Grain Thickness
GWAS analysis of related SNP information for grain thickness in 115 rice accesssions
| QTL | Chr | Start | End | Sig_SNP_number | Peak_SNP | P-value | -log10(P) | Known genes |
|---|---|---|---|---|---|---|---|---|
| qGT1-1 | chr01 | 4922831 | 8081279 | 6 | 8081279 | 1.24073E-09 | 8.91 | NA |
| qGT1-2 | chr01 | 23166439 | 42039077 | 65 | 24879078 | 4.07268E-13 | 12.39 | OFP2(LOC_Os01g43610)(Schmitz 2015) |
| qGT3-1 | chr03 | 5041952 | 8157781 | 8 | 7256282 | 1.0866E-10 | 9.96 | LPA1(LOC_Os03g13400)(Wu 2013) LPA1(LOC_Os03g13400)(Wu 2013) |
| qGT3-2 | chr03 | 13176641 | 16686122 | 14 | 13680215 | 4.83635E-10 | 9.32 | NA |
| qGT4-1 | chr04 | 18079276 | 18479276 | 1 | 18279276 | 1.66837E-07 | 6.78 | NA |
| qGT4-2 | chr04 | 30620651 | 33068547 | 8 | 30993742 | 3.16769E-09 | 8.50 | NA |
| qGT5 | chr05 | 1779677 | 2191939 | 13 | 1923048 | 2.89591E-09 | 8.54 | NA |
| qGT6-1 | chr06 | 571308 | 971308 | 1 | 771308 | 5.56212E-08 | 7.25 | NA |
| qGT6-2 | chr06 | 22342511 | 22742511 | 1 | 22542511 | 1.0055E-07 | 7.00 | NA |
| qGT7 | chr07 | 18237767 | 18637767 | 1 | 18437767 | 1.34884E-08 | 7.87 | NA |
| qGT8 | chr08 | 22494856 | 22894856 | 1 | 22694856 | 3.10214E-08 | 7.51 | NA |
| qGT9 | chr09 | 18010741 | 18363530 | 4 | 18092604 | 8.34288E-11 | 10.08 | NA |
| qGT10 | chr10 | 10492732 | 13814503 | 44 | 12020503 | 1.32687E-12 | 11.88 | NA |
| qGT11 | chr11 | 143815 | 2353352 | 8 | 2192950 | 5.6285E-10 | 9.25 | NA |
| qGT12-1 | chr12 | 4107060 | 4699735 | 9 | 4492519 | 2.37727E-09 | 8.62 | NA |
| qGT12-2 | chr12 | 24090016 | 25521433 | 6 | 24090908 | 3.1288E-09 | 8.50 | NA |
Manhattan Plot of Grain Thickness(GLM_CovTopFivePCA Model)
QQ Plot of Grain Thickness(GLM_CovTopFivePCA Model)
| QTL | Chr | Start | End | Sig_SNP_number | Peak_SNP | P-value | -log10(P) | Known genes |
|---|---|---|---|---|---|---|---|---|
| qGT1-3 | chr01 | 36859882 | 37259882 | 1 | 37059882 | 8.18000E-08 | 7.09 | NA |
| qGT1-4 | chr01 | 37305826 | 37705826 | 1 | 37505826 | 1.09000E-07 | 6.96 | NA |
| qGT10-2 | chr10 | 13519346 | 13919346 | 2 | 13719346 | 2.13000E-08 | 7.67 | NA |
| qGT12-3 | chr12 | 3426853 | 3826853 | 1 | 3626853 | 1.73000E-08 | 7.76 | NA |
Manhattan Plot of Grain Thickness(emmax-CovKinship Model)
QQ Plot of Grain Thickness(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).