GWAS of resistance to three bacterial diseases in the Andean common bean diversity panel

Authors: SOLER-GARZON, ALVARO - Washington State University Extension Service; MULUBE, MWIINGA - University Of Zambia; KAMFWA, KELVIN - University Of Zambia; LUNGU, DAVIES - University Of Zambia; HAMABWE, SWIVIA - University Of Zambia; ROY, JAYANTA - North Dakota State University; SALEGUA, VENANCIO - Agricultural Research Council Of South Africa; Porch, Timothy - Tim; MCCLEAN, PHIL - North Dakota State University; Miklas, Phillip - Phil

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/2024
Publication Date: 9/5/2024
Citation: Soler-Garzon, A., Mulube, M., Kamfwa, K., Lungu, D., Hamabwe, S., Roy, J., Salegua, V., Porch, T.G., Mcclean, P., Miklas, P.N. 2024. GWAS of resistance to three bacterial diseases in the Andean common bean diversity panel. Frontiers in Plant Science. 15:1469381. https://doi.org/10.3389/fpls.2024.1469381.
DOI: https://doi.org/10.3389/fpls.2024.1469381

Interpretive Summary: The three most globally prevalent bacterial diseases in common bean are bacterial brown spot (BBS), common bacterial blight (CBB), and halo bacterial blight (HBB). With favorable conditions, these pathogens can cause up to 50% yield loss and reduced seed quality. Our goal was to gain a better understanding of the genetics of resistance to all three diseases to facilitate breeding Andean dry beans with improved resistance. A large Andean Diversity Panel (ADP) with 444 accessions was evaluated for reaction to the three bacterial blight diseases in field and screenhouse trials. We detected 24 gene regions which influenced resistance to the three diseases. Five regions possessed genes which conditioned resistance to two or more bacterial diseases. These results will be used by breeders to incorporate and deploy new sources and combinations of resistance genes in the development of new culitvars with increased sustainability to bacterial blight epidemics.

Technical Abstract: Bacterial brown spot (BBS) caused by Pseudomonas syringae pv. syringae (Pss), common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli (Xap) and Xanthomonas fuscans subsp. fuscans (Xff), and halo bacterial blight (HBB) caused by Pseudomonas syringae pv. phaseolicola (Psph) are major bacterial diseases which severely impact common bean yields, affecting global food security. Andean-origin dry beans, representing large-seeded market classes, are particularly susceptible. Using 140,325 SNPs, a multi-locus GWAS was conducted on subsets of the Andean diversity panel (ADP) phenotyped for BBS in South Africa, CBB in Puerto Rico, South Africa, and Zambia, and HBB in South Africa through natural infection, artificial inoculation, or both. Twenty-four QTL associated with resistance were identified: nine QTL for BBS, eight for CBB, and seven for HBB. Four QTL intervals on Pv01, Pv03, Pv05, and Pv08 possessed overlapping BBS and HBB resistance. A genomic interval on Pv01near to the fin gene, which conditions determinate growth habit, was linked to resistance to all three pathogens. Different QTL for BBS and CBB resistance were detected under natural infection and artificial inoculations. These results underscore the importance of combining both methods in multi-GWAS to capture the full genetic spectrum. Previously recognized CBB resistance QTL SAP6 and SU91 and HBB resistance QTL HB4.2 and HB5.1 were observed. Other common (MAF >0.25) and rare (MAF <0.05) resistance QTL were also detected. Overall, these findings enhance the understanding and utilization of the bacterial resistance present in the ADP for developing common beans with improved resistance.