Genomic insights of leafminer resistance in spinach through GWAS approach and genomic prediction

The Leafminers, representing a diverse group of insects from various genera within the Agromyzidae family, pose a significant threat to spinach (Spinacia oleracea L.) production. This study aimed to identify single nucleotide polymorphism (SNP) markers associated with leafminer resistance through a genome-wide association study (GWAS) and to evaluate the prediction accuracy (PA) for selecting resistant spinach using genomic prediction (GP). Using a dataset of 84301 SNPs obtained from whole-genome resequencing, seven GWAS models, including BLINK, FarmCPU, MLM, and MLMM in GAPIT 3, as well as MLM, GLM, and SMR in TASSEL 5, were employed to perform GWAS on a panel of 286 USDA spinach germplasm accessions. Three SNP markers, namely 1_115279256_C_T, 3_157082529_C_T, and 4_168510908_T_G on chromosomes 1, 3, and 4, respectively, were identified as associated with leafminer resistance. In the 30 kb flanking regions of these markers, four candidate genes (SOV1g031330, SOV1g031340, SOV4g047270, and SOV4g047280), encoding LOB domain-containing protein, KH domain-containing protein, were discovered. Nodulin-like domain-containing protein, and SAM domain-containing protein, were discovered. The PA for leafminer resistance selection was estimated using ten different SNP sets, including two GWAS-derived marker sets (three and 51 SNPs) and eight random marker sets (ranging from 51 to 10 K SNPs) analyzed by seven GP models. The findings emphasized the superior performance of GWAS-derived SNP sets, reaching a PA of up to 0.79 using the cBLUP model. Notably, this research marks the pioneering application of GP in the context of insect resistance, providing a significant advancement in the understanding and management of leafminer resistance in spinach cultivation.