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Table 2 SNPs associated with each of the wild soybean seed composition traits

From: A genome-wide association study of seed composition traits in wild soybean (Glycine soja)

Trait SNP Chr bp P - Log10 P   Allelic effect % h2
PROTEIN ss715617976 14 24367698 3.10E-05 4.51 A 0.551 3.41 0.22
PROTEIN ss715631057 18 45438677 3.42E-05 4.47 A 0.574 3.09  
OIL ss715585518 3 34839398 9.21E-06 5.04 A 0.527 3.53 0.32
OIL ss715637730 20 36705945 1.31E-05 4.88 A 0.479 3.31  
OIL ss715637732 20 36710220 3.24E-05 4.49 A 0.422 2.99
PALMITIC ACID ss715595323 6 5303094 1.91E-05 4.72 A −0.567 3.87 0.45
PALMITIC ACID ss715597684 7 37911072 5.07E-06 5.29 A −0.646 3.40  
PALMITIC ACID ss715617910 14 22537916 4.15E-05 4.38 C 0.801 3.13
STEARIC ACID ss715618427 14 17499955 5.17E-05 4.29 A 0.704 2.95 0.50
STEARIC ACID ss715618430 14 17561477 3.37E-05 4.47 A 0.753 3.15  
STEARIC ACID ss715625341 16 6804502 5.31E-06 5.27 C −0.745 3.76
OLEIC ACID ss715596070 7 11603310 1.25E-05 4.90 G 0.545 3.39
OLEIC ACID ss715617910 14 22537916 2.06E-05 4.69 C 0.693 3.13 0.36
OLEIC ACID ss715623399 16 1258943 2.23E-06 5.65 A −0.472 2.93  
OLEIC ACID ss715623400 16 1260003 6.66E-06 5.18 A −0.374 2.76
OLEIC ACID ss715633271 19 12874336 5.24E-05 4.28 G −0.588 2.49
LINOLEIC ACID ss715582510 2 39934224 8.71E-06 5.06 A −0.691 3.60 0.49
LINOLEIC ACID ss715582512 2 39940256 1.57E-05 4.80 A −0.692 3.41  
LINOLEIC ACID ss715596075 7 11584261 2E-05 4.70 C 0.546 2.72
LINOLEIC ACID ss715596074 7 11585878 1.39E-05 4.86 C −0.562 3.35
LINOLEIC ACID ss715596072 7 11592971 9.15E-06 5.04 C −0.577 3.52
LINOLEIC ACID ss715596071 7 11602516 1.88E-05 4.73 A −0.549 3.64
LINOLEIC ACID ss715596070 7 11603310 2.10E-06 5.68 G −0.636 3.38
LINOLEIC ACID ss715596058 7 11756838 3.62E-06 5.44 C 0.696 4.17
LINOLEIC ACID ss715604488 9 44197778 3.2E-05 4.50 A −0.430 4.04
LINOLENIC ACID ss715583655 2 573749 5.04E-05 4.30 C 0.745 3.72 0.44
LINOLENIC ACID ss715583662 2 578327 1.46E-05 4.84 C 0.741 3.34  
LINOLENIC ACID ss715617909 14 22514991 3.99E-05 4.40 C −0.842 3.01
LINOLENIC ACID ss715617910 14 22537916 6.71E-06 5.17 C −0.891 2.92
  1. Shown are the locations (in base pairs, bp), standardized allelic effects, and the percentage (%) of the total phenotypic variation explained for SNPs (r 2 X 100) on all chromosomes (Chr) associated with the wild soybean traits. The allelic effect is the standardized effect of the allele listed (A, C, G) compared with the alternate allele and also represents the standardized difference in the means of the two homozygous genotypes. All –log10 P scores (where P = the probability of SNP/trait associations) exceeding 5.348 are significant at the 5% experimentwise level and those exceeding 4.248 are significant at the chromosome-wide level. Heritabilities (h2) calculated using all SNPS also are given for each trait