Table 2.
Single nucleotide polymorphisms (SNPs) associated with hundred seed weight of soybean and known QTL overlapped with peak SNP
| Locus name | Environmental | Chr.b | Position | Alleles | Allelic effect | -Log10(P) | MAF | R2(%) | Known QTLs |
|---|---|---|---|---|---|---|---|---|---|
| HSW-3-1 | E3 | 3 | 40,302,935 | G:T | 2.25 | 4.2 | 0.07 | 31.96 |
Seed weight per plant 5-3_40168335–42,675,829 (Kuroda et al. 2013); Seed yield 27-4_40375902–41,065,116 (Kim et al. 2012); Seed yield 30-4_40375902–41,065,116 (Kim et al. 2012); |
| HSW-4-1 | E2 | 4 | 33,447,909 | A:G | 2.3 | 3.7 | 0.14 | 31.85 | Seed width 1-10_32617784–45,860,827 (Salas et al. 2006) |
| HSW-4-2 | E2 | 4 | 33,617,714 | A:G | 2.3 | 3.7 | 0.14 | 31.93 | Seed width 1-10_32617784–45,860,827(Salas et al. 2006) |
| HSW-5-1 | E2, E3 | 5 | 431,686 | A:G | −1.68/− 1.61 | 4.15/3.97 | 0.14 | 32.33/32.11 | |
| HSW-5-2 | E5 | 5 | 38,064,280 | G:T | 1.01 | 3.58 | 0.28 | 32.49 | |
| HSW-6-1 | E6 | 6 | 18,590,024 | G:T | 1.59 | 3.77 | 0.09 | 34.19 | |
| HSW-6-2 | E6 | 6 | 34,877,639 | A:G | 1.99 | 3.68 | 0.07 | 33.33 | |
| HSW-6-3 | E5 | 6 | 41,987,021 | G:T | 1.77 | 3.79 | 0.08 | 32.85 | |
| HSW-8-1 | E1, E2, E3 | 8 | 20,122,716 | G:T | 1.84/1.7/1.64 | 4.28/3.69/3.67 | 0.10 | 33.22/32.46/32.64 | |
| HSW-8-2 | E2 | 8 | 43,658,396 | A:G | −2.36 | 4.53 | 0.07 | 32.45 | |
| HSW-9-1 | E2, E4, E5 | 9 | 19,237,332 | G:T | 1.8/2.05/1.98 | 4.73/4.14/4.84 | 0.09 | 30.85/31.95/31.18 | |
| HSW-10-1 | E1 | 10 | 48,019,613 | A:G | −1.64 | 4.12 | 0.13 | 33.4 | Seed weight per plant 3-2_47716772–48,485,990 (Liu et al. 2011) |
| HSW-12-1 | E1, E2, E3, E4 | 12 | 6,618,366 | C:T | 2.32/1.93/2.17/2.29 | 4.64/4.07/3.76/4.71 | 0.07 | 33.5/32.43/31.92/31.07 | Seed weight 23–2_6653096–7,980,959 (Li et al. 2008) |
| HSW-12-2 | E6 | 12 | 10,343,129 | G:T | 1.56 | 3.71 | 0.12 | 32.28 | |
| HSW-12-3 | E1, E2 | 12 | 19,897,222 | A:G | −1.92/−1.93 | 3.67/3.88 | 0.10 | 32.66/31.39 | |
| HSW-12-4 | E1, E2, E4 | 12 | 32,409,801 | A:C | −1.94/−2.15/−2.43 | 3.77/3.54/4.85 | 0.06 | 31.91/32.68/34.9 | |
| HSW-12-5 | E5 | 12 | 33,768,654 | A:T | 1.31 | 3.85 | 0.20 | 33.03 | |
| HSW-13–1 | E4 | 13 | 10,148,283 | C:T | 2.4 | 3.64 | 0.07 | 31.05 | |
| HSW-13 − 2 | E3 | 13 | 29,533,558 | A:C | 1.31 | 3.64 | 0.22 | 30.71 |
Seed yield 28–11_29609521–32,196,800 (Rossi et al. 2013); Seed weight 40-1_29609521–32,196,800 (Rossi et al. 2013); Seed weight 49–13_29609521–31,661,129 (Teng et al. 2009) |
| HSW-13-3 | E5 | 13 | 37,094,696 | G:T | 1.81 | 3.59 | 0.07 | 30.71 | Seed weight 45-6_32,196,800–39,208,429 (Yan et al. 2014) |
| HSW-14–1 | E3, E4 | 14 | 981,334 | A:G | -2/−1.81 | 3.81/3.54 | 0.07 | 34.09 | Seed weight 29–1_439027–971,657 (Liu et al. 2011) |
| HSW-16–1 | E5 | 16 | 20,127,714 | A:G | −2.11 | 4.34 | 0.07 | 34.6 | Seed weight 30-6_16724085–27,167,274 (Kim et al. 2010) |
| HSW-16–3 | E3, E4, E5, E6 | 16 | 30,250,524 | G:T | 1.94/1.66/1.6/1.76 | 4.96/3.84/4.18/4.68 | 0.10 | 35.54/35.39/34.04/33.33 | |
| HSW-17-1 | E5 | 17 | 1,004,800 | A:G | 3 | 3.57 | 0.10 | 32.55 | Seed weight 3–1_961346–2,201,427 (Mian et al. 1996) |
| HSW-17-2 | E3 | 17 | 19,283,709 | C:T | 1.66 | 3.75 | 0.10 | 36.28 | |
| HSW-17-3 | E1 | 17 | 29,346,634 | A:G | −2.15 | 3.58 | 0.06 | 31.8 | Seed weight 34–17_24110077–37,831,244(Han et al. 2012) |
| HSW-18–1 | E5 | 18 | 27,066,313 | G:T | −2.11 | 3.96 | 0.07 | 36.03 | Seed weight per plant 6-7_22375695–48,185,138 (Yao et al. 2015) |
| HSW-18–2 | E3 | 18 | 56,307,027 | C:G | 1.65 | 3.92 | 0.12 | 35.43 | |
| HSW-18-3 | E3,E5 | 18 | 56,316,047 | G:T | −1.65 | 4.18/3.97 | 0.14 | 34.42/31.38 | |
| HSW-19–1 | E1 | 19 | 36,849,383 | A:C | −2.27 | 4.91 | 0.07 | 36.31 | |
| HSW-20-1 | E1 | 20 | 19,267,460 | C:T | 2.24 | 3.97 | 0.07 | 31.57 | Seed yield 9–1_3903416–27,664,504 (Yao et al. 2015) |
| HSW-20-2 | E3 | 20 | 26,794,777 | C:T | −1.38 | 3.74 | 0.31 | 31.37 | Seed yield 10–1_2716974–25,498,552 (Yao et al. 2015) |
| HSW-20-3 | E3,E4 | 20 | 35,358,859 | A:G | −1.11/− 1.07 | 3.57/3.67 | 0.46 | 32.63/37.25 | Seed weight 36-5_34302228–46,787,225(Han et al. 2012) |
| HSW-20-4 | E3 | 20 | 37,897,358 | G:T | −1.95 | 3.57 | 0.07 | 31.62 |
aE1: at Harbin in 2015, E2:at Harbin in 2016, E3: at Gongzhuling in 2015, E4: at Gongzhuling in 2016, E5: at Shenyang in 2015, E6 at Shenyang in 2016; b Chromosome