Grain Length
GWAS analysis of related SNP information for grain length in 115 rice accesssions
| QTL | Chr | Start | End | Sig_SNP_number | Peak_SNP | P-value | -log10(P) | Known genes |
|---|---|---|---|---|---|---|---|---|
| qGL1-1 | chr01 | 4759314 | 5159314 | 2 | 4959314 | 7.74819E-08 | 7.11 | NA |
| qGL1-2 | chr01 | 23167049 | 42039077 | 89 | 24987297 | 3.05185E-16 | 15.52 | OFP2(LOC_Os01g43610)(Schmitz 2015) |
| qGL3-1 | chr03 | 6576407 | 7256282 | 11 | 6576407 | 2.22428E-09 | 8.65 | LPA1(LOC_Os03g13400)(Wu 2013) |
| qGL3-2 | chr03 | 13180082 | 16733441 | 27 | 13262435 | 4.36555E-13 | 12.36 | NA |
| qGL4 | chr04 | 18251859 | 18505087 | 2 | 18251859 | 3.31938E-08 | 7.48 | NA |
| qGL4-5 | chr04 | 30476832 | 30876832 | 3 | 30676832 | 1.71E-07 | 6.77 | NA |
| qGL4-6 | chr04 | 32865336 | 33265336 | 1 | 33065336 | 1.91E-07 | 6.72 | NA |
| qGL5-1 | chr05 | 1579677 | 1979677 | 1 | 1779677 | 1.28271E-07 | 6.89 | NA |
| qGL5-2 | chr05 | 27702623 | 28295260 | 8 | 27702623 | 1.23192E-10 | 9.91 | NA |
| qGL6 | chr06 | 22342511 | 22742511 | 1 | 22542511 | 9.81225E-08 | 7.01 | NA |
| qGL8-1 | chr08 | 21879783 | 22279783 | 1 | 22079783 | 1.40E-07 | 6.85 | NA |
| qGL8-2 | chr08 | 22494856 | 22894856 | 1 | 22694856 | 2.37E-10 | 9.63 | NA |
| qGL9 | chr09 | 17892604 | 18292604 | 2 | 18092604 | 1.20E-07 | 6.92 | NA |
| qGL10 | chr10 | 10405411 | 13719346 | 64 | 10580067 | 4.54638E-13 | 12.34 | NA |
| qGL11 | chr11 | 826120 | 2353352 | 6 | 2192950 | 1.55024E-09 | 8.81 | NA |
| qGL12 | chr12 | 24594467 | 25521433 | 6 | 24594467 | 3.74526E-10 | 9.43 | NA |
Manhattan Plot of Grain Length(GLM_CovTopFivePCA Model)
QQ Plot of Grain Length(GLM_CovTopFivePCA Model)
| QTL | Chr | Start | End | Sig_SNP_number | Peak_SNP | P-value | -log10(P) | Known genes |
|---|---|---|---|---|---|---|---|---|
| qGL1-3 | chr01 | 29758103 | 30158103 | 1 | 29958103 | 1.03000E-07 | 6.99 | NA |
| qGL3-3 | chr03 | 12997031 | 13397031 | 1 | 13197031 | 1.87000E-09 | 8.73 | NA |
| qGL4-2 | chr04 | 18079276 | 18479276 | 1 | 18279276 | 4.15000E-08 | 7.38 | NA |
| qGL4-3 | chr04 | 30296914 | 30696914 | 1 | 30496914 | 1.82000E-07 | 6.74 | NA |
| qGL4-4 | chr04 | 34264311 | 34664311 | 1 | 34464311 | 6.35000E-08 | 7.20 | NA |
| qGL8 | chr08 | 25439616 | 25839616 | 1 | 25639616 | 1.79000E-07 | 6.75 | NA |
| qGL12-2 | chr12 | 24444052 | 24844052 | 1 | 24644052 | 2.42000E-08 | 7.62 | NA |
Manhattan Plot of Grain Length(emmax-CovKinship Model)
QQ Plot of Grain Length(emmax-CovKinship Model)
Reference
Schmitz AJ, et al. Rice Ovate Family Protein 2 (OFP2) alters hormonal homeostasis and vasculature development. Plant Sci 241, 177-188 (2015).
Wu, et al. Loose plant architecture1, an indeterminate domain protein involved in shoot gravitropism, regulates plant architecture in rice. Plant Physiol 161, 317-329 (2013).