A robust SNP-haplotype assay for resistance to beet curly top virus in common bean (Phaseolus vulgaris L.)

Authors: SOLER-GARZON, ALVARO - Washington State University; GOLDOFF, DEIDRAH - Harris Moran Seed Company; THORNTON, ALYSON - Harris Moran Seed Company; Swisher Grimm, Kylie; Hart, John; Song, Qijian; Strausbaugh, Carl; Miklas, Phillip - Phil

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/12/2023
Publication Date: 7/14/2023
Citation: Soler-Garzon, A., Goldoff, D., Thornton, A., Swisher Grimm, K.D., Hart, J.P., Song, Q., Strausbaugh, C.A., Miklas, P.N. 2023. A robust SNP-haplotype assay for resistance to beet curly top virus in common bean (Phaseolus vulgaris L.). Frontiers in Plant Science. 14:e1215950. https://doi.org/10.3389/fpls.2023.1215950.
DOI: https://doi.org/10.3389/fpls.2023.1215950

Interpretive Summary: Beet curly top virus is a major disease plaguing common bean (dry bean and garden or snap beans) production in the Western United States. The best control method is to plant bean varieties that carry the Bct gene making them resistant to beet curly top virus. A major challenge in developing new resistant cultivars is that each genetic line must be screened for susceptibility to the pathogen, which is labor intensive and time consuming. Researchers with the USDA-ARS, Washington State University, and Harris Moran Seed mapped the Bct gene region and identified robust genetic markers for detecting the Bct gene in breeding populations. These new tools will allow breeders to use marker-assisted selection to develop snap and dry bean cultivars that are resistance to beet curly top virus.

Technical Abstract: Beet curly top virus (BCTV), which is synonymous with Curly Top Virus (CTV), causes significant yield loss in common bean (snap and dry beans) cultivars and several other important crops. Common bean cultivars have been found to be resistant to CTV, but screening for resistance is challenging due to the cyclical nature of epidemics and spotty feeding by the leafhopper that vectors the virus. We used a SNP dataset for the Snap Bean Association Panel (SnAP) agro-inoculated with CTV-Logan (CA/Logan) strain to locate the Bct gene region to a 1.7 Mb interval on chromosome Pv07 using Genome-wide association study (GWAS) analysis. Recombinant lines from the SnAP were used to further narrow the Bct region to a 58.0 Kb interval. A missense SNP (S07_2970381) in candidate gene Phvul.007G036300 Exonuclease V (EXO5) was identified as the most likely causal mutation, and it was the most significant SNP detected by GWAS in a Dry Bean Population (DBP) naturally infected by the CTV-Worland (Wor) strain. Tm-shift assay markers developed for SNP S07_2970381 and two linked SNPs, S07_2970276 and S07_2966197, were useful for tracking different origins of the Bct EXO5 candidate gene resistance to CTV in common bean. The three SNPs identified four haplotypes, with haplotype 3-1 (Haplo3-1) of Middle American origin associated with the highest levels of CTV resistance. This SNP-haplotype assay will enable breeders to track resistance sources and to develop cultivars with better CTV resistance.