 kb window containing pentatricopeptide repeat (PPR)-encoding genes, and eleven were close to leucine-rich repeat (LRR)-encoding genes, suggesting that these two classes are of outsized importance for snap bean resistance to white mold.

Linked candidate genes of different functions for white mold resistance in common bean (Phaseolus vulgaris L) are identified by multiple QTL mapping approaches

“…These results support our identification of three independent QTL within the 3.11 to 23.21 Mb physical position on Pv02. A recent GWAS of WM resistance in snap bean germplasm identified significant SNPs located on 34.9, 41.8, and 51.3 Mb on Pv02 ( Arkwazee et al., 2022 ). However, none of the identified SNPs were found to overlap with our reported genomic interval.…”

Novel SNP markers for flowering and seed quality traits in faba bean (Vicia faba L.): characterization and GWAS of a diversity panel

“…It should be noted that the choice of MAF threshold affects the power of GWAS and is commonly set to 0.05 ( Alqudah et al., 2020 ). However, to capture rare alleles in diverse panels which can be of interest as targets for further genetic and biological studies, the MAF threshold in the GWAS can be lowered to not exclude any potential markers of interest ( Stanton-Geddes et al., 2013 ; Arkwazee et al., 2022 ; Kim et al., 2022 ). In the current study, the MAF was therefore set to >0.01, however, it is noteworthy, that the markers identified as significantly associated with traits all had a MAF exceeding 0.05.…”

The alleles bc‐ud and bc‐ur (previously bc‐4 gene), representing coding mutations within Vps4 AAA+ ATPase ESCRT protein, interact with other genes to condition resistance to BCMV and BCMNV in common bean

“…Recently, the SnAP was used for genome‐wide association studies (GWAS) for resistance to white mold ( Sclerotinia sclerotiorum Lib. de Bary) (Arkwazee et al., 2022) and to beet curly top virus (Soler‐Garzón et al., 2023). A subset of 59 accessions from the DDP were selected for presence of either I / bc‐1 / bc‐u d (nine accessions), bc‐1 / bc‐u d (47 accessions), or bc‐1 / bc‐4 (three accessions) genotypes (Table S2).…”