Genome-wide association study of resistance to Xanthomonas gardneri in USDA pepper (Capsicum) collection

Authors: POTNIS, NEHA - Auburn University; Branham, Sandra; JONES, JEFF - University Of Florida; Wechter, William - Pat

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/12/2019
Publication Date: 6/18/2019
Citation: Potnis, N., Branham, S.E., Jones, J.B., and Wechter, W.P. 2019. Genome-wide association study of resistance to Xanthomonas gardneri in the USDA pepper (Capsicum) collection. https://doi.org/10.1094/PHYTO-06-18-0211-R
DOI: https://doi.org/10.1094/phyto-06-18-0211-r

Interpretive Summary: The bacterial phytopathogen Xanthomonas gardneri is a serious threat to peppers and tomato in the U.S. This emerging and expanding pathogen was first identified in the Midwest around 2010, and has since caused extreme crop losses in those regions. The pathogen is now being identified in other tomato and pepper growing States throughout the U.S. To date, no resistance to this pathogen exists in any pepper cultivar. ARS scientists in Cahrleston in cooperation with univeristy scientists in Florida and Alabama screened the U.S. pepper core collection for resistance to this pathogen, identifying several Plant Introductions with resistance. Using a recently developed technique called genome-wide association study, the scientists identified genetic regions that are linked to the resistance. These genetic “markers” are being developed into molecular tools to allow breeders to track incorporation of this new resistance into existing pepper cultivars.

Technical Abstract: Bacterial spot Xanthomonas species cause significant disease outbreaks on tomato and pepper in tropical and subtropical regions throughout the world. Host resistance has been one of the key components of integrated disease management approaches to mitigate plant pathogens. Although a number of resistance genes have been identified in pepper against bacterial spot xanthomonads, emergence of bacterial spot pathogen variants capable of overcoming these sources and changing pathogen distributions reinforce the importance of identifying novel candidates to incorporate into breeding programs. We have conducted a genome-wide association study (GWAS) on a diverse USDA collection of pepper germplasm including different species of Capsicum to identify novel sources of disease resistance against a highly virulent X. gardneri strain isolated from a recent outbreak. GWAS identified highly significant SNPs associated with disease severity and defoliation. Functionally relevant candidate genes encoded products involved in disease resistance/susceptibility, hormone signaling, and basal resistance against multiple pathogens in various host-pathogen systems. The X. gardneri resistant genotypes and quantitative trait loci (QTL) identified in this study provide alleles which could be used for a resistance gene pyramiding effort against different species of bacterial spot xanthomonads in pepper.