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