Association Analysis of Stemphylium Leaf Spot Resistance in Spinach

Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia, is an important disease of spinach. The use of genetic resistance is an efficient, economical, and environmentally sound method to manage this disease. The objective of this research was to conduct association analysis to identify single nucleotide polymorphism (SNP) markers associated with Stemphylium leaf spot resistance in spinach germplasm. A total of 295 spinach genotypes, including 275 accessions of the USDA spinach germplasm collection and 20 commercial cultivars, were used for genotyping by sequencing (GBS) with 794 SNPs for genetic diversity and association analyses. Spinach genotypes showed a near-normal distribution for Stemphylium leaf spot resistance, with a range from 0 to 100% disease incidence, suggesting that Stemphylium leaf spot resistance in spinach is a complex, quantitative trait controlled by minor genes. Association analysis indicated that seven SNP markers were associated with Stemphylium leaf spot resistance, with a log of odds (LOD) >2.5. Of the seven SNP markers, AYZV02031464_90, AYZV02031464_94, and AYZV02031464_95 were located on the same contig, AYZV02031464, at a 5 bp distance; AYZV02076752_426 and AYZV02076752_431 were on contig AYZV02076752 with a 5 bp distance; and AYZV02124848_365 and AYZV02149880_108 were on contigs AYZV02124848 and AYZV02149880, respectively. This indicated four genomic regions, or quantitative trait loci (QTLs), were associated with Stemphylium leaf spot resistance in spinach. SNP markers may be useful to select for Stemphylium leaf spot resistance in spinach breeding programs through marker-assisted selection.