Leaf base color in spinach (Spinacia oleracea L.) exhibits substantial phenotypic variation, potentially influencing consumer preference and nutritional content. To elucidate the genetic basis of this variation, we conducted a genome-wide association study (GWAS) utilizing a diverse panel of 313 USDA-GRIN accessions of spinach. This population, characterized by a predominance of white (65%) and red (35%) leaf base colors, was genotyped using whole-genome resequencing (WGR) resulting in the identification of 83,261 high-quality single nucleotide polymorphisms (SNPs) after rigorous filtering. Genetic diversity analyses and association mapping were performed using multiple statistical models, including mixed linear model (MLM), generalized linear model (GLM), BLINK, and FarmCPU, implemented in GAPIT 3, TASSEL 5, and rMVP software. The GWAS identified three significantly associated SNPs (SOVchr3_140405053, SOVchr3_140405474, SOVchr3_140412359) located on chromosome 03, which collectively contribute to leaf base color variation. Within a 50kb flanking region of these SNPs, we identified three candidate genes: SOV3g042000 (membrane protein), SOV3g041980 (mariner transposase), SOV3g041990 (pentatricopeptide repeat). These genetic loci explained 30.55% of the phenotypic variation observed in leaf base color. These findings provide critical insights into genetic architecture governing leaf base color in spinach. The identified SNPs and candidate genes represent valuable targets for marker-assisted selection and gene editing, facilitating the development of improved spinach cultivars with desired leaf base color. Overall, this study contributes to a comprehensive understanding of the genetic control of leaf pigmentation, ultimately supporting targeted breeding strategies for spinach varieties.
