Table 3.
SNPs significantly associated with salt tolerance indices and SNC in the three growth environments.
| Trait | SNPsa | Chr | Site (b) | Allele | MAF | Q | Q + K | Envc | ||
|---|---|---|---|---|---|---|---|---|---|---|
| −Log10P | R2(%)b | −Log10P | R2(%)b | |||||||
| ST-RL | Bn-A01-p1372430 | A01 | 973485 | A/G | 0.135 | 4.67 | 5.96 | 4.15 | 5.67 | E1 |
| 4.26 | 5.37 | E2 | ||||||||
| Bn-A03-p9873327 | A03 | 9088303 | T/C | 0.41 | 4.12 | 5.59 | E1 | |||
| 4.12 | 5.54 | E2 | ||||||||
| Bn-A06-p3066372 | A06 | 2959211 | A/G | 0.16 | 5.73 | 7.44 | 4.33 | 6.69 | E1 | |
| 4.95 | 6.27 | E2 | ||||||||
| 5.11 | 6.5 | AVE | ||||||||
| ST-SL | Bn-A04-p11164883 | A04 | 12315774 | A/G | 0.305 | 4.45 | 5.65 | E1 | ||
| 4.15 | 5.24 | AVE | ||||||||
| Bn-A04-p14778146 | A04 | 15229011 | A/G | 0.395 | 4.85 | 6.17 | E1 | |||
| Bn-A05-p1744534 | A05 | 1887184 | A/C | 0.465 | 4.16 | 4.27 | E1 | |||
| Bn-A05-p2246038 | A05 | 2366787 | A/C | 0.304 | 4.14 | 4.24 | E1 | |||
| 4.35 | 4.46 | 4.04 | 4.3 | E2 | ||||||
| Bn-A05-p17420613 | A05 | 14469584 | T/C | 0.419 | 5.5 | 7.69 | E1 | |||
| 4.39 | 6.02 | E3 | ||||||||
| 4.96 | 6.88 | AVE | ||||||||
| Bn-A07-p15589001 | A07 | 17485098 | T/C | 0.15 | 4.18 | 4.78 | E1 | |||
| Bn-A09-p33179406 | A09 | 30892924 | T/C | 0.17 | 4.32 | 5.56 | E1 | |||
| Bn-A08-p3269074 | A08 | 2746242 | T/C | 0.117 | 6.48 | 8.04 | 4.81 | 6.24 | E1 | |
| 4.81 | 5.8 | E2 | ||||||||
| 4.72 | 5.71 | AVE | ||||||||
| Bn-Scaffold000211-p65635 | A10 | 4230491 | T/G | 0.467 | 4.11 | 4.21 | E1 | |||
| Bn-scaff_15838_1-p1804241 | C01 | 2159899 | T/C | 0.424 | 6.69 | 9.23 | 4.09 | 6.06 | E1 | |
| 5.89 | 8.03 | 4.25 | 6.23 | E2 | ||||||
| 4.93 | 6.68 | E3 | ||||||||
| 6.33 | 8.71 | 4.16 | 6.19 | AVE | ||||||
| Bn-scaff_15908_1-p535407 | C04 | 5694092 | A/G | 0.259 | 4.35 | 5.19 | E1 | |||
| ST-SFW | Bn-A01-p7574355 | A01 | 6916594 | T/C | 0.276 | 5.03 | 6.2 | 4.61 | 6.02 | E1 |
| 5.82 | 7.26 | 5.36 | 7.05 | E2 | ||||||
| 5.24 | 6.48 | 4.78 | 6.31 | AVE | ||||||
| Bn-A01-p21855770 | A01 | 18441121 | T/C | 0.212 | 5.84 | 7.53 | 4.77 | 6.43 | E1 | |
| 6.58 | 8.49 | 5.55 | 7.75 | E2 | ||||||
| 5.32 | 6.81 | 4.54 | 6.21 | AVE | ||||||
| Bn-A06-p7703242 | A06 | 7333685 | T/G | 0.23 | 4.54 | 4.71 | E1 | |||
| Bn-A08-p20091818 | A08 | 17365577 | T/C | 0.173 | 4.67 | 5.51 | E1 | |||
| 4.35 | 5.09 | AVE | ||||||||
| Bn-A10-p15741819 | A10 | 15808392 | A/G | 0.477 | 4.2 | 5.59 | E2 | |||
| Bn-scaff_16116_1-p406330 | C06 | 28299662 | T/G | 0.191 | 4.92 | 5.15 | E1 | |||
| 4.6 | 4.78 | AVE | ||||||||
| SNC | Bn-A03-p8032849 | A03 | 7321761 | A/G | 0.266 | 4.12 | 4.85 | E1 | ||
| 5.81 | 7.04 | 5.19 | 6.37 | E2 | ||||||
| 4.56 | 5.45 | 4.48 | 5.29 | E3 | ||||||
| 5.46 | 6.6 | 5.05 | 6.11 | AVE | ||||||
| Bn-A09-p13614414 | A09 | 10135644 | T/G | 0.411 | 4.65 | 4.81 | E2 | |||
| Bn-scaff_16268_1-p640088 | C05 | 12621782 | A/G | 0.493 | 4.28 | 5.52 | E2 | |||
| Bn-scaff_18206_1-p435713 | C06 | 18701952 | A/G | 0.362 | 4.07 | 5.39 | E2 | |||
| 4.2 | 5.59 | AVE | ||||||||
| Bn-scaff_16110_1-p3586046 | C07 | 41328003 | T/C | 0.213 | 4.81 | 5.74 | 4.49 | 5.42 | E1 | |
a
Only the lead SNPs at a defined locus are shown.
b
Percentage of phenotypic variance explained by the lead SNP.
c
E1 greenhouse in 2013, E2 greenhouse in 2014, E3 natural environment in 2014, AVE, average values across three environments.