1000 Grain Weight
GWAS analysis of related SNP information for 1000 grain weight in 115 rice accesssions
| QTL | Chr | Start | End | Sig_SNP_number | Peak_SNP | P-value | -log10(P) | Known genes |
|---|---|---|---|---|---|---|---|---|
| qTGW1-1 | chr01 | 4955331 | 8147243 | 51 | 8081279 | 1.83982E-11 | 10.74 | NA |
| qTGW1-2 | chr01 | 24879078 | 42885037 | 118 | 24902823 | 1.9131E-11 | 10.72 | OFP2(LOC_Os01g43610)(Schmitz 2015) |
| qTGW2 | chr02 | 25647151 | 26047151 | 1 | 25847151 | 1.18805E-07 | 6.93 | NA |
| qTGW3-1 | chr03 | 5041952 | 8157781 | 13 | 7256282 | 1.91083E-11 | 10.72 | LPA1(LOC_Os03g13400)(Wu 2013) LPA1(LOC_Os03g13400) |
| qTGW3-2 | chr03 | 13193965 | 16686122 | 8 | 13193965 | 6.06777E-11 | 10.22 | NA |
| qTGW4-1 | chr04 | 18072707 | 19172190 | 6 | 18072707 | 1.00169E-09 | 9.00 | NA |
| qTGW4-2 | chr04 | 30993742 | 32961143 | 5 | 32862891 | 4.05807E-09 | 8.39 | NA |
| qTGW5 | chr05 | 1779677 | 1923048 | 3 | 1779677 | 1.16877E-08 | 7.93 | NA |
| qTGW6 | chr06 | 22542511 | 22660899 | 2 | 22542511 | 1.59913E-07 | 6.80 | NA |
| qTGW7 | chr07 | 18155535 | 18451468 | 5 | 18437767 | 3.38597E-08 | 7.47 | NA |
| qTGW8 | chr08 | 21103731 | 21503731 | 1 | 21303731 | 5.59699E-08 | 7.25 | NA |
| qTGW10-1 | chr10 | 9556200 | 15736503 | 104 | 12020503 | 1.5379E-11 | 10.81 | NA |
| qTGW10-2 | chr10 | 393709 | 793709 | 1 | 593709 | 1.74E-07 | 6.76 | NA |
| qTGW11 | chr11 | 626120 | 1026120 | 1 | 826120 | 1.15618E-07 | 6.94 | NA |
| qTGW12-1 | chr12 | 4107060 | 4870867 | 34 | 4699735 | 2.40321E-13 | 12.62 | NA |
| qTGW12-2 | chr12 | 24090016 | 25816873 | 15 | 24090908 | 9.97002E-11 | 10.00 | NA |
Manhattan Plot of 1000 Grain Weight(GLM_CovTopFivePCA Model)
QQ Plot of 1000 Grain Weight(GLM_CovTopFivePCA Model)
| QTL | Chr | Start | End | Sig_SNP_number | Peak_SNP | P-value | -log10(P) | Known genes |
|---|---|---|---|---|---|---|---|---|
| qTGW1-3 | chr01 | 38822463 | 39222463 | 3 | 39022463 | 2.85000E-08 | 7.54 | NA |
| qTGW2-2 | chr02 | 26841591 | 27241591 | 4 | 27041591 | 1.96000E-07 | 6.71 | OsPIP1;1(LOC_Os02g44630)(Liu 2013) |
| qTGW3-3 | chr03 | 7961341 | 8361341 | 4 | 8161341 | 3.68000E-09 | 8.43 | NA |
| qTGW4-3 | chr04 | 18026310 | 18426310 | 7 | 18226310 | 1.61000E-07 | 6.79 | NA |
| qTGW7-2 | chr07 | 17014554 | 17414554 | 1 | 17214554 | 1.73000E-08 | 7.76 | NA |
| qTGW8-2 | chr08 | 3973699 | 4373699 | 1 | 4173699 | 2.46000E+08 | 6.98 | NA |
| qTGW8-3 | chr08 | 24142451 | 24542451 | 1 | 24342451 | 2.66000E+08 | 7.68 | NA |
| qTGW9 | chr09 | 6172037 | 6572037 | 1 | 6372037 | 1.36000E-07 | 6.87 | NA |
| qTGW10-1 | chr10 | 11559302 | 11959302 | 2 | 11759302 | 1.11000E-07 | 6.95 | NA |
| qTGW10-2 | chr10 | 11831110 | 12231110 | 3 | 12031110 | 1.08000E-08 | 7.97 | NA |
| qTGW10-3 | chr10 | 13449344 | 13849344 | 3 | 13649344 | 6.13000E-08 | 7.21 | NA |
| qTGW12-1 | chr12 | 4783744 | 5183744 | 2 | 4983744 | 7.22000E-08 | 7.14 | NA |
| qTGW12-2 | chr12 | 23891793 | 24291793 | 1 | 24091793 | 1.92000E-07 | 6.72 | NA |
Manhattan Plot of 1000 Grain Weight(emmax-CovKinship Model)
QQ Plot of 1000 Grain Weight(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).
Liu,et al. Patatin-related phospholipase A, pPLAIIIα, modulates the longitudinal growth of vegetative tissues and seeds in rice. J Exp Bot 66, 6945-6955 (2015).
Liu, et al. Aquaporin OsPIP1;1 promotes rice salt resistance and seed germination. Plant Physiology and Biochemistry 63, 151-158 (2013).