Table 3 Predicted functional genes present inside and adjacent to the main, epistatic and MET- QTLs and their distances from the QTLs peak.
Trait/QTL | Environment | Chromo-some | Peak marker | Position (Mb) | Number of genes in QTL interval | Starting - ending gene at QTL interval | Nearest functional gene (RAP DB ID/Q-TARO ID) | Gene function | Gene Position (Mb) | Distance (gene-QTL) (Mb) |
|---|---|---|---|---|---|---|---|---|---|---|
qGPC1.1 | Env.1, Env.2, Env.3, MET | 1 | CSCWR_Os01g02590__61041 | 0.861041 | 186 | Os01G0111600-Os01g0119500 | Os01g0111900 | Glutelin family protein. (Os01t0111900-01) | 0.6264975 | 0.23454 |
qSGPC1.1 | Env.1 | |||||||||
qSGPC7.1 | Env.1, Env.2, MET | 7 | SCR100_Os07g37440_17971 | 22.24752 | 28 | Os07g0556500 – Os07g0558500 | Os07g0570100, Os07g0570300, Os07g0570500 | Gene cluster of three peptidase proteins | 23.614 | 1.35 |
qSGPC11.1 | Env.1, MET | 11 | SCR200_Os11g07480_87716 | 3.788 | 35 | Os11g0175300 – Os11g0177200 | Os11g0184800 (OsAsp1) | OsAsp1 | 4.34 | 0.62 |
ep-qSGPC11.1 | Epistatic in Env.1 and Env.2 | 11 | SCR100_Os11g08270_33249 | 4.333 | — | — | Os11g0184800 (OsAsp1) | OsAsp1 | 4.34 | 0.01 |
qGPC2.1 | Env.2 | 2 | SCR200_Os02g17350_76316 | 9.976316 | 251 | Os02g0265700 – Os02g0281200 | Os02g0268100 | Similar to Glutelin (Fragment). (Os02t0268100-01) | 9.5814845 | 0.394 |
Os02g0268300 | Similar to Glutelin (Fragment). (Os02t0268300-00) | 9.587016 | 0.389 | |||||||
Os02g0252400 (RPBF) | Prolamin box binding factor | 8.62 | 1.35 | |||||||
Eq-GPC2.1 | MET | 2 | SCR200_Os02g17350_76316 | 26 | Os02g0272900- Os02g0274100 | Os02g0268100 | Similar to Glutelin (Fragment). (Os02t0268100-01) | 9.5814845 | 0.394 | |
qSGPC1.2 | Env.2 | 1 | SCR100_Os01g66690_66361 | 39.06636 | 28 | Os01g0897700- Os01g0899100 | Os01g0878700 (OsAAP6) | Amino acid transporter, transmembrane domain containing protein | 39.89 | 0.83 |
qSGPC1.3 | Env.2 | 1 | CSCWR_Os01g14920__57875 | 8.357875 | 36 | Os01g0251400- Os01g0253800 | Os01g0254000 (Sar1c) | Seed storage protein.Pro-gultelin content in seed. Floury endosperm. | 8.41 | 0.06 |
qSGPC3.1 | Env.2 | 3 | CSCWR_Os03g64360_22659 | 36.32266 | 383 | Os03g0840200 – Os03g0862200 | Os03g0826500 | Anthranilate synthase alpha 1 | 35.57 | 0.75 |
Eq-GPC3.1 | MET | 3 | SCR200_Os03g62388_78948 | 35.28 | 32 | Os03g0838400 – Os03g0826500 | Os03g0826500 | Anthranilate synthase alpha 1 | 35.57 | 0.29 |
