Date of Graduation


Document Type


Degree Name

Master of Science in Crop, Soil & Environmental Sciences (MS)

Degree Level



Food Science


Pengyin Chen

Committee Member

Andy Pereira

Second Committee Member

Kenneth L. Korth

Third Committee Member

Kristofor R. Brye

Fourth Committee Member

Vibha Srivastava


Biological sciences, Candidate genes, Genome-wide association mapping, Qtl, Salt tolerance, Snp, Soybean


Salinity is a common abiotic stress causing soybean yield loss worldwide. Use of tolerant cultivars is an effective and economic approach to coping with this stress. Toward this, research is needed to identify salt-tolerant germplasm and better understand the genetic and molecular basis of salt tolerance in soybean. The objectives of this study were to identify salt-tolerant genotypes, to search for SNPs and QTLs associated with salt tolerance, and to identify candidate salt tolerance genes. A total of 192 diverse soybean lines and cultivars were screened for salt tolerance in the greenhouse based on visual leaf scorch scores after 15 - 18 days of 120 ml NaCl stress, among which 94 were tolerant while 87 were sensitive. These genotypes were further genotyped using the SoySNP50K iSelect BeadChip with 52,041 single nucleotide polymorphism (SNP) markers, among which 37,281 SNPs were polymorphic with minor allele frequency (MAF) > 5% and present in 75% of all genotypes. Genome-wide association mapping showed that 62 SNP markers representing 6 genomic regions on Chromosomes 2, 3, 5, 6, 8, and 18, respectively were significantly associated with salt tolerance (P < 0.001). 52 SNP markers on Chromosome 3 are mapped at or near the major salt tolerance QTL previously identified in S-100 (Lee et al., 2004). Three SNPs on Chromosome 18 map near the salt tolerance QTL previously identified in Nannong1138-2 (Chen et al., 2008). The other significant SNPs represent four putative minor QTLs for salt tolerance newly identified in this study. Ten genes, which are mapped at or near (< 35 kb) the significant SNPs, appear to be potential candidates involved in ion metabolisms and salt stress responses in soybean. Gene expression analysis indicated that GmUBC2, an ubiquitin-conjugating enzyme, and GmNHX1, a vacuolar Na+/H+ antiporter, are both up-regulated in salt-tolerant (Lee 68 and S-100) and salt-sensitive genotypes (Dare and Glenn). However, GmUBC2 expression is higher in salt-tolerant genotypes than in salt-sensitive genotypes. As for GmNHX1, Dare exhibited a higher level of expression than the other three genotypes. These results imply potential roles of GmUBC2 and GmNHX1 in conferring salt tolerance in soybean.