Abstract: To identify the genetic components of salt tolerance at the seedling stage of tomato，the contents of sodium（Na+）and potassium（K+）were determined，and genome-wide association analysis was further performed for shoot Na+/K+ ratio in a population consisting of 501 tomato accessions. The decrease in salt tolerance from wild tomatoes to large-fruited tomatoes is due to the decrease in Na+ content and Na+/K+ ratio during tomato domestication and improvement. The most significant loci associated with shoot Na+ content and Na+/K+ ratio were identified on chromosome 7，which contained two genes with known function，HKT1;1 and HKT1;2. Sequence analysis，and haplotype analysis identified a 6 bp InDel（InDel_6）on the promoter of HKT1;2 showed highly correlated with Na+ content and Na+/K+ ratio，and salt treatment of different genotype accessions based on the InDel_6 confirmed that this mutation was the causative variant associated with Na+/K+ ratio and confer salt tolerance in tomato. Based on this causative variant，a codominant molecular marker that can quickly and accurately verify the salt tolerance of tomatoes at the seedling stage were developed.

Key words: tomato, salt tolerance, sodium, potassium, genome-wide association analysis, molecular marker