Genome-wide study of salt tolerance in USDA tomato germplasm at seedling stage

Salinity is a major constraint on tomato production, increasingly intensified by climate change. This study aimed to develop superior salt-tolerant tomato cultivars by evaluating genetic variation in salt tolerance, identifying associated single-nucleotide polymorphism (SNP) markers through genome-wide association studies (GWAS), and applying genomic prediction (GP). A total of 265 tomato accessions from the USDA germplasm collection were evaluated at the seedling stage under controlled greenhouse conditions with saline stress (200 mM NaCl). Nineteen accessions were identified as salt-tolerant, exhibiting a leaf injury score (LIS) ≤ 3.0 (on a 1–7 scale) and less than 40% chlorophyll reduction compared to non-stressed controls. GWAS was conducted using 27,046 SNPs generated via genotyping-by-sequencing (GBS), utilizing five models in GAPIT3 (GLM, MLM, MLMM, FarmCPU, and BLINK), three models in TASSEL 5 (SMR, GLM, and MLM), and three models in rMVP (GLM, MLM, and FarmCPU). Eight SNPs with LOD scores > 5.73 were significantly associated with salt tolerance (RST_C), located on chromosomes 1, 3, 4, 5, 6, and 7. One SNP (SL4.0CH05_60973295) was also associated with LIS. Candidate genes near these loci included Solyc05g051265 (encoding an alpha/beta-hydrolase superfamily protein and calmodulin-binding heat shock protein) on Chr 5, Solyc06g005680 (a homeodomain-like superfamily protein) on Chr 6, and Solyc06g005690 (a tetratricopeptide repeat [TPR]-like superfamily protein) on Chr 6. Genomic prediction models using GWAS-derived SNPs achieved prediction accuracies (r-values) up to 0.38 for salt tolerance in cross-population analyses. These findings provide insights into the genetic architecture of salt tolerance and valuable tools for molecular breeding of salt-tolerant tomato cultivars.