Genome-wide association study and genomic prediction of fruit weight in spinach

Fruit weight is a fundamental agronomic trait in spinach (Spinacia oleracea L.) that influences germination, seedling vigor, early growth, storage quality, seed nutrient reserves, and seed yield. In this study, fruit weight variation was evaluated in a panel of 364 USDA germplasm accessions that were phenotyped for this trait and genotyped using 68,561 single-nucleotide polymorphisms (SNPs) generated through whole-genome resequencing. Genome-wide association study (GWAS) analyses were conducted using GAPIT3 with the MLM, MLMM, FarmCPU, and BLINK models, and six SNPs significantly associated with fruit weight were identified: SOVchr1_36331932 and SOVchr1_12344662 on chromosome 1; SOVchr3_151819671, SOVchr3_56703 and SOVchr3_90402076 on chromosome 3; and SOVchr6_21959181 on chromosome 6. Two candidate genes were identified in proximity to two SNPs: gene SOV3g032190 on chromosome 3, encoding a BHLH transcription factor (90,472,330–90,479,952 bp), and gene SOV6g047020 on chromosome 6, encoding a NAC domain-containing protein (148,214,848–148,218,323 bp). Genomic prediction (GP) models further determined genomic estimated breeding values (GEBVs) for fruit weight, achieving prediction accuracies up to r = 0.51 using the 6-marker GWAS-derived SNP set (m6; detected by at least two models) and r = 0.59 using the 49-marker set (m49; detected by at least one model) in cross-population analysis. These findings provide new insights into the genetic architecture of fruit weight in spinach and demonstrate the utility of integrating GWAS and GP to support marker-assisted breeding strategies for spinach improvement and enhanced economic returns.