Genome-Wide Association Study Identifies Loci and a Candidate Gene Regulating Tomato Seed Germination

Seed germination is the first critical transition in the plant life cycle, strongly influencing seedling establishment, crop uniformity, and subsequent productivity. However, the genetic basis of seed germination in tomato remains incompletely understood. Here, we performed a genome-wide association study (GWAS) using 319 diverse tomato accessions to identify new loci and candidate genes associated with seed germination. Five significant variants were detected across the genome. Among them, SNP_59508294 on chromosome 3 was consistently associated with the seed germination index (SGI), and accessions carrying the GG haplotype exhibited a significantly higher SGI than those carrying the TT haplotype. Seven α-expansin (EXPA) genes were located within or near the associated interval. Integration of transcriptomic data from contrasting accessions and expression profiles across tomato tissues showed SlEXPA10 to be the most plausible candidate gene. The InDels in the SlEXPA10 promoter were highly associated with its low expression level in low SGI varieties. CRISPR/Cas9-mediated disruption of SlEXPA10 significantly reduced the rate and speed of seed germination relative to the wild type. Collectively, these results identify SlEXPA10 as a positive regulator of tomato seed germination and provide a candidate locus for improving seed vigor and emergence uniformity.