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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #431887
Research Project: Harnessing Genomic Technologies Toward Improving Vegetable Health in Field and Controlled Environments

Location: Vegetable Research

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

Author
item ALATAWI, IBITISAM - University Of Arkansas
item XIONG, HAIZHENG - University Of Arkansas
item ALKABKABI, HANAN - University Of Arkansas
item CHIWINA, KENANI - University Of Arkansas
item QU, YUEJUN - University Of Arkansas
item DU, RENJIE - University Of Arkansas
item LUO, QUN - University Of Arkansas
item Ling, Kai Shu
item SHI, AINONG - University Of Arkansas

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/26/2026
Publication Date: 3/1/2026
Citation: Alatawi, I., Xiong, H., Alkabkabi, H., Chiwina, K., Qu, Y., Du, R., Luo, Q., Ling, K., Shi, A. 2026. Genome-wide study of salt-tolerance in USDA tomato germplasm at seedling stage. Meeting Abstract. https://doi.org/10.1038/s41598-025-30759-y.
DOI: https://doi.org/10.1038/s41598-025-30759-y

Interpretive Summary: Tomato (Solanum lycopersicum L.) is a major horticultural crop worldwide, valued not only for its culinary versatility but also for its nutritional contents that contribute to human health. Salinity is a major constraint on tomato production, which disrupt water uptake, nutrient acquisition, and photosynthetic efficiency due to osmotic stress and ion toxicity. Although significant efforts have been placed in screening tomato germplasm for salt tolerance, the molecular mechanism underlying its salt-tolerance is still poorly understood. In this study, ARS researcher at Charleston, SC in collaboration with a team of scientists at the University of Arkansas conducted a genome-wide association study (GWAS) using a core collection of 265 accessions of the USDA tomato germplasm for their salt-tolerance at seedling stage. GWAS helps pinpoint the crucial loci that are associated with the salt-tolerance. With the identified single-nucleotide polymorphisms, marker-assisted selection could be used to facilitate the development of salt-tolerant cultivars. Considering the complex genetic architecture of salt tolerance in tomato, a combined approach leveraging GWAS and genome prediction is critical for identifying key loci and enhancing breeding efficiency. The outcomes will provide valuable insights to guide the development of salt-tolerant tomato cultivars suited for saline environments.

Technical Abstract: 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.