Identification of GmSALT3 haplotypes and development of molecular markers based on their diversity associated with salt tolerance in soybean

Soybean [Glycine max (L.) Merr.] is a major agricultural crop and generally known as a salt-sensitive crop. In a previous study, GmSALT3 was identified as a salt tolerance gene in soybean, and its nine haplotypes (H1 to H9) were reported in Chinese soybean accessions. In the present study, we aimed to identify new haplotypes of GmSALT3 in soybean accessions and to develop molecular markers for selection of salt-tolerant and -sensitive accessions. To do so, we examined genomic variations in the GmSALT3 coding region of 216 accessions of G. max and G. soja from Korea, China, and Japan. As a result, 40 different haplotypes, including three known haplotypes (H1, H2, and H5), were identified. Performing salt tolerance tests for the haplotypes, we were able to classify them into salt-tolerant (8) and salt-sensitive (32) categories. We also found that more variations in the haplotype composition of G. soja accessions exist than in that of G. max accessions. Quantitative expression analysis showed that almost all of the salt-tolerant haplotypes had much higher levels of GmSALT3 expression than the salt-sensitive haplotypes did. Finally, we developed molecular markers and applied them to screen salt tolerance of soybean accessions. The molecular markers performed well with an accuracy of 98.8% in identifying phenotypes of soybean accessions.