Chromosome 1 QTLs associated with response to bacterial leaf spot in Beta vulgaris

Bacterial leaf spot (BLS), caused by Pseudomonas syringae pathovar aptata (Psa), is a seedborne, foliar disease affecting members of the Amaranthaceae and Cucurbitaceae families, including table beet and Swiss chard crops. There is no known resistance to BLS in beet or chard. A diversity panel, modified from the Wisconsin Beta Diversity Panel (WBDP) and comprised of 219 accessions from the Beta vulgaris crop complex, was assembled and genotyped for single nucleotide polymorphism data. These accessions were screened by foliar inoculation of Psa and visually evaluated for percentage of diseased leaf tissue. Overall, sugar beet and Beta vulgaris subsp. maritima accessions had the lowest BLS response, whereas table beet accessions had the largest range of responses. Phenotypic means were adjusted using best linear unbiased estimates, and two different software programs, GWASpoly and GAPIT3, were utilized to conduct a genome-wide association study (GWAS). Leaf color was found to be significantly associated with and correlated with BLS response scores, and was used as a covariate in GWAS analysis. An association with BLS response was detected on chromosome 1 in the full WBDP, explaining upward of 21% of the variation in the phenotype. The marker associated with this quantitative trait locus (QTL), Chr1_61344476, showed an additive relationship between dosage and BLS response. Eleven candidate genes, described and annotated in sugar beet, were associated with this QTL. Some of these include F Box domains, RNA-binding proteins, and calcium-dependent kinases, all of which have roles in plant defense responses. Marker Chr1_61344476 may be useful in breeding for BLS resistance in members of the Beta vulgaris crop complex.