Candidate lncRNAs for seed size, oil content and seed coat color were identified from transcriptome analysis of developing seeds in three different stages, of two contrasting Brassica juncea varieties.
(Reference: https://doi.org/10.1016/j.cpb.2023.100306)
| Seed Trait | lncRNA ID | Target Transcript | Gene Symbol | Function | Reference |
|---|---|---|---|---|---|
| Seed size | A03_VARUNA_g3751.t1 | A02_VARUNA_g2629.t1 | DA2 | Involved in peptidase cativity of DA1 which further cleave growth regulators | http://www.genesdev.org/cgi/doi/10.1101/gad.292235.116 |
| Seed size | A03_VARUNA_g3751.t1 | B02_VARUNA_g7424.t1 | DA2 | Involved in peptidase cativity of DA1 which further cleave growth regulators | http://www.genesdev.org/cgi/doi/10.1101/gad.292235.116 |
| Seed size | A03_VARUNA_g5010.t1 | A04_VARUNA_g2621.t1 | IKU1 | Regulate endosperm development, positive regulator of seed size | https://doi.org/10.1104/pp.102.018762 |
| Seed size | A03_VARUNA_g5339.t1 | A04_VARUNA_g1016.t1 | AHKs | Negative regulator of seed size, core cytokinin signaling component | https://doi.org/10.1146/annurev-arplant-042811-105503 |
| Seed size | A03_VARUNA_g5913.t1 | B01_VARUNA_g2936.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | A05_VARUNA_g1.t1 | B08_VARUNA_g4686.t1 | AGG3 | Overexpression leads to an increase in silique length, and seed size due to cell proliferation | https://doi.org/10.1111/j.1469-8137.2012.04083.x |
| Seed size | A05_VARUNA_g130.t1 | A05_VARUNA_g2339.t1 | SAMBA | Restrict cell proliferation in integuments by modulating the stability of cyclins | https://doi.org/10.1016/j.tplants.2015.11.012 |
| Seed size | A05_VARUNA_g2366.t1 | MSTRG.17518.1 | DA2 | Involved in peptidase cativity of DA1 which further cleave growth regulators | http://www.genesdev.org/cgi/doi/10.1101/gad.292235.116 |
| Seed size | A06_VARUNA_g2416.t1 | B05_VARUNA_g1915.t1 | BZR1 | Affected by PP2C-1 which is encooded by seed weight QTL | https://doi.org/10.1016/j.molp.2017.03.006 |
| Seed size | A06_VARUNA_g3302.t1 | A05_VARUNA_g901.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | A06_VARUNA_g3302.t1 | B04_VARUNA_g454.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | A06_VARUNA_g3302.t1 | MSTRG.28157.1 | AGB1 | Interacts with BIN2 for seed size regulation | https://doi.org/10.1093/jxb/ert159 |
| Seed size | A06_VARUNA_g3302.t1 | B02_VARUNA_g382.t1 | AGB1 | Interacts with BIN2 for seed size regulation | https://doi.org/10.1093/jxb/ert159 |
| Seed size | A06_VARUNA_g3302.t1 | B02_VARUNA_g48.t1 | BRI1 | Involved in BR signalling which play key role in seed size regulation | https://doi.org/10.1111/jipb.12081 |
| Seed size | A06_VARUNA_g3302.t1 | A05_VARUNA_g1629.t1 | MINI3 | Involved in endosperm development, positive regulator of seed size | https://doi.org/10.1073/pnas.0508418102 |
| Seed size | A06_VARUNA_g3302.t1 | B03_VARUNA_g4053.t1 | MKK4 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | A07_VARUNA_g1982.t1 | A04_VARUNA_g2621.t1 | IKU1 | Regulate endosperm development, positive regulator of seed size | https://doi.org/10.1104/pp.102.018762 |
| Seed size | A09_VARUNA_g1463.t1 | A06_VARUNA_g182.t1 | ABA2 | Play key role in IKU pathway, positive regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | A09_VARUNA_g1463.t1 | A03_VARUNA_g3964.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | A09_VARUNA_g2765.t1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | A09_VARUNA_g2765.t1 | B01_VARUNA_g2936.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | A09_VARUNA_g2765.t1 | B01_VARUNA_g2935.t1 | AGG3 | Overexpression leads to an increase in silique length, and seed size due to cell proliferation | https://doi.org/10.1111/j.1469-8137.2012.04083.x |
| Seed size | A10_VARUNA_g2552.t1 | A05_VARUNA_g1832.t1 | MKK4 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | A10_VARUNA_g2936.t1 | B05_VARUNA_g2844.t1 | KLU | Positive regulator of seed size and encodes cytochrome P450 | https://doi.org/10.1007/s11103-015-0392-0 |
| Seed size | B01_VARUNA_g1662.t1 | B08_VARUNA_g8054.t1 | KLU | Positive regulator of seed size and encodes cytochrome P450 | https://doi.org/10.1007/s11103-015-0392-0 |
| Seed size | B01_VARUNA_g1863.t1 | A06_VARUNA_g949.t1 | KLU | Positive regulator of seed size and encodes cytochrome P450 | https://doi.org/10.1007/s11103-015-0392-0 |
| Seed size | B01_VARUNA_g1863.t1 | A03_VARUNA_g3964.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B01_VARUNA_g1973.t1 | A09_VARUNA_g1151.t1 | CKX2 | Modulates cytokinin breakdown which further cause enlarged seeds | https://doi.org/10.1105/tpc.014928 |
| Seed size | B01_VARUNA_g1973.t1 | A04_VARUNA_g86.t1 | CYP78A9 | Positive regulator of seed size through KLUH pathway | https://doi.org/10.1111/j.1365-313X.2012.04907.x |
| Seed size | B02_VARUNA_g7380.t1 | MSTRG.246.2 | AGB1 | Interacts with BIN2 for seed size regulation | https://doi.org/10.1093/jxb/ert159 |
| Seed size | B02_VARUNA_g7380.t1 | MSTRG.37892.1 | EOD1/BB | Involved in peptidase cativity of DA1, Negative regulator of seed size | http://www.genesdev.org/cgi/doi/10.1101/gad.292235.116 |
| Seed size | B02_VARUNA_g7380.t1 | A03_VARUNA_g3964.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B02_VARUNA_g7380.t1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B02_VARUNA_g7380.t1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B02_VARUNA_g910.t1 | B04_VARUNA_g454.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | B02_VARUNA_g910.t1 | B05_VARUNA_g5787.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | B02_VARUNA_g910.t1 | MSTRG.40219.2 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | B03_VARUNA_g2499.t1 | MSTRG.37892.1 | EOD1/BB | Involved in peptidase cativity of DA1, Negative regulator of seed size | http://www.genesdev.org/cgi/doi/10.1101/gad.292235.116 |
| Seed size | B03_VARUNA_g2581.t1 | A06_VARUNA_g1510.t1 | ARF2 | Restrict cell proliferation in integuments | https://doi.org/10.1242/dev.02194 |
| Seed size | B03_VARUNA_g2581.t1 | B02_VARUNA_g1940.t1 | ARF2 | Restrict cell proliferation in integuments | https://doi.org/10.1242/dev.02194 |
| Seed size | B03_VARUNA_g3517.t1 | B06_VARUNA_g239.t1 | ARF2 | Restrict cell proliferation in integuments | https://doi.org/10.1242/dev.02194 |
| Seed size | B03_VARUNA_g3517.t1 | MSTRG.37892.1 | EOD1/BB | Involved in peptidase cativity of DA1, Negative regulator of seed size | http://www.genesdev.org/cgi/doi/10.1101/gad.292235.116 |
| Seed size | B03_VARUNA_g3683.t1 | B06_VARUNA_g5140.t1 | MINI3 | Involved in endosperm development, positive regulator of seed size | https://doi.org/10.1073/pnas.0508418102 |
| Seed size | B03_VARUNA_g3683.t1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B03_VARUNA_g6234.t1 | B05_VARUNA_g3711.t1 | MKK4 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B04_VARUNA_g1164.t1 | A06_VARUNA_g1510.t1 | ARF2 | Restrict cell proliferation in integuments | https://doi.org/10.1242/dev.02194 |
| Seed size | B04_VARUNA_g77.t1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B05_VARUNA_g1788.t1 | A08_VARUNA_g2347.t1 | BRI1 | Involved in BR signalling which play key role in seed size regulation | https://doi.org/10.1111/jipb.12081 |
| Seed size | B05_VARUNA_g2886.t1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B05_VARUNA_g4205.t1 | B01_VARUNA_g2936.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B05_VARUNA_g5231.t1 | A08_VARUNA_g255.t1 | MKK4 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B05_VARUNA_g6592.t1 | MSTRG.18590.1 | RPT2A | Interacts with BIN2 for seed size regulation | https://doi.org/10.1242/dev.02604 |
| Seed size | B05_VARUNA_g6592.t1 | A05_VARUNA_g2339.t1 | SAMBA | Restrict cell proliferation in integuments by modulating the stability of cyclins | https://doi.org/10.1016/j.tplants.2015.11.012 |
| Seed size | B05_VARUNA_g823.t1 | MSTRG.37892.1 | EOD1/BB | Involved in peptidase cativity of DA1, Negative regulator of seed size | http://www.genesdev.org/cgi/doi/10.1101/gad.292235.116 |
| Seed size | B05_VARUNA_g823.t1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B05_VARUNA_g823.t1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B05_VARUNA_g823.t1 | B01_VARUNA_g2936.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | B06_VARUNA_g1164.t1 | MSTRG.37892.1 | EOD1/BB | Involved in peptidase cativity of DA1, Negative regulator of seed size | http://www.genesdev.org/cgi/doi/10.1101/gad.292235.116 |
| Seed size | B08_VARUNA_g3935.t1 | B07_VARUNA_g1763.t1 | BZR1 | Affected by PP2C-1 which is encooded by seed weight QTL | https://doi.org/10.1016/j.molp.2017.03.006 |
| Seed size | B08_VARUNA_g656.t1 | B05_VARUNA_g5787.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | B08_VARUNA_g656.t1 | MSTRG.40219.2 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | B08_VARUNA_g7619.t1 | A01_VARUNA_g3840.t1 | IKU2 | Acts zygotically to regulate endosperm development | https://doi.org/10.1104/pp.102.018762 |
| Seed size | MSTRG.10296.1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.10944.1 | B07_VARUNA_g4871.t1 | AGB1 | Interacts with BIN2 for seed size regulation | https://doi.org/10.1093/jxb/ert159 |
| Seed size | MSTRG.13236.2 | A02_VARUNA_g4621.t1 | ARF2 | Restrict cell proliferation in integuments | https://doi.org/10.1242/dev.02194 |
| Seed size | MSTRG.13236.2 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.13236.2 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.13637.2 | A04_VARUNA_g2707.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | MSTRG.13637.2 | A05_VARUNA_g901.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | MSTRG.13637.2 | B04_VARUNA_g454.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | MSTRG.13637.2 | B05_VARUNA_g5787.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | MSTRG.13637.2 | MSTRG.40219.2 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | MSTRG.13637.2 | MSTRG.9859.2 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | MSTRG.13637.2 | A01_VARUNA_g3716.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.13866.1 | MSTRG.13718.4 | ARF2 | Restrict cell proliferation in integuments | https://doi.org/10.1242/dev.02194 |
| Seed size | MSTRG.13866.1 | A01_VARUNA_g4441.t1 | SOD7/NGAL2 | Maternally regulate seed size by inhibiting cell proliferation in integuments | https://doi.org/10.1007/s11103-015-0392-0 |
| Seed size | MSTRG.13928.1 | B05_VARUNA_g5716.t1 | IKU1 | Regulate endosperm development, positive regulator of seed size | https://doi.org/10.1104/pp.102.018762 |
| Seed size | MSTRG.15584.1 | A07_VARUNA_g137.t1 | CKX2 | Modulates cytokinin breakdown which further cause enlarged seeds | https://doi.org/10.1105/tpc.014928 |
| Seed size | MSTRG.15584.1 | A08_VARUNA_g3068.t1 | SOD2/UBP15 | Required for cell proliferation in integuments during seed development | https://doi.org/10.1105/tpc.114.122663 |
| Seed size | MSTRG.15584.1 | MSTRG.19219.2 | SOD2/UBP15 | Required for cell proliferation in integuments during seed development | https://doi.org/10.1105/tpc.114.122663 |
| Seed size | MSTRG.15776.1 | MSTRG.118.2 | DAR1 | Mutant exhibit larger seeds | https://doi.org/10.1105/tpc.114.132274 |
| Seed size | MSTRG.16320.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.16320.1 | B01_VARUNA_g2936.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.16320.1 | A03_VARUNA_g5521.t1 | RPT2A | Negative regulator of seed size by inhibiting cell expansion | https://doi.org/10.1104/pp.109.135970 |
| Seed size | MSTRG.17830.1 | A03_VARUNA_g3964.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.17991.1 | A03_VARUNA_g3964.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.18149.1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.18149.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.18149.1 | B01_VARUNA_g2936.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.2937.1 | A05_VARUNA_g1629.t1 | MINI3 | Involved in endosperm development, positive regulator of seed size | https://doi.org/10.1073/pnas.0508418102 |
| Seed size | MSTRG.29546.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.29984.1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.31128.1 | A03_VARUNA_g3964.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.31128.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.31128.1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.34939.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.34939.1 | A06_VARUNA_g1235.t1 | SOD2/UBP15 | Required for cell proliferation in integuments during seed development | https://doi.org/10.1105/tpc.114.122663 |
| Seed size | MSTRG.38109.1 | A08_VARUNA_g2347.t1 | BRI1 | Involved in BR signalling which play key role in seed size regulation | https://doi.org/10.1111/jipb.12081 |
| Seed size | MSTRG.38109.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.38109.1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.38109.1 | MSTRG.18590.1 | RPT2A | Negative regulator of seed size by inhibiting cell expansion | https://doi.org/10.1104/pp.109.135970 |
| Seed size | MSTRG.38350.2 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.38487.4 | MSTRG.20079.2 | ARF2 | Restrict cell proliferation in integuments | https://doi.org/10.1242/dev.02194 |
| Seed size | MSTRG.38487.4 | A08_VARUNA_g2347.t1 | BRI1 | Involved in BR signalling which play key role in seed size regulation | https://doi.org/10.1111/jipb.12081 |
| Seed size | MSTRG.38570.1 | A05_VARUNA_g901.t1 | ABI5 | Inhibit transcription of SHB1, negative regulator of seed size | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | MSTRG.38570.1 | B07_VARUNA_g172.t1 | CKX2 | Modulates cytokinin breakdown which further cause enlarged seeds | https://doi.org/10.1105/tpc.014928 |
| Seed size | MSTRG.38570.1 | A03_VARUNA_g3964.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.38570.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.38570.1 | B01_VARUNA_g2935.t1 | MKK5 | Mutant exhibit larger seeds | https://doi.org/10.1105/tpc.114.132274 |
| Seed size | MSTRG.38991.1 | A01_VARUNA_g117.t1 | ANT | Directly regulates COR15A expression which is positive regulator of seed size | https://doi.org/10.1242/jcs.171207 |
| Seed size | MSTRG.38991.1 | B07_VARUNA_g6292.t1 | KLU | Positive regulator of seed size and encodes cytochrome P450 | https://doi.org/10.1007/s11103-015-0392-0 |
| Seed size | MSTRG.38991.1 | B04_VARUNA_g4817.t1 | SOD7/NGAL2 | Maternally regulate seed size by inhibiting cell proliferation in integuments | https://doi.org/10.1007/s11103-015-0392-0 |
| Seed size | MSTRG.43473.1 | B01_VARUNA_g1074.t1 | IKU2 | Acts zygotically to regulate endosperm development | https://doi.org/10.1104/pp.102.018762 |
| Seed size | MSTRG.43473.1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.43747.1 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.45024.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737S |
| Seed size | MSTRG.45827.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.46047.1 | B04_VARUNA_g562.t1 | IKU1 | Regulate endosperm development, positive regulator of seed size | https://doi.org/10.1104/pp.102.018762 |
| Seed size | MSTRG.4661.1 | MSTRG.37892.1 | EOD1/BB | Involved in peptidase cativity of DA1, Negative regulator of seed size | http://www.genesdev.org/cgi/doi/10.1101/gad.292235.116 |
| Seed size | MSTRG.47588.4 | B04_VARUNA_g319.t1 | DET2 | Mutant have decreased endosperm volume and integument length, resulting in smaller and less elongated seeds | https://doi.org/10.1104/pp.113.217703 |
| Seed size | MSTRG.47588.4 | A08_VARUNA_g255.t1 | MKK4 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.48794.1 | B01_VARUNA_g5726.t1 | MKK4 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.49706.1 | B01_VARUNA_g2936.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.49706.1 | MSTRG.18590.1 | RPT2A | Negative regulator of seed size by inhibiting cell expansion | https://doi.org/10.1104/pp.109.135970 |
| Seed size | MSTRG.50766.1 | MSTRG.18590.1 | RPT2A | Negative regulator of seed size by inhibiting cell expansion | https://doi.org/10.1104/pp.109.135970 |
| Seed size | MSTRG.50782.2 | MSTRG.14103.1 | ARF2 | Restrict cell proliferation in integuments | https://doi.org/10.1242/dev.02194 |
| Seed size | MSTRG.50782.2 | A06_VARUNA_g2542.t1 | ARF2 | Restrict cell proliferation in integuments | https://doi.org/10.1242/dev.02194 |
| Seed size | MSTRG.50782.2 | B01_VARUNA_g2935.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.50922.1 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.50922.1 | B01_VARUNA_g2935.t1 | MKK5 | Mutant have decreased endosperm volume and integument length, resulting in smaller and less elongated seeds | https://doi.org/10.1104/pp.113.217703 |
| Seed size | MSTRG.6182.2 | A03_VARUNA_g3965.t1 | MKK5 | Control embryogenesis and required for cell proliferation | https://doi.org/10.1111/tpj.13737 |
| Seed size | MSTRG.8794.1 | A08_VARUNA_g2347.t1 | BRI1 | Involved in BR signalling which play key role in seed size regulation | https://doi.org/10.1111/jipb.12081 |
| Oil content | A01_VARUNA_g3533.t1 | MSTRG.38484.2 | LACS9 | Found in plastid and essential for activation of long-chain fatty acids for both synthesis of cellular lipids and degradation. | https://doi.org/10.1104/pp.003251 |
| Oil content | A04_VARUNA_g1633.t1 | A09_VARUNA_g2792.t1 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Oil content | A07_VARUNA_g4355.t1 | A07_VARUNA_g4358.t1 | GK | Found in endoplasmic reticulum | https://doi.org/10.1186/s13068-019-1557-x |
| Oil content | A08_VARUNA_g2447.t1 | A03_VARUNA_g1603.t1 | HSI2/VAL1 | Acts as negative regulator for oil content and seed storage proteins | https://doi.org/10.1073/pnas.0607940104 |
| Oil content | A08_VARUNA_g2540.t1 | MSTRG.4270.3 | KAS I | Involved in fatty acid biosynthesis by increase acyl chain from C12-C16. | https://doi.org/10.1199/tab.0161 |
| Oil content | A08_VARUNA_g2540.t1 | MSTRG.4270.2 | KAS I | Involved in fatty acid biosynthesis by increase acyl chain from C12-C16. | https://doi.org/10.1199/tab.0161 |
| Oil content | A08_VARUNA_g2540.t1 | A02_VARUNA_g3475.t1 | KAS I | Involved in fatty acid biosynthesis by increase acyl chain from C12-C16. | https://doi.org/10.1199/tab.0161 |
| Oil content | A09_VARUNA_g2645.t1 | A05_VARUNA_g3512.t1 | FAD2 | Mutants are deficient in oleate desaturase99 | https://doi.org/10.1371/journal.pone.0030355 |
| Oil content | A09_VARUNA_g4342.t1 | B08_VARUNA_g2647.t1 | KAS I | Involved in fatty acid biosynthesis by increase acyl chain from C12-C16. | https://doi.org/10.1199/tab.0161 |
| Oil content | A10_VARUNA_g1097.t1 | B05_VARUNA_g3986.t1 | PDHC | Mutants are deficient in acety-coA | https://doi.org/10.1186/s13068-019-1557-x |
| Oil content | A10_VARUNA_g1893.t1 | MSTRG.29327.1 | PDAT | Found in Endoplasmic reticulum and with DGAT1 are involved in seed oil accumulation and epoxy or hydroxy fatty acid accumulation in developing seed. | https://doi.org/10.1007/s11745-010-3385-4 |
| Oil content | B01_VARUNA_g1973.t1 | A06_VARUNA_g4220.t1 | KAS I | Involved in fatty acid biosynthesis by increase acyl chain from C12-C16. | https://doi.org/10.1199/tab.0161 |
| Oil content | B01_VARUNA_g1973.t1 | MSTRG.16626.13 | LACS9 | Found in plastid and essential for activation of long-chain fatty acids for both synthesis of cellular lipids and degradation. | https://doi.org/10.1104/pp.003251 |
| Oil content | B01_VARUNA_g1973.t1 | MSTRG.16626.4 | LACS9 | Found in plastid and essential for activation of long-chain fatty acids for both synthesis of cellular lipids and degradation. | https://doi.org/10.1104/pp.003251 |
| Oil content | B01_VARUNA_g1973.t1 | MSTRG.16626.3 | LACS9 | Found in plastid and essential for activation of long-chain fatty acids for both synthesis of cellular lipids and degradation. | https://doi.org/10.1104/pp.003251 |
| Oil content | B01_VARUNA_g1973.t1 | MSTRG.16626.8 | LACS9 | Found in plastid and essential for activation of long-chain fatty acids for both synthesis of cellular lipids and degradation. | https://doi.org/10.1104/pp.003251 |
| Oil content | B01_VARUNA_g1973.t1 | B05_VARUNA_g6331.t1 | SAD | Involved in TAG biosynthesis | https://doi.org/10.1007/s00438-016-1265-1 |
| Oil content | B01_VARUNA_g2112.t1 | MSTRG.11850.3 | PLD | Found in Endoplasmic reticulum and hydrolyzes glycerol-phospholipids to generate phosphatidic acids (PA). | https://doi.org/10.1104/pp.010928 |
| Oil content | B01_VARUNA_g2179.t1 | MSTRG.15364.2 | DGAT1 | Seed-specific overexpression of DGAT1 increases oil content from 11% to 28% in Arabidopsis | https://doi.org/10.1105/tpc.109.071795 |
| Oil content | B01_VARUNA_g2965.t1 | B04_VARUNA_g982.t1 | HSI2/VAL1 | Acts as negative regulator for oil content and seed storage proteins | https://doi.org/10.1073/pnas.0607940104 |
| Oil content | B01_VARUNA_g4888.t1 | B03_VARUNA_g3285.t1 | HSD1,MID1 | Ectopic expression deprived the accumulation of fatty acids in seed oil bodies | https://doi.org/10.1093/pcp/pcp092 |
| Oil content | B02_VARUNA_g5961.t1 | B06_VARUNA_g3013.t1 | FATB | Determine the fatty acid composition | https://doi.org/10.1016/j.pbi.2013.02.015 |
| Oil content | B02_VARUNA_g7380.t1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Oil content | B02_VARUNA_g910.t1 | MSTRG.36636.3 | PLD | Found in Endoplasmic reticulum and hydrolyzes glycerol-phospholipids to generate phosphatidic acids (PA) | https://doi.org/10.1104/pp.010928 |
| Oil content | B03_VARUNA_g2499.t1 | B04_VARUNA_g4763.t1 | FAD2 | Mutants are deficient in oleate desaturase | https://doi.org/10.1371/journal.pone.0030355 |
| Oil content | B03_VARUNA_g2499.t1 | MSTRG.12095.2 | FAD2 | Mutants are deficient in oleate desaturase | https://doi.org/10.1371/journal.pone.0030355 |
| Oil content | B03_VARUNA_g2882.t1 | A04_VARUNA_g2256.t1 | MCMT | Involved in acyl-ACP synthesis in plastids | https://doi.org/10.1186/s13068-020-01728-6 |
| Oil content | B03_VARUNA_g3450.t1 | A03_VARUNA_g2133.t1 | ABI4 | Mutants showed TAG accumulation and reduced expression of DGAT1 | https://doi.org/10.1104/pp.111.175950 |
| Oil content | B03_VARUNA_g3517.t1 | B02_VARUNA_g303.t1 | GPAT 9 | Localized to the endoplasmic reticulum (ER) and catalyzes triacyglycerol (TAG) accumulation for plant mebrane lipid and oil biosynthesis. | https://doi.org/10.1104/pp.15.01563 |
| Oil content | B03_VARUNA_g3517.t1 | A04_VARUNA_g3028.t1 | GPDH | overexpression leads to increased oil content | https://doi.org/10.1111/jipb.13094 |
| Oil content | B03_VARUNA_g3517.t1 | B08_VARUNA_g2647.t1 | KAS I | Involved in fatty acid biosynthesis by increase acyl chain from C12-C16. | https://doi.org/10.1199/tab.0161 |
| Oil content | B03_VARUNA_g3517.t1 | B04_VARUNA_g4318.t1 | PLD | Found in Endoplasmic reticulum and hydrolyzes glycerol-phospholipids to generate phosphatidic acids (PA) | https://doi.org/10.1104/pp.010928 |
| Oil content | B03_VARUNA_g3517.t1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Oil content | B03_VARUNA_g7043.t1 | B03_VARUNA_g7052.t1 | FAX1 | Acts as primary transporter of fatty acid. Involved in oil content aacumulation | https://doi.org/10.1104/pp.19.01344 |
| Oil content | B05_VARUNA_g1788.t1 | MSTRG.29327.1 | PDAT | Found in Endoplasmic reticulum and with DGAT1 are involved in seed oil accumulation and epoxy or hydroxy fatty acid accumulation in developing seed | https://doi.org/10.1007/s11745-010-3385-4 |
| Oil content | B05_VARUNA_g2886.t1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Oil content | B05_VARUNA_g4205.t1 | B02_VARUNA_g2390.t1 | PDAT | Found in Endoplasmic reticulum and with DGAT1 are involved in seed oil accumulation and epoxy or hydroxy fatty acid accumulation in developing seed | https://doi.org/10.1007/s11745-010-3385-4 |
| Oil content | B05_VARUNA_g823.t1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Oil content | B06_VARUNA_g1164.t1 | A03_VARUNA_g2133.t1 | ABI4 | Mutants showed TAG accumulation and reduced expression of DGAT1 | https://doi.org/10.1104/pp.111.175950 |
| Oil content | B06_VARUNA_g1164.t1 | A03_VARUNA_g4555.t1 | DGAT2 | Mutants show defective TAG biosynthesis | https://doi.org/10.1105/tpc.106.043695 |
| Oil content | B06_VARUNA_g1164.t1 | A03_VARUNA_g1603.t1 | HSI2/VAL1 | Acts as negative regulator for oil content and seed storage proteins | https://doi.org/10.1073/pnas.0607940104 |
| Oil content | B06_VARUNA_g1164.t1 | A04_VARUNA_g2256.t1 | MCMT | Involved in acyl-ACP synthesis in plastids | https://doi.org/10.1186/s13068-020-01728-6 |
| Oil content | B06_VARUNA_g1164.t1 | B05_VARUNA_g4660.t1 | MCMT | Involved in acyl-ACP synthesis in plastids | https://doi.org/10.1186/s13068-020-01728-6 |
| Oil content | B06_VARUNA_g1164.t1 | A03_VARUNA_g2295.t1 | SAD | Invovled in determination of oil composition | https://doi.org/10.1007/s00438-016-1265-1 |
| Oil content | B06_VARUNA_g1164.t1 | A09_VARUNA_g2792.t1 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Oil content | B06_VARUNA_g2218.t1 | B04_VARUNA_g4318.t1 | PLD | Found in Endoplasmic reticulum and hydrolyzes glycerol-phospholipids to generate phosphatidic acids (PA) | https://doi.org/10.1104/pp.010928 |
| Oil content | B07_VARUNA_g2781.t1 | A01_VARUNA_g4407.t1 | FAD2 | Mutants are deficient in oleate desaturase | https://doi.org/10.1371/journal.pone.0030355 |
| Oil content | B07_VARUNA_g3381.t1 | A03_VARUNA_g414.t1 | FAE1 | Involved in eurcic acid content | https://doi.org/10.1007/s11032-019-0971-x |
| Oil content | B07_VARUNA_g3381.t1 | MSTRG.47560.2 | OLE1 | Deficiency in OLE1 caused a decrease in total lipid content | https://doi.org/10.1105/tpc.106.041269 |
| Oil content | B08_VARUNA_g5727.t1 | A07_VARUNA_g144.t1 | DGAT1 | Seed-specific overexpression of DGAT1 increases oil content from 11% to 28% in Arabidopsis | https://doi.org/10.1105/tpc.109.071795 |
| Oil content | B08_VARUNA_g656.t1 | MSTRG.45235.2 | LEC2 | Ectopic expression causes accumulation of seed storage proteins and lipid oil bodies in vegetative and reproductive organs | https://doi.org/10.1073/pnas.0712364105 |
| Oil content | B08_VARUNA_g8376.t1 | A06_VARUNA_g866.t1 | LACAT1 | Found in endoplasmic reticulum, involved in TAG biosynthesis | https://doi.org/10.1186/s13068-020-01728-6 |
| Oil content | MSTRG.11274.1 | A09_VARUNA_g5490.t1 | HAD | Found in plastids, key role in fatty acid metabolism | https://doi.org/10.1186/s13068-020-01728-6 |
| Oil content | MSTRG.1389.1 | A05_VARUNA_g1403.t1 | HSI2/VAL1 | Acts as negative regulator for oil content and seed storage proteins | https://doi.org/10.1073/pnas.0607940104 |
| Oil content | MSTRG.15776.1 | MSTRG.41351.1 | KAS I | Involved in fatty acid biosynthesis by increase acyl chain from C12-C16. | https://doi.org/10.1199/tab.0161 |
| Oil content | MSTRG.16131.1 | MSTRG.12095.2 | FAD2 | Mutants are deficient in oleate desaturase | https://doi.org/10.1371/journal.pone.0030355 |
| Oil content | MSTRG.16320.1 | A06_VARUNA_g539.t1 | FATB | Determine the fatty acid composition | https://doi.org/10.1016/j.pbi.2013.02.015 |
| Oil content | MSTRG.17991.1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Oil content | MSTRG.18149.1 | MSTRG.9632.1 | MCMT | Involved in acyl-ACP synthesis in plastids | https://doi.org/10.1186/s13068-020-01728-6 |
| Oil content | MSTRG.30925.2 | B08_VARUNA_g7105.t1 | HAD | Found in plastids, key role in fatty acid metabolism | https://doi.org/10.1186/s13068-020-01728-6 |
| Oil content | MSTRG.38487.4 | MSTRG.29327.1 | PDAT | Found in Endoplasmic reticulum and with DGAT1 are involved in seed oil accumulation and epoxy or hydroxy fatty acid accumulation in developing seed. | https://doi.org/10.1007/s11745-010-3385-4 |
| Oil content | MSTRG.38570.1 | A06_VARUNA_g539.t1 | FATB | Determine the fatty acid composition | https://doi.org/10.1016/j.pbi.2013.02.015 |
| Oil content | MSTRG.38570.1 | MSTRG.9632.1 | MCMT | Involved in acyl-ACP synthesis in plastids | https://doi.org/10.1186/s13068-020-01728-6 |
| Oil content | MSTRG.41746.1 | B06_VARUNA_g1082.t1 | KAS I | Involved in fatty acid biosynthesis by increase acyl chain from C12-C16. | https://doi.org/10.1199/tab.0161 |
| Oil content | MSTRG.43179.1 | A07_VARUNA_g1169.t1 | LEC2 | Ectopic expression causes accumulation of seed storage proteins and lipid oil bodies in vegetative and reproductive organs | https://doi.org/10.1073/pnas.0712364105 |
| Oil content | MSTRG.4572.1 | A06_VARUNA_g4220.t1 | KAS I | Involved in fatty acid biosynthesis by increase acyl chain from C12-C16. | https://doi.org/10.1199/tab.0161 |
| Oil content | MSTRG.4661.1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Oil content | MSTRG.47588.4 | B03_VARUNA_g2458.t1 | ABI4 | Mutants showed TAG accumulation and reduced expression of DGAT1 | https://doi.org/10.1104/pp.111.175950 |
| Oil content | MSTRG.47588.4 | A06_VARUNA_g539.t1 | FATB | Determine the fatty acid composition | https://doi.org/10.1016/j.pbi.2013.02.015 |
| Oil content | MSTRG.47588.4 | MSTRG.12932.1 | FATB | Determine the fatty acid composition | https://doi.org/10.1016/j.pbi.2013.02.015 |
| Oil content | MSTRG.50571.1 | A06_VARUNA_g1443.t1 | KAS II | Found in plastid and involved in fatty acid elongation from 16:0-ACP to 18:0-ACP. Mutants produced embryo lethal. | https://doi.org/10.1046/j.1365-313X.2002.01253.x |
| Oil content | MSTRG.50766.1 | B04_VARUNA_g4763.t1 | FAD2 | Mutants are deficient in oleate desaturase | https://doi.org/10.1371/journal.pone.0030355 |
| Oil content | MSTRG.50766.1 | MSTRG.12095.2 | FAD2 | Mutants are deficient in oleate desaturase | https://doi.org/10.1371/journal.pone.0030355 |
| Oil content | MSTRG.50766.1 | A09_VARUNA_g2792.t1 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | A03_VARUNA_g3156.t1 | MSTRG.5035.1 | PAL | It catalyses the first step in the phenylpropanoid pathway, the deamination of phenylalanine to cinnamate and ammonia. | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | A04_VARUNA_g1633.t1 | A09_VARUNA_g2792.t1 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | A06_VARUNA_g1615.t1 | MSTRG.14480.3 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | A06_VARUNA_g1861.t1 | A06_VARUNA_g1849.t1 | FLS1 | Overexpression altered seed coat color in a light brown color and also affected flavonoid metabolism | https://doi.org/10.1016/j.plaphy.2016.03.010 |
| Seed coat color | A06_VARUNA_g3302.t1 | A09_VARUNA_g4016.t1 | MYB3 | Involved in regulation of phenylpropanoid pathway and flavonoid biosynthesis | https://doi.org/10.1104/pp.15.01831 |
| Seed coat color | A06_VARUNA_g3302.t1 | B02_VARUNA_g2630.t1 | TT19 | Mutants have anthocyanins but do not have the brown pigments | https://doi.org/10.1046/j.1365-313X.2003.01943.x |
| Seed coat color | A06_VARUNA_g3302.t1 | A06_VARUNA_g3192.t1 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | A09_VARUNA_g1463.t1 | A06_VARUNA_g3192.t1 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | A09_VARUNA_g4116.t1 | MSTRG.19436.2 | MYB61 | Mutant seeds lack mucilage extrusion and deposition | https://doi.org/10.1105/tpc.010265 |
| Seed coat color | A10_VARUNA_g1370.t1 | B08_VARUNA_g3647.t1 | TT7 | Mutants show altered level and patterns of proanthocyanidin deposition in the cell | https://doi.org/10.1104/pp.006189 |
| Seed coat color | B01_VARUNA_g1973.t1 | A05_VARUNA_g1831.t1 | 4CL | A critical function in directing carbon flow into phenylpropanoid metabolism's many branch routes | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | B01_VARUNA_g2166.t1 | B08_VARUNA_g5638.t1 | OMT | Overexpression leads to black seed coat color | https://doi.org/10.1186/1471-2164-12-381 |
| Seed coat color | B01_VARUNA_g2179.t1 | MSTRG.14480.3 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | B01_VARUNA_g2965.t1 | B05_VARUNA_g1350.t1 | TT12 | Recessive mutant seeds show a pale brown color with a reduction of proanthocyanidins deposition in endothelium | https://doi.org/10.1105/tpc.13.4.853 |
| Seed coat color | B02_VARUNA_g7009.t1 | A05_VARUNA_g1402.t1 | C4H | Defects in C4H activity showed reduction in the phenylpropanoid metabolism | https://doi.org/10.1111/j.1365-313X.2009.03996.x |
| Seed coat color | B02_VARUNA_g7380.t1 | MSTRG.20051.1 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | B02_VARUNA_g7380.t1 | MSTRG.20051.4 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | B02_VARUNA_g7380.t1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | B03_VARUNA_g3517.t1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | B03_VARUNA_g5397.t1 | B08_VARUNA_g1491.t1 | TT6 | Mutants showed complete or reduction in seed coat color pigmentation | https://doi.org/10.1016/S0168-9452(03)00344-3 |
| Seed coat color | B03_VARUNA_g5397.t1 | MSTRG.47970.1 | TT6 | Mutants showed complete or reduction in seed coat color pigmentation | https://doi.org/10.1016/S0168-9452(03)00344-3 |
| Seed coat color | B03_VARUNA_g5397.t1 | A10_VARUNA_g1142.t1 | UFGT | Mutants showed drastically reduction of anthocyanin | https://doi.org/10.1111/j.1365-313X.2011.04779.x |
| Seed coat color | B03_VARUNA_g5397.t1 | B08_VARUNA_g1491.t1 | TT6 | Mutants showed complete or reduction in seed coat color pigmentation | https://doi.org/10.1016/S0168-9452(03)00344-3 |
| Seed coat color | B03_VARUNA_g5397.t1 | MSTRG.47970.1 | TT6 | Mutants showed complete or reduction in seed coat color pigmentation | https://doi.org/10.1016/S0168-9452(03)00344-3 |
| Seed coat color | B03_VARUNA_g5397.t1 | A10_VARUNA_g1142.t1 | UFGT | Mutants showed drastically reduction of anthocyanin | https://doi.org/10.1111/j.1365-313X.2011.04779.x |
| Seed coat color | B05_VARUNA_g2886.t1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | B05_VARUNA_g3037.t1 | B08_VARUNA_g1307.t1 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | B05_VARUNA_g3037.t1 | MSTRG.47859.1 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | B05_VARUNA_g3037.t1 | MSTRG.47859.2 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | B05_VARUNA_g3037.t1 | MSTRG.40928.4 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | B05_VARUNA_g3935.t1 | MSTRG.44763.2 | 4CL | A critical function in directing carbon flow into phenylpropanoid metabolism's many branch routes | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | B05_VARUNA_g823.t1 | A05_VARUNA_g2597.t1 | 4CL | A critical function in directing carbon flow into phenylpropanoid metabolism's many branch routes | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | B05_VARUNA_g823.t1 | MSTRG.11589.1 | 4CL | A critical function in directing carbon flow into phenylpropanoid metabolism's many branch routes | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | B05_VARUNA_g823.t1 | MSTRG.11589.2 | 4CL | A critical function in directing carbon flow into phenylpropanoid metabolism's many branch routes | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | B05_VARUNA_g823.t1 | MSTRG.49693.1 | TT19 | Mutants have anthocyanins but do not have the brown pigments | https://doi.org/10.1046/j.1365-313X.2003.01943.x |
| Seed coat color | B05_VARUNA_g823.t1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | B06_VARUNA_g1164.t1 | A09_VARUNA_g2792.t1 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | B06_VARUNA_g2218.t1 | B03_VARUNA_g181.t1 | PAL | It catalyses the first step in the phenylpropanoid pathway, the deamination of phenylalanine to cinnamate and ammonia. | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | MSTRG.10296.1 | B08_VARUNA_g1207.t1 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | MSTRG.10418.1 | MSTRG.47798.1 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | MSTRG.1389.1 | MSTRG.9638.2 | C4H | Defects in C4H activity showed reduction in the phenylpropanoid metabolism | https://doi.org/10.1111/j.1365-313X.2009.03996.x |
| Seed coat color | MSTRG.13909.4 | A02_VARUNA_g536.t1 | CHS(TT4) | Catalyse first step in biosynthesis of flavonoid | https://doi.org/10.1016/S0378-1119(00)00304-8 |
| Seed coat color | MSTRG.16320.1 | B08_VARUNA_g1207.t1 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | MSTRG.1709.1 | A10_VARUNA_g2403.t1 | CHS(TT4) | Catalyse first step in biosynthesis of flavonoid | https://doi.org/10.1016/S0378-1119(00)00304-8 |
| Seed coat color | MSTRG.17991.1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | MSTRG.23086.1 | MSTRG.9638.2 | C4H | Defects in C4H activity showed reduction in the phenylpropanoid metabolism | https://doi.org/10.1111/j.1365-313X.2009.03996.x |
| Seed coat color | MSTRG.2652.1 | MSTRG.9638.2 | C4H | Defects in C4H activity showed reduction in the phenylpropanoid metabolism | https://doi.org/10.1111/j.1365-313X.2009.03996.x |
| Seed coat color | MSTRG.29984.1 | MSTRG.7558.3 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | MSTRG.29984.1 | MSTRG.7558.1 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | MSTRG.30925.2 | MSTRG.14480.3 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | MSTRG.38109.1 | A10_VARUNA_g2403.t1 | CHS(TT4) | Catalyse first step in biosynthesis of flavonoid | https://doi.org/10.1016/S0378-1119(00)00304-8 |
| Seed coat color | MSTRG.38685.1 | B08_VARUNA_g1207.t1 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | MSTRG.43179.1 | A04_VARUNA_g553.t1 | TT6 | Mutants showed complete or reduction in seed coat color pigmentation | https://doi.org/10.1016/S0168-9452(03)00344-3 |
| Seed coat color | MSTRG.43473.1 | MSTRG.16890.3 | 4CL | A critical function in directing carbon flow into phenylpropanoid metabolism's many branch routes | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | MSTRG.43473.1 | B02_VARUNA_g1382.t1 | TT18 | Regulatory role in anthocyanin accumulation | https://doi.org/10.1186/s12870-019-1821-z |
| Seed coat color | MSTRG.43473.1 | B08_VARUNA_g942.t1 | TT18 | Regulatory role in anthocyanin accumulation | https://doi.org/10.1186/s12870-019-1821-z |
| Seed coat color | MSTRG.43473.1 | MSTRG.28803.2 | TT18 | Regulatory role in anthocyanin accumulation | https://doi.org/10.1186/s12870-019-1821-z |
| Seed coat color | MSTRG.43747.1 | MSTRG.20051.1 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | MSTRG.43747.1 | MSTRG.20051.4 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/TPC.010098 |
| Seed coat color | MSTRG.44053.1 | B05_VARUNA_g444.t1 | GT | Overexpression leads to accumulation of anthocyanin | https://doi.org/10.1186/1471-2164-12-381 |
| Seed coat color | MSTRG.45433.1 | B08_VARUNA_g3706.t1 | FLS1 | Overexpression altered seed coat color in a light brown color and also affected flavonoid metabolism | https://doi.org/10.1016/j.plaphy.2016.03.010 |
| Seed coat color | MSTRG.45568.1 | A03_VARUNA_g3966.t1 | 4CL | A critical function in directing carbon flow into phenylpropanoid metabolism's many branch routes | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | MSTRG.45827.1 | A02_VARUNA_g716.t1 | TT19 | Mutants have anthocyanins but do not have the brown pigments | https://doi.org/10.1046/j.1365-313X.2003.01943.x |
| Seed coat color | MSTRG.4661.1 | MSTRG.46872.1 | MYB61 | Mutant seeds lack mucilage extrusion and deposition | https://doi.org/10.1105/tpc.010265 |
| Seed coat color | MSTRG.4661.1 | MSTRG.21084.2 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | MSTRG.48910.1 | A10_VARUNA_g3054.t1 | PAL | It catalyses the first step in the phenylpropanoid pathway, the deamination of phenylalanine to cinnamate and ammonia. | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | MSTRG.50391.1 | B08_VARUNA_g1207.t1 | TTG1 | Involved in seed coat mucilage production | https://doi.org/10.1104/pp.010410 |
| Seed coat color | MSTRG.50766.1 | A09_VARUNA_g2792.t1 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | MSTRG.6182.2 | MSTRG.47970.1 | TT6 | Mutants showed complete or reduction in seed coat color pigmentation | https://doi.org/10.1016/S0168-9452(03)00344-3 |
| Seed coat color | MSTRG.6182.2 | MSTRG.34244.2 | TT6 | Mutants showed complete or reduction in seed coat color pigmentation | https://doi.org/10.1016/S0168-9452(03)00344-3 |
| Seed coat color | MSTRG.6182.2 | B08_VARUNA_g3647.t1 | TT7 | Mutants show altered level and patterns of proanthocyanidin deposition in the cell | https://doi.org/10.1104/pp.006189 |
| Seed coat color | MSTRG.8794.1 | MSTRG.5035.2 | PAL | It catalyses the first step in the phenylpropanoid pathway, the deamination of phenylalanine to cinnamate and ammonia. | https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001735.3/ |
| Seed coat color | MSTRG.8794.1 | MSTRG.29452.2 | TT19 | Mutants have anthocyanins but do not have the brown pigments | https://doi.org/10.1046/j.1365-313X.2003.01943.x |