Table 3 The GWAS-based QTNs identified in at least two models in low light (LL) and ambient light (AL), their chromosomal positions (Chr), minor allele frequency (MAF), and the additive effect.
From: Identification and analysis of low light responsive yield enhancing QTLs in rice
Traits | QTN | Chr | Position | p-value | Min Allele | Add | Model |
|---|---|---|---|---|---|---|---|
GY_LL | 1163456 | 1 | 35825579 | 9.33E − 09 | 0.37 | − 2.1 | BLINK |
1163456 | 1 | 35825579 | 1.86E − 09 | 0.37 | − 1.6 | FarmCPU | |
1163456 | 1 | 35825579 | 9.65E − 06 | 0.37 | 1.7 | IIIVmrMLM | |
1163456 | 1 | 35825579 | 7.40E − 06 | 0.37 | − 1.6 | FASTmrMLM | |
PN_LL | 1163456 | 1 | 35825579 | 2.10E − 09 | 0.37 | 0.7 | BLINK |
1163456 | 1 | 35825579 | 6.71E − 07 | 0.37 | 0.5 | FarmCPU | |
1163456 | 1 | 35825579 | 5.46E − 05 | 0.37 | 0.5 | IIIVmrMLM | |
1163456 | 1 | 35825579 | 0.00017 | 0.37 | − 0.42 | mrMLM | |
1163456 | 1 | 35825579 | 8.91E − 05 | 0.37 | − 0.38 | FASTmrMLM | |
PN_LL | 465718 | 1 | 14375630 | 4.95E − 07 | 0.19 | 1.2 | BLINK |
465718 | 1 | 14375630 | 6.71E − 07 | 0.19 | 1 | FarmCPU | |
GPP_LL | SNP-2.25351027 | 2 | 25356897 | 1.35E − 07 | 0.13 | 26.5 | BLINK |
SNP-2.25351027 | 2 | 25356897 | 1.90E − 05 | 0.13 | 20.34 | mrMLM | |
TW_AL | SNP-3.16841419 | 3 | 16842546 | 1.40E − 06 | 0.39 | 1.8 | FarmCPU |
SNP-3.16841419 | 3 | 16842546 | 2.05E − 07 | 0.39 | 2.1 | IIIVmrMLM | |
GY_AL | SNP-4.3704513 | 4 | 3708908 | 2.95E − 06 | 0.25 | 2.2 | BLINK |
SNP-4.3704513 | 4 | 3708908 | 1.34E − 06 | 0.25 | 1.8 | IIIVmrMLM | |
GPP-LL | 3956648 | 4 | 7825479 | 1.14E − 04 | 0.43 | 9.1 | mrMLM |
PW_LL | 3956648 | 4 | 7825479 | 2.03E − 07 | 0.43 | 10.1 | FASTmrMLM |
3956648 | 4 | 7825479 | 4.21E − 06 | 0.43 | 14.2 | mrMLM | |
GY_LL | 5951985 | 6 | 4680281 | 2.07E − 10 | 0.17 | 3 | FarmCPU |
PN_LL | 5951985 | 6 | 4680281 | 5.59E − 06 | 0.17 | 2.61 | FASTmrMLM |
5951985 | 6 | 4680281 | 6.71E − 07 | 0.17 | 0.5 | FarmCPU | |
PW_AL | wd7002824 | 7 | 19590130 | 1.78E − 08 | 0.10 | 0.7 | BLINK |
wd7002824 | 7 | 19590130 | 3.10E − 10 | 0.10 | 0.6 | FarmCPU | |
TW_LL | 9657687 | 9 | 14851680 | 2.31E − 07 | 0.33 | 1.90 | mrMLM |
9657687 | 9 | 14851680 | 8.31E − 05 | 0.33 | 1.34 | FASTmrMLM | |
TW_LL | id12002740 | 12 | 6819391 | 6.54E − 05 | 0.14 | − 1.83 | FASTmrMLM |
id12002740 | 12 | 6819391 | 6.69E − 05 | 0.14 | − 1.42 | mrMLM |
