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Table 3 The most significant SNPs on each chromosome associated with salt tolerance traits detected in an association analysis using the WGRS-derived SNP dataset in the subset of 234 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
1:4591993-SNV 1 4,591,993 1.1 ns 2.3 ns 5.5* 4.9* 100 T 0.50 T/C No gene
2:38974662-SNV 2 38,974,662 4.5* 3.0 ns 0.7 ns 3.4 ns 100 T 0.41 T/A No gene
2:43513959-SNV 2 43,513,959 4.0 ns 2.3 ns 1.1 ns 4.4* 100 C 0.49 T/C Glyma.02 g247400
Salt-20 3 38,610,964 29.0* 25.6* 7.2* 27.4* 99.6 C 0.45 C/G Glyma03g32900 b
Salt14056 3 38,619,995 32.4* 28.2* 8.2* 29.6* 100 G 0.46 C/G Glyma03g32900 b
Salt11655 3 38,622,492 27.2* 24.1* 6.2* 25.7* 99.6 T 0.45 G/T Glyma03g32900 b
5:2725777-SNV 5 2,725,777 1.1 ns 2.3 ns 5.5* 4.9* 100 T 0.50 T/C Glyma.05 g031300
6:3536892-SNV 6 3,536,892 1.1 ns 2.3 ns 5.5* 4.9* 100 A 0.50 A/G No gene
6:38850839-SNV 6 38,850,839 4.8* 2.9 ns 2.2 ns 5.2* 100 A 0.25 A/G No gene
8:11762527-SNV 8 11,762,527 4.2 ns 3.7 ns 5.2* 6.6* 100 T 0.35 T/A No gene
8:11859355-SNV 8 11,859,355 4.3* 3.4 ns 3.6 ns 5.3* 100 T 0.32 T/A No gene
8:11869912-SNV 8 11,869,912 4.1 ns 3.3 ns 3.5 ns 5.0* 100 T 0.3 T/C Glyma.08 g153800
8:11897542-SNV 8 11,897,542 4.1 ns 3.3 ns 3.3 ns 4.6* 100 C 0.3 C/T Glyma.08 g154400
8:12168563-SNV 8 12,168,563 3.3 ns 3.5 ns 6.7* 4.4* 100 G 0.38 G/A Glyma.08 g157400
8:12177874-SNV 8 12,177,874 2.9 ns 3.7 ns 6.9* 3.4 ns 100 A 0.48 A/T Glyma.08 g157400
8:12198547-SNV 8 12,198,547 3.8 ns 4.1 ns 7.6* 4.6* 100 C 0.4 C/T No gene
8:12221598-SNV 8 12,221,598 3.0 ns 2.8 ns 6.7* 4.3 ns 100 G 0.4 G/A Glyma.08 g157700
8:18197526-SNV 8 18,197,526 3.5 ns 3.2 ns 3.1 ns 5.0* 100 T 0.07 T/C Glyma.08 g224400
8:18363900-SNV 8 18,363,900 4.5* 3.6 ns 2.2 ns 4.6* 100 A 0.47 A/G No gene
8:18378659-SNV 8 18,378,659 4.8* 4.5* 3.3 ns 3.7 ns 100 G 0.48 T/G No gene
14:8102511-SNV 14 8,102,511 4.6* 3.7 ns 1.2 ns 2.2 ns 100 T 0.49 T/C No gene
14:47627721-SNV 14 47,627,721 1.2 ns 0.9 ns 5.6* 0.9 ns 100 A 0.06 A/G Glyma.14 g211300
15:11833367-SNV 15 11,833,367 3.0 ns 2.4 ns 3.4 ns 5.0* 100 C 0.49 C/T Glyma.15 g143900
16:34944055-SNV 16 34,944,055 4.9* 4.1 ns 1.3 ns 2.4 ns 100 C 0.37 C/A No gene
18:56065139-SNV 18 56,065,139 1.1 ns 2.3 ns 5.5* 4.9* 100 G 0.50 G/T Glyma.18 g294400
18:57153685-SNV 18 57,153,685 3.2 ns 5.3* 0.8 ns 3.2 ns 100 T 0.23 T/C No gene
18:57203235-SNV 18 57,203,235 4.9* 4.1 ns 2.5 ns 2.9 ns 100 A 0.17 A/T No gene
19:43567289-SNV 19 43,567,289 7.5* 6.7* 2.1 ns 5.1* 100 T 0.20 T/G Glyma.19 g175600
20:37261341-SNV 20 37,261,341 3.3 ns 4.6* 0.5 ns 1.6 ns 100 C 0.06 T/C No gene
-log10(P) threshold c 4.3 4.4 5.1 4.3      
  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 consisting 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