TABLE 4.
Gene reference Table with fsnps added.
| Gene_ID | Gene symbol synonym(s) | CGSNL Gene name | Gene name synonym(s) | Chr. No. | RAP ID | RAPDB start (bp) | RAPDB end (bp) | MSU ID |
| Rc | RC, OsbHLH017, OsbHLH17 | BROWN PERICARP AND SEED COAT | Brown pericarp and seed coat, basic helix loop helix 17 | 7 | Os07g0211500 | 6,062,889 | 6,069,317 | LOC_Os07g11020.1 |
| Rd | RD, DFR, OsDFR, OS-DFR | RED PERICARP AND SEED COAT | Red pericarp and seed coat, dihydroflavonol 4-reductase, dihydroflavonol-4-reductase | 1 | Os01g0633500 | 25,382,714 | 25,384,678 | LOC_Os01g44260.1 |
| Bh4 | Bh4, OsATL14, ATL14 | BLACK HULL 4 | Black hull 4, amino acid transporter-like 14 | 4 | Os04g0460200 | 22,969,845 | 22,971,859 | LOC_Os04g38670.1; LOC_Os04g38660.1 |
| Ph | BHC, Bhc(Po), Bhc, Po, Ph, Bh3, PPO, Phr1, BH1 | BLACK HULL C | Phenol staining, polyphenol oxidase, PPO enzyme, BLACK HULL1 | 4 | Os04g0624500 | 31,749,141 | 31,751,604 | LOC_Os04g53300.1 |
| OsbHLH016 | OsbHLH016, Kala4, OsB2 | Basic helix-loop-helix protein 016 Key gene for black coloration by anthocyanin accumulation on chromosome 4 | Os04g0557500 | 27,915,598 | 27,939,357 | LOC_Os04g47059.1 | ||
| SH4 | Sh4, SHAT2, SHA1, qSH4, OsSh4, | SHATTERING 4 | Shattering 4, grain shattering quantitative trait locus on chromosome 4, SHATTERING ABORTION2 | 4 | Os04g0670900 | 34,231,186 | 34,233,221 | LOC_Os04g57530.1 |
| qSH1 | qSH1, qsh1, Qsh1, qSH-1, RIL1, OsRIL1 | Shattering (QTL)-1 | QTL of seed shattering on chromosome 1, RI-LIKE1, erticillate rachis-like 1 | 1 | Os01g0848400 | 36,445,456 | 36,449,951 | LOC_Os01g62920.1 |
| OsSh1 | YAB2, OsYAB2, OsSh1, Sh1, SH1, OsFIL2, OsSH1, Osh1, qSH3 | SHATTERING1 | YABBY2, Os YABBY2, Shattering1, FIL homolog 2 | 3 | Os03g0650000 | 25,197,057 | 25,206,948 | LOC_Os03g44710.1 |
| RFT1 | FT-L 3, OsFTL3, FT-L3, RFT, OsRFT1 | RICE FLOWERING- LOCUS T 1 | Rice Flowering-locus T 1, FT-like gene 3, RFT | 6 | Os06g0157500 | 2,926,823 | 2,928,474 | LOC_Os06g06300.1 |
| Hd3a | HD3A, FT, OsHd3a, qHD3(t)*, FT-L 2, OsFTL2 | HEADING DATE 3A | Heading date-3a, Heading date (QTL)-3(t), Flowering locus T, FT-like gene 2 | 6 | Os06g0157700 | 2,940,004 | 2,942,452 | LOC_Os06g06320.1 |
| Hd1 | Se1, Se1(Lm,Lf,Rs,Fl), HD1, K, Se-1, Hd1(t), qHD1(t), OsA, OsBBX18, BBX18, Hd1/OsA, OsCCT21 | PHOTOSENSITIVITY 1 | Photosensitivity1, Heading date, HEADING DATE 1, Arabidopsis CONSTANS(CO) gene ortholog, B-box- containing protein 18, CCT domain-containing gene 21, CCT (CO, CO-LIKE and TOC1) domain protein 21 | 6 | Os06g0275000 | 9,336,376 | 9,338,569 | LOC_Os06g16370.1 |
| Ghd7 | Ghd2, OsCCT26, OsCMF8, OsI, OsEH7 Ghd7/Hd4, EH7-1/Hd4, Ghd7-0a, | HEADING DATE 7 | heading date 7, “\Grain number, plant height, and heading date7\,” CCT domain-containing gene 26, CCT (CO, CO-LIKE and TOC1) domain protein 26, Early heading 7 | 7 | Os07g0261200 | 9,152,377 | 9,155,030 | LOC_Os07g15770.1 |
| Ehd1 | Ef1, Ef2, Ehd1, Eh1(t)*, qEHD-10- 1(t) (qEhd1), OsRR30, OsRR22 | EARLINESS 1 | Earliness1, EARLY HEADING DATE 1 | 10 | Os10g0463400 | 17,076,098 | 17,081,344 | LOC_Os10g32600.1 |
| Pi-ta | PITA, Pita (sl, Pi4a, Pi-ta), Pita2, Pi4a, Pi-4, OsTRXh6, OsTrx30 | PYRICULARIA ORYZAE RESISTANCE TA | Pyricularia oryzae resistance-ta, Magnaporthe grisea resistance-ta, Blast resistance ta, Thioredoxin H-type 6, Thioredoxin 30 | 12 | Os12g0281300 | 10,606,359 | 10,611,917 | LOC_Os12g18360.2 LOC_Os12g18360.1 |
| GS3 | LK3, lk3(t), SG3, SG3-GS3, OsGS3, OsGW3, RGG3, GGC1 Mi, OsGGC1, | LONG KERNEL 3 | long kernel 3, grain size, grain length and weight protein, GRAIN SIZE 3, G gamma subunit GS3, Heterotrimeric G Protein gamma Subunit | 3 | Os03g0407400 | 16,729,501 | 16,735,109 | Not annotated |
| ALK | alk, OsSSIIa, SSIIa, SSS2A, SS2a, OsSSII-3 | ALKALI DEGENERATION | ALKALI DEGENERATION, Soluble starch synthase 2–3, chloroplast precursor, Soluble starch synthase 2–3, chloroplastic/amyloplastic, Soluble starch synthase II- 3, Starch synthase IIa, soluble starch synthase Iia | 6 | Os06g0229800 | 6,748,398 | 6,753,302 | LOC_Os06g12450.1 |
| Waxy | WX1, Wx, WX-B, OsWx, GBSS, OsGBSSI, GBSS1, GSS | GLUTINOUS ENDOSPERM | glutinous endosperm, WAXY, Granule-bound starch synthase 1/chloroplastic/amyloplastic, Granule- bound starch synthase I, UDP-glycogen synthase, Granule-bound starch synthase/chloroplast precursor, glycogen [starch] synthase, UDPG-glycogen transglucosylase, uridine diphosphoglucose-glycogen glucosyltransferase | 6 | Os06g0133000 | 1,765,622 | 1,770,653 | LOC_Os06g04200.4 LOC_Os06g04200.3 LOC_Os06g04200.2 LOC_Os06g04200.1 |