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Table 2 Several SNPs significantly associated with salt tolerance evaluated in GWAS using the SoySNP50K dataset for 305 soybean accessions

From: Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping

Marker Chr. Position -log10(P) Call Rate (%) MA MAF Allele Refer Cloned/Candidate genes a
LSS CCR LSC LCC
Salt-20 3 38,610,964 23.9* 22.3* 7.2* 25.7* 99.7 C 0.40 C/G Glyma03g32900 b
Salt14056 3 38,619,995 28.9* 24.7* 10.3* 29.1* 100 G 0.44 C/G Glyma03g32900 b
Salt11655 3 38,622,492 24.4* 22.5* 7.8* 27.9* 99.7 T 0.41 G/T Glyma03g32900 b
ss715592375 5 7,534,622 2.5 ns 3.1 ns 2.4 ns 4.7* 98.0 G 0.22 A/G No gene
ss715609949 11 27,743,052 3.8 ns 2.6 ns 5.6* 4.1 ns 99.0 A 0.06 G/A No gene
ss715611871 12 20,568,054 2.6 ns 2.5 ns 4.8* 3.3 ns 99.3 T 0.10 G/T No gene
ss715616720 13 16,871,244 5.8* 4.9* 1.8 ns 3.2 ns 99.7 T 0.31 C/T No gene
ss715623199 15 9,138,970 4.4* 2.2 ns 1.0 ns 1.3 ns 100 T 0.24 C/T Glyma.15 g116200
-log10(P) threshold c 4.4 4.3 4.8 4.2      
  1. LSS leaf scorch score, CCR chlorophyll content ratio, LSC leaf sodium content, LCC leaf chloride content (LCC)
  2. *: Significant association with salt tolerant traits; ns: None significant association with trait
  3. a: The candidate gene in Soybase Wm82 Genome Browser version 2 consist of significant SNP; b: The cloned gene for salt tolerance is named Glyma03g32900 in SoyBase Wm82 Genome Browser version 1; c: Threshold was calculated based on P-value using False Discovery Rate correction (Benjamini-Hochberg); MA: Minor allele; MAF: Minor allele frequency