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Table 3 SNPs signifcantly associated with the four yield-related traits and previously reported QTLs at similar genome regions

From: Genome-wide association study of four yield-related traits at the R6 stage in soybean

Traits SNPa MAFb Physical position Significant region Meanc Effectd Enve Known QTLsf
Chr. Position Start End -Log10(P) R2(%)    
PFW AX-90490395 0.34 2 46,440,530 46,321,460 46,559,600 6.41 27.72 3.81 15,16,mean seed weight 50–12
AX-90483564 0.27 3 36,787,728 36,668,658 36,906,798 6.60 29.19 4.57 15,16,mean  
AX-90435834 0.18 4 1,402,717 1,283,647 1,521,787 6.08 25.12 11.06 15,16,mean Seed weight per plant 6–2; Seed weight 47–3; Seed height 1–12, Seed length 1–13
AX-90328574 0.11 9 39,625,218 39,506,148 39,744,288 6.52 27.10 11.46 15,16,mean Seed weight 50–5; Seed yield 31–10
AX-90481424 0.24 14 5,733,475 5,614,405 5,852,545 6.52 27.22 4.58 15,16,mean Seed weight 36–14
AX-90512978 0.14 14 45,661,649 45,542,579 45,780,719 6.49 27.16 15.43 15,16,mean Seed yield 31–1
AX-90496773 0.07 16 1,617,227 1,498,157 1,736,297 7.03 29.99 16.33 15,16,mean Seed yield 23–6; Pod maturity 19–6; Pod maturity 9–1
AX-90370125 0.08 16 5,791,933 5,672,863 5,911,003 7.54 33.61 0.53 15,16,mean Seed yield 29–2
AX-90519309 0.35 17 4,197,693 4,078,623 4,316,763 7.34 32.14 8.22 15,16,mean Seed weight 21–2; Seed weight 22–3; Seed weight 22–4
SFW AX-90490395 0.34 2 46,440,530 46,321,460 46,559,600 6.26 26.86 0.64 15,16,mean Seed weight 50–12
AX-90481424 0.24 14 5,733,475 5,614,405 5,852,545 6.45 26.54 0.75 15,16,mean Seed weight 36–14
AX-90370125 0.08 16 5,791,933 5,672,863 5,911,003 6.37 27.80 0.01 15,16,mean Seed yield 29–2
AX-90519309 0.35 17 4,197,693 4,078,623 4,316,763 6.35 27.47 1.74 15,16,mean Seed weight 21–2;, Seed weight 22–3, Seed weight 22–4
SDW AX-90505318 0.12 1 50,248,686 50,129,616 50,367,756 7.31 17.69 3.71 15,16,mean Seed weight 15–2; Seed weight 45–2
AX-90395822 0.14 1 50,267,101 50,148,031 50,386,171 7.12 19.42 3.79 15,16,mean Seed weight 15–2; Seed weight 45–2
AX-90328574 0.11 9 39,625,218 39,506,148 39,744,288 5.84 16.24 0.48 15,16,mean Seed weight 50–5; Seed yield 31–10
AX-90501040 0.05 14 42,496,533 42,377,463 42,615,603 9.58 24.87 5.81 15,16,mean Seed yield 32–3; Pod maturity 27–3
AX-90367415 0.05 14 42,696,630 42,577,560 42,815,700 6.58 18.05 3.69 15,16,mean Seed yield 32–3; Pod maturity 27–3
AX-90480993 0.05 14 42,700,090 42,581,020 42,819,160 6.58 18.05 3.69 15,16,mean Seed yield 32–3; Pod maturity 27–3
AX-90496773 0.07 16 1,617,227 1,498,157 1,736,297 6.16 17.29 0.60 15,16,mean Seed yield 23–6; Pod maturity 19–6; Pod maturity 9–1
AX-90421382 0.09 16 5,520,943 5,401,873 5,640,013 5.51 13.46 2.76 15,16,mean Seed yield29–2
MCFS AX-90441957 0.46 5 41,791,118 41,672,048 41,910,188 7.38 19.52 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90371675 0.47 5 41,797,554 41,678,484 41,916,624 7.36 19.32 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90525251 0.46 5 41,807,238 41,688,168 41,926,308 7.38 19.52 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90320946 0.47 5 41,807,727 41,688,657 41,926,797 7.36 19.32 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90347760 0.46 5 41,808,982 41,689,912 41,928,052 7.38 19.52 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90335134 0.46 5 41,815,650 41,696,580 41,934,720 7.38 19.52 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90418462 0.47 5 41,818,004 41,698,934 41,937,074 7.36 19.32 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90492796 0.47 5 41,818,197 41,699,127 41,937,267 7.36 19.32 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90363684 0.47 5 41,818,450 41,699,380 41,937,520 7.36 19.32 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90392895 0.46 5 41,828,027 41,708,957 41,947,097 7.38 19.52 3.39 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90333199 0.46 5 41,831,486 41,712,416 41,950,556 7.18 18.99 3.36 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90344127 0.44 5 41,833,722 41,714,652 41,952,792 7.64 20.59 3.36 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90494650 0.46 5 41,853,747 41,734,677 41,972,817 7.36 19.32 3.36 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90424180 0.47 5 41,866,507 41,747,437 41,985,577 7.75 20.30 3.47 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90335974 0.46 5 41,882,999 41,763,929 42,002,069 7.00 20.68 3.51 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90435701 0.47 5 41,903,235 41,784,165 42,022,305 7.34 21.56 3.51 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90460290 0.47 5 41,927,984 41,808,914 42,047,054 8.19 21.56 3.51 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90337409 0.47 5 41,932,683 41,813,613 42,051,753 8.09 21.17 3.47 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90391337 0.48 5 41,947,344 41,828,274 42,066,414 7.36 19.34 3.37 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
AX-90415951 0.48 5 41,955,229 41,836,159 42,074,299 7.36 19.34 3.37 15,16,mean Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3
  1. aThe significant SNP ID, bMinor allele frequency for each associated marker, cThe average across two years was used to association analysis -Log10(P) and R2 were listed, dPhenotypic differences between different genotypes classified on alleles of associated markers, e15 and 16 represented the environments of years 2015 and 2016, respectively. “mean” represented associations detected with the mean values across two years, fComparision of trait-marker associations identified in this study with QTLs identified in previous studies. Based on the QTL list on SoyBase (http://www.soybase.org), The underlined SNPs were common markers detected in two traits