Genome-wide association study and genomic prediction of leaf spot (Stemphylium vesicarium) resistance in spinach diversity panel

Stemphylium leaf spot (SLP), caused by <i>Stemphylium vesicarium</i>, has emerged as an increasing threat to spinach production in the United States, with widespread outbreaks reported across major spinach-growing regions over the past two decades. The objectives of this study were to: (1) evaluate global USDA spinach germplasm collections and commercial cultivars for resistance to <i>S. vesicarium</i>; (2) perform genome-wide association studies (GWAS) to identify genomic regions associated with resistance; and (3) conduct genomic prediction (GP) to enhance selection accuracy. A total of 311 diverse spinach genotypes, including USDA germplasm accessions and commercial cultivars, were evaluated under greenhouse conditions at the University of Arkansas using the <i>S. vesicarium</i> isolate Sb-1-St001 from 2019 to 2021. The panel exhibited a wide range of disease responses. GWAS using disease severity index (DSI) values and whole-genome resequencing (WGR)-based SNP markers identified four SNPs-SOVchr1_127757911 (127,757,911 bp, Chr1), SOVchr2_21962694 (21,962,694 bp, Chr2), SOVchr4_114674293 (114,674,293 bp, Chr4), and SOVchr5_37417509 (37,417,509 bp, Chr5)-that were significantly associated with DSI for SLP resistance. Genomic prediction of DSI was performed using seven GP models across nine randomly selected SNP datasets and two GWAS-derived SNP sets. The GWAS-derived marker sets produced higher prediction accuracies in cross-population prediction, with r-values of 0.45 and 0.51 for the 4- and 18-SNP sets, respectively. These results underscore the potential of marker-assisted selection (MAS) and genomic selection (GS) to accelerate the development of spinach cultivars resistant to Stemphylium leaf spot.