Candidates for seed size, oil content and seed coat colour were identified from transcriptome analysis in three different stages, of two contrasting Brassica juncea varieties.
(Reference: https://doi.org/10.1038/s41598-022-15938-5)
Candidate Genes
| Seed Trait | Brassica juncea Transcript ID | Orthologous Arabidopsis Gene ID | Gene Symbol | Function | Reference |
|---|---|---|---|---|---|
| Seed size | A04_VARUNA_g3379.t1 | AT2G46660 | ENHANCER OF DA1 (EOD3)/CYP78A6 | Loss of function mutation produced small seeds. Overexpression increased the seed size, Promotes cell expansion and proliferation of cotyledons maternally | https://doi.org/10.1111/j.1365-313X.2012.04907.x , https://doi.org/10.1016/j.pbi.2016.05.008 |
| Seed size | B05_VARUNA_g6603.t1 | AT2G46660 | ENHANCER OF DA1 (EOD3)/CYP78A6 | Loss of function mutation produced small seeds. Overexpression increased the seed size, Promotes cell expansion and proliferation of cotyledons maternally | https://doi.org/10.1111/j.1365-313X.2012.04907.x , https://doi.org/10.1016/j.pbi.2016.05.008 |
| Seed size | A04_VARUNA_g90.t1 | AT3G61830 | ARF18 | Regulates seed weight negatively through auxin response pathway, and acts maternally, Overexpression of this gene in Arabidopsis showed change in seed weight | https://doi.org/10.1073/pnas.1502160112 |
| Seed size | A09_VARUNA_g5135.t1 | AT3G61830 | ARF18 | Regulates seed weight negatively through auxin response pathway, and acts maternally, Overexpression of this gene in Arabidopsis showed change in seed weight | https://doi.org/10.1073/pnas.1502160112 |
| Seed size | B05_VARUNA_g650.t1 | AT3G61830 | ARF18 | Regulates seed weight negatively through auxin response pathway, and acts maternally, Overexpression of this gene in Arabidopsis showed change in seed weight | https://doi.org/10.1073/pnas.1502160112 |
| Seed size | B03_VARUNA_g7431.t1 | AT3G61830 | ARF18 | Regulates seed weight negatively through auxin response pathway, and acts maternally, Overexpression of this gene in Arabidopsis showed change in seed weight | https://doi.org/10.1073/pnas.1502160112 |
| Seed size | B08_VARUNA_g22.t1 | AT4G38600 | UPL3 | Codes for a HECT E3 ubiquitin ligase which regulates seed weight negatively by proteosomal degradation of LEC2 responsible for seed maturation | https://doi.org/10.1105/tpc.18.00577 |
| Seed size | A03_VARUNA_g2832.t1 | AT3G61880 | CYP78A9 | Codes for a cytochrome P450 monooxygenase CYP78A9 and regulates seed weight positively through auxin metabolism pathway, cyp78a9-KO mutants had smaller and lighter seeds than the wild type | https://doi.org/10.1111/tpj.14236 |
| Seed size | A04_VARUNA_g456.t1 | AT3G61880 | CYP78A9 | Codes for a cytochrome P450 monooxygenase CYP78A9 and regulates seed weight positively through auxin metabolism pathway, cyp78a9-KO mutants had smaller and lighter seeds than the wild type | https://doi.org/10.1111/tpj.14236 |
| Seed size | A04_VARUNA_g86.t1 | AT3G61880 | CYP78A9 | Codes for a cytochrome P450 monooxygenase CYP78A9 and regulates seed weight positively through auxin metabolism pathway, cyp78a9-KO mutants had smaller and lighter seeds than the wild type | https://doi.org/10.1111/tpj.14236 |
| Seed size | A09_VARUNA_g5141.t1 | AT3G61880 | CYP78A9 | Codes for a cytochrome P450 monooxygenase CYP78A9 and regulates seed weight positively through auxin metabolism pathway, cyp78a9-KO mutants had smaller and lighter seeds than the wild type | https://doi.org/10.1111/tpj.14236 |
| Seed size | B03_VARUNA_g7439.t1 | AT3G61880 | CYP78A9 | Codes for a cytochrome P450 monooxygenase CYP78A9 and regulates seed weight positively through auxin metabolism pathway, cyp78a9-KO mutants had smaller and lighter seeds than the wild type | https://doi.org/10.1111/tpj.14236 |
| Seed size | B05_VARUNA_g653.t1 | AT3G61880 | CYP78A9 | Codes for a cytochrome P450 monooxygenase CYP78A9 and regulates seed weight positively through auxin metabolism pathway, cyp78a9-KO mutants had smaller and lighter seeds than the wild type | https://doi.org/10.1111/tpj.14236 |
| Seed size | B05_VARUNA_g6233.t1 | AT2G44810 | DEFECTIVE IN ANTHER DEHISCENCE 1 (DAD1; Bna.A05DAD1) | Suppressed the negative regulation by ARF18 and upregulates auxin genes by promoting JA signaling | https://doi.org/10.1016/j.indcrop.2021.113576 |
| Seed size | MSTRG.34420.1 | AT3G54320 | Wrinled1 (WRI1) | Regulates the cell size of embryo positively | https://doi.org/10.1016/j.plaphy.2009.09.007 |
| Seed size | B04_VARUNA_g2725.t1 | AT5G35750 | Bna-A03g37960D | Histidine kinase gene, ahk2, 3, 4 triple mutant produced large seeds | https://doi.org/10.1093/jxb/eru549 |
| Seed size | B08_VARUNA_g7826.t1 | AT5G35750 | Bna-A03g37960D | Histidine kinase gene, ahk2, 3, 4 triple mutant produced large seeds | https://doi.org/10.1093/jxb/eru549 |
| Seed size | B02_VARUNA_g6083.t1 | AT1G65480 | FT | Regulates seed weight negatively | https://doi.org/10.1093/jxb/eru549 |
| Seed size | B07_VARUNA_g2747.t1 | AT1G65480 | FT | Regulates seed weight negatively | https://doi.org/10.1093/jxb/eru549 |
| Seed size | A06_VARUNA_g949.t1 | AT1G13710 | KLUH | Loss of function mutation produced large seeds | https://doi.org/10.5958/0975-6906.2015.00055.3 |
| Seed size | A09_VARUNA_g5986.t1 | AT1G13710 | KLUH | Loss of function mutation produced large seeds | https://doi.org/10.5958/0975-6906.2015.00055.3 |
| Seed size | B05_VARUNA_g2844.t1 | AT1G13710 | KLUH | Loss of function mutation produced large seeds | https://doi.org/10.5958/0975-6906.2015.00055.3 |
| Seed size | A09_VARUNA_g1148.t1 | AT2G19450 | DGAT1 | Loss of function mutation produced large seeds | https://doi.org/10.1139/cjb-2015-0218 |
| Seed size | A06_VARUNA_g24.t1 | AT1G55600 | MINISEED 3 (MINI3) | Loss of function mutation produced small seeds due to precocious cellularisation of the endosperm | https://doi.org/10.1073/pnas.0508418102 |
| Seed size | A08_VARUNA_g55.t1 | AT1G55600 | MINISEED 3 (MINI3) | Loss of function mutation produced small seeds due to precocious cellularisation of the endosperm | https://doi.org/10.1073/pnas.0508418102 |
| Seed size | A08_VARUNA_g57.t1 | AT1G55600 | MINISEED 3 (MINI3) | Loss of function mutation produced small seeds due to precocious cellularisation of the endosperm | https://doi.org/10.1073/pnas.0508418102 |
| Seed size | B01_VARUNA_g5995.t1 | AT1G55600 | MINISEED 3 (MINI3) | Loss of function mutation produced small seeds due to precocious cellularisation of the endosperm | https://doi.org/10.1073/pnas.0508418102 |
| Seed size | B02_VARUNA_g6049.t1 | AT1G55600 | MINISEED 3 (MINI3) | Loss of function mutation produced small seeds due to precocious cellularisation of the endosperm | https://doi.org/10.1073/pnas.0508418102 |
| Seed size | A02_VARUNA_g2629.t1 | AT1G78420 | DA2 | Loss of function mutation produced large seeds | https://doi.org/10.1105/tpc.113.115063 / https://doi.org/10.1105/tpc.113.115063 |
| Seed size | B02_VARUNA_g7424.t1 | AT1G78420 | DA2 | Loss of function mutation produced large seeds | https://doi.org/10.1105/tpc.113.115063 / https://doi.org/10.1105/tpc.113.115063 |
| Seed size | MSTRG.37892.1 | AT3G63530 | ENHANCER1 OF DA1 (EOD1) | Loss of function mutation produced large seeds | https://doi.org/10.1105/tpc.113.115063 |
| Seed size | A05_VARUNA_g2339.t1 | AT1G32310 | SAMBA | Loss of function mutation produced large seeds | https://doi.org/10.1073/pnas.1211418109 |
| Seed size | A10_VARUNA_g1910.t1 | AT5G20635 | ARABIDOPSIS G PROTEIN GAMMA SUBUNIT (AGG3) | Loss of function mutation produced small seeds | https://doi.org/10.1111/j.1365-313X.2011.04638.x |
| Seed size | A01_VARUNA_g38.t1 | AT4G39400 | BRASSINOSTEROID INSENSITIV E 1 (BRI1) | Loss of function mutation produced small seeds | https://doi.org/10.1104/pp.113.217703 |
| Seed size | A06_VARUNA_g4464.t1 | AT4G39400 | BRASSINOSTEROID INSENSITIV E 1 (BRI1) | Loss of function mutation produced small seeds | https://doi.org/10.1104/pp.113.217703 |
| Seed size | A08_VARUNA_g2347.t1 | AT4G39400 | BRASSINOSTEROID INSENSITIV E 1 (BRI1) | Loss of function mutation produced small seeds | https://doi.org/10.1104/pp.113.217703 |
| Seed size | B04_VARUNA_g2725.t1 | AT5G35750 | DE- ETIOLATED 2 (DET2) | Histidine kinase gene | https://doi.org/10.1105/tpc.20.00057 |
| Seed size | B08_VARUNA_g7826.t1 | AT5G35750 | DE- ETIOLATED 2 (DET2) | Histidine kinase gene | https://doi.org/10.1105/tpc.20.00057 |
| Seed size | A07_VARUNA_g1228.t1 | AT1G27320 | ARABIDOPSIS HISTIDINE KINASE 3 (AHK3) | ahk2, 3, 4 triple mutant produced large seeds | https://doi.org/10.1105/tpc.106.045674 |
| Seed size | A01_VARUNA_g3691.t1 | AT3G21510 | ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 1 (AHP1) | ahp1, 2, 3, 4, 5 quintuple mutants produced large seeds quintuple mutants produced large seeds | https://doi.org/10.1105/tpc.106.045674 |
| Seed size | A09_VARUNA_g382.t1 | AT3G29350 | ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 2 (AHP2) | ahp1, 2, 3, 4, 5 quintuple mutants produced large seeds | https://doi.org/10.1105/tpc.106.045674 |
| Seed size | B01_VARUNA_g2468.t1 | AT3G29350 | ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 2 (AHP2) | ahp1, 2, 3, 4, 5 quintuple mutants produced large seeds | https://doi.org/10.1105/tpc.106.045674 |
| Seed size | A02_VARUNA_g4621.t1 | AT5G62000 | AUXIN RESPONSE FACTOR (ARF2) | Loss of function mutant produced large seeds | https://doi.org/10.1242/dev.02194 |
| Seed size | MSTRG.14103.1 | AT5G62000 | AUXIN RESPONSE FACTOR (ARF2) | Loss of function mutant produced large seeds | https://doi.org/10.1242/dev.02194 |
| Seed size | A06_VARUNA_g182.t1 | AT1G52340 | ABA DEFICIENT 2 (ABA2) | Loss of function mutant produced large seeds | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | A05_VARUNA_g901.t1 | AT2G36270 | ABA INSENSITIVE 5 (ABI5) | Loss of function mutant produced large seeds | https://doi.org/10.1105/tpc.113.121566 |
| Seed size | A05_VARUNA_g828.t1 | AT2G37260 | TRANSPARENT TESTA GLABRA 2 (TTG2) | Loss of function produced small seeds | https://doi.org/10.1016/j.pbi.2016.05.008 |
| Seed size | A01_VARUNA_g4441.t1 | AT3G11580 | SUPPRESSOR 7 OF DA1 (SOD7) | Loss of function mutants produced large seeds | https://doi.org/10.1105%2Ftpc.114.135368 |
| Seed size | B04_VARUNA_g4817.t1 | AT3G11580 | SUPPRESSOR 7 OF DA1 (SOD7) | Loss of function mutants produced large seeds | https://doi.org/10.1105%2Ftpc.114.135368 |
| Seed size | A01_VARUNA_g117.t1 | AT4G37750 | AINTEGUMENTA (ANT) | Overexpression produced large seeds | https://doi.org/10.1093/plcell/koab084 |
| Seed size | A08_VARUNA_g2267.t1 | AT4G37750 | AINTEGUMENTA (ANT) | Overexpression produced large seeds | https://doi.org/10.1093/plcell/koab084 |
| Seed size | B02_VARUNA_g135.t1 | AT4G37750 | AINTEGUMENTA (ANT) | Overexpression produced large seeds | https://doi.org/10.1093/plcell/koab084 |
| Seed size | B07_VARUNA_g5453.t1 | AT4G37750 | AINTEGUMENTA (ANT) | Overexpression produced large seeds | https://doi.org/10.1093/plcell/koab084 |
| Seed size | B08_VARUNA_g101.t1 | AT4G37750 | AINTEGUMENTA (ANT) | Overexpression produced large seeds | https://doi.org/10.1093/plcell/koab084 |
| Seed size | A06_VARUNA_g949.t1 | AT1G13710 | KLUH (KLU) | Loss of function mutation produced large seeds | https://doi.org/10.1073/pnas.0907024106 |
| Seed size | A09_VARUNA_g5986.t1 | AT1G13710 | KLUH (KLU) | Loss of function mutation produced large seeds | https://doi.org/10.1073/pnas.0907024106 |
| Seed size | B05_VARUNA_g2844.t1 | AT1G13710 | KLUH (KLU) | Loss of function mutation produced large seeds | https://doi.org/10.1073/pnas.0907024106 |
| Seed size | A04_VARUNA_g3379.t1 | AT2G46660 | ENHANCER 3 OF DA1 (EOD3) | Promotes cell expansion and proliferation of cotyledons maternally, Loss of function mutation produced small seeds Overexpression increased the seed size | https://doi.org/10.1016/j.pbi.2016.05.008 |
| Seed size | B05_VARUNA_g6603.t1 | AT2G46660 | ENHANCER 3 OF DA1 (EOD3) | Promotes cell expansion and proliferation of cotyledons maternally, Loss of function mutation produced small seeds Overexpression increased the seed size | https://doi.org/10.1016/j.pbi.2016.05.008 |
| Seed size | A05_VARUNA_g1832.t1 | AT2G46660 | ENHANCER 3 OF DA1 (EOD3) | Promotes cell expansion and proliferation of cotyledons maternally, Loss of function mutation produced small seeds Overexpression increased the seed size | https://doi.org/10.1016/j.pbi.2016.05.008 |
| Seed size | A03_VARUNA_g3964.t1 | AT3G21220 | MITOGEN ACTIVATED PROTEIN KINASE KINASE 5 (MKK5) | mkk4 mkk5 double mutant contained smaller seeds than the wild type | https://doi.org/10.1104/pp.16.01386 |
| Seed size | A03_VARUNA_g3965.t1 | AT3G21220 | MITOGEN ACTIVATED PROTEIN KINASE KINASE 5 (MKK5) | mkk4 mkk5 double mutant contained smaller seeds than the wild type | https://doi.org/10.1104/pp.16.01386 |
| Seed size | B01_VARUNA_g2935.t1 | AT3G21220 | MITOGEN ACTIVATED PROTEIN KINASE KINASE 5 (MKK5) | mkk4 mkk5 double mutant contained smaller seeds than the wild type | https://doi.org/10.1104/pp.16.01386 |
| Seed size | B01_VARUNA_g2936.t1 | AT3G21220 | MITOGEN ACTIVATED PROTEIN KINASE KINASE 5 (MKK5) | mkk4 mkk5 double mutant contained smaller seeds than the wild type | https://doi.org/10.1104/pp.16.01386 |
| Seed size | A02_VARUNA_g2403.t1 | AT1G75080 | BRASSINAZ OLE- RESISTANT 1 (BZR1) | No significant difference in seed weight, area and shape between gain of function mutant and the wild type | https://doi.org/10.1105/tpc.114.133678 |
| Seed size | B07_VARUNA_g1763.t1 | AT1G75080 | BRASSINAZ OLE- RESISTANT 1 (BZR1) | No significant difference in seed weight, area and shape between gain of function mutant and the wild type | https://doi.org/10.1105/tpc.114.133678 |
| Seed size | A07_VARUNA_g137.t1 | AT2G19500 | CYTOKININ OXIDASE 2 (CKX2) | Transcriptional target of the IKU pathway. Overexpression in iku2-2 mutants caused significant seed enlargement | https://doi.org/10.1186/s12284-015-0070-5 |
| Seed size | B06_VARUNA_g2433.t1 | AT2G19500 | CYTOKININ OXIDASE 2 (CKX2) | Transcriptional target of the IKU pathway. Overexpression in iku2-2 mutants caused significant seed enlargement | https://doi.org/10.1186/s12284-015-0070-5 |
| Seed size | B07_VARUNA_g172.t1 | AT2G19500 | CYTOKININ OXIDASE 2 (CKX2) | Transcriptional target of the IKU pathway. Overexpression in iku2-2 mutants caused significant seed enlargement | https://doi.org/10.1186/s12284-015-0070-5 |
| Oil content | B07_VARUNA_g4392.t1 | AT3G24650 | ABI3 | Overexpression causes enhanced lipid content | https://doi.org/10.1071/fp19260 |
| Oil content | MSTRG.7408.1 | AT3G24650 | ABI3 | Overexpression causes enhanced lipid content | https://doi.org/10.1071/fp19260 |
| Oil content | B03_VARUNA_g2458.t1 | AT2G40220 | ABI4 | Mutants showed TAG accumulation and reduced expression of DGAT1 | https://doi.org/10.1104%2Fpp.111.175950 |
| Oil content | A05_VARUNA_g590.t1 | AT2G40220 | ABI4 | Mutants showed TAG accumulation and reduced expression of DGAT1 | https://doi.org/10.1104%2Fpp.111.175950 |
| Oil content | B05_VARUNA_g6109.t1 | AT2G40220 | ABI4 | Mutants showed TAG accumulation and reduced expression of DGAT1 | https://doi.org/10.1104%2Fpp.111.175950 |
| Oil content | MSTRG.39372.1 | AT3G44460 | bZIP67 / DPBF2 | Overexpression inhibits the expression of FAD3, which results in increased 18:1 and decreased 18:3 levels in seeds | https://doi.org/10.1105/tpc.113.116343 |
| Oil content | A06_VARUNA_g2114.t1 | AT3G44460 | bZIP67 / DPBF2 | Overexpression inhibits the expression of FAD3, which results in increased 18:1 and decreased 18:3 levels in seeds | https://doi.org/10.1105/tpc.113.116343 |
| Oil content | A09_VARUNA_g1148.t1 | AT2G19450 | DGAT1 | Seed-specific overexpression of DGAT1 increases oil content from 11% to 28% | https://doi.org/10.1105/tpc.109.071795 |
| Oil content | A03_VARUNA_g4555.t1 | AT3G51520 | DGAT2 | Mutants show defective TAG biosynthesis | https://doi.org/10.1105/tpc.106.043695 |
| Oil content | A05_VARUNA_g3512.t1 | AT3G12120 | FAD2 | Mutants are deficient in oleate desaturase | https://doi.org/10.1371/journal.pone.0030355 |
| Oil content | A05_VARUNA_g1444.t1 | AT2G29980 | FAD3 | Loss of function mutant show increased activity of C18:2 desaturase and drastically lower C18:3 content in the endoplasmic reticulum | https://doi.org/10.1104%2Fpp.114.4.1533 |
| Oil content | B03_VARUNA_g1718.t1 | AT2G29980 | FAD3 | Loss of function mutant show increased activity of C18:2 desaturase and drastically lower C18:3 content in the endoplasmic reticulum | https://doi.org/10.1104%2Fpp.114.4.1533 |
| Oil content | B05_VARUNA_g4686.t1 | AT2G29980 | FAD3 | Loss of function mutant show increased activity of C18:2 desaturase and drastically lower C18:3 content in the endoplasmic reticulum | https://doi.org/10.1104%2Fpp.114.4.1533 |
| Oil content | B04_VARUNA_g1017.t1 | AT2G29980 | FAD3 | Loss of function mutant show increased activity of C18:2 desaturase and drastically lower C18:3 content in the endoplasmic reticulum | https://doi.org/10.1104%2Fpp.114.4.1533 |
| Oil content | A04_VARUNA_g2237.t1 | AT2G29980 | FAD3 | Loss of function mutant show increased activity of C18:2 desaturase and drastically lower C18:3 content in the endoplasmic reticulum | https://doi.org/10.1104%2Fpp.114.4.1533 |
| Oil content | A03_VARUNA_g1569.t1 | AT2G29980 | FAD3 | Loss of function mutant show increased activity of C18:2 desaturase and drastically lower C18:3 content in the endoplasmic reticulum | https://doi.org/10.1104%2Fpp.114.4.1533 |
| Oil content | A02_VARUNA_g3954.t1 | AT3G26790 | FUS3 | Overexpression increases oil content | https://doi.org/10.1111/tpj.13233 |
| Oil content | B08_VARUNA_g2257.t1 | AT3G26790 | FUS3 | Overexpression increases oil content | https://doi.org/10.1111/tpj.13233 |
| Oil content | B06_VARUNA_g751.t1 | AT3G26790 | FUS3 | Overexpression increases oil content | https://doi.org/10.1111/tpj.13233 |
| Oil content | A06_VARUNA_g3829.t1 | AT3G26790 | FUS3 | Overexpression increases oil content | https://doi.org/10.1111/tpj.13233 |
| Oil content | A02_VARUNA_g1642.t1 | AT5G50700 | HSD1, MID1 | Ectopic expression deprived the accumulation of fatty acids in seed oil bodies | https://doi.org/10.1093/pcp/pcp092 |
| Oil content | B03_VARUNA_g3285.t1 | AT5G50700 | 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_g5986.t1 | AT5G50700 | HSD1, MID1 | Ectopic expression deprived the accumulation of fatty acids in seed oil bodies | https://doi.org/10.1093/pcp/pcp092 |
| Oil content | A03_VARUNA_g2629.t1 | AT5G50700 | HSD1, MID1 | Ectopic expression deprived the accumulation of fatty acids in seed oil bodies | https://doi.org/10.1093/pcp/pcp092 |
| Oil content | A04_VARUNA_g2274.t1 | AT2G30470 | HSI2 / VAL1 | Acts as negative regulator for oil content and seed storage proteins | https://doi.org/10.1073/pnas.0607940104 |
| Oil content | B04_VARUNA_g982.t1 | AT2G30470 | HSI2 / VAL1 | Acts as negative regulator for oil content and seed storage proteins | https://doi.org/10.1073/pnas.0607940104 |
| Oil content | A03_VARUNA_g1603.t1 | AT2G30470 | HSI2 / VAL1 | Acts as negative regulator for oil content and seed storage proteins | https://doi.org/10.1073/pnas.0607940104 |
| Oil content | B03_VARUNA_g1756.t1 | AT2G30470 | HSI2 / VAL1 | Acts as negative regulator for oil content and seed storage proteins | https://doi.org/10.1073/pnas.0607940104 |
| Oil content | MSTRG.15960.1 | AT1G21970 | LEC1 | Loss-of-function cause defects in storage protein and lipid accumulation | https://doi.org/10.1104/pp.108.126342 |
| Oil content | A09_VARUNA_g4072.t1 | AT1G21970 | LEC1 | Loss-of-function cause defects in storage protein and lipid accumulation | https://doi.org/10.1104/pp.108.126342 |
| Oil content | B06_VARUNA_g3502.t1 | AT1G21970 | LEC1 | Loss-of-function cause defects in storage protein and lipid accumulation | https://doi.org/10.1104/pp.108.126342 |
| Oil content | MSTRG.45383.2 | AT1G21970 | LEC1 | Loss-of-function cause defects in storage protein and lipid accumulation | https://doi.org/10.1104/pp.108.126342 |
| Oil content | A09_VARUNA_g3595.t1 | AT1G28300 | 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 | B07_VARUNA_g5614.t1 | AT4G25140 | OLE1 | Deficiency in OLE1 caused a decrease in total lipid content | https://doi.org/10.1105/tpc.106.041269 |
| Oil content | A03_VARUNA_g5249.t1 | AT4G25140 | OLE1 | Deficiency in OLE1 caused a decrease in total lipid content | https://doi.org/10.1105/tpc.106.041269 |
| Oil content | A01_VARUNA_g1620.t1 | AT4G25140 | OLE1 | Deficiency in OLE1 caused a decrease in total lipid content | https://doi.org/10.1105/tpc.106.041269 |
| Oil content | B02_VARUNA_g1185.t1 | AT4G25140 | OLE1 | Deficiency in OLE1 caused a decrease in total lipid content | https://doi.org/10.1105/tpc.106.041269 |
| Oil content | A08_VARUNA_g2121.t1 | AT4G25140 | OLE1 | Deficiency in OLE1 caused a decrease in total lipid content | https://doi.org/10.1105/tpc.106.041269 |
| Oil content | B07_VARUNA_g5614.t1 | AT4G25140 | OLE1 | Deficiency in OLE1 caused a decrease in total lipid content | https://doi.org/10.1105/tpc.106.041269 |
| Oil content | B04_VARUNA_g2151.t1 | AT5G40420 | OLE2 | Suppression in OLE2 causes enlarged oilbodies | https://doi.org/10.1111/j.1365-313x.2008.03553.x |
| Oil content | A04_VARUNA_g1362.t1 | AT5G40420 | OLE2 | Suppression in OLE2 causes enlarged oilbodies | https://doi.org/10.1111/j.1365-313x.2008.03553.x |
| Oil content | A07_VARUNA_g2032.t1 | AT5G40420 | OLE2 | Suppression in OLE2 causes enlarged oilbodies | https://doi.org/10.1111/j.1365-313x.2008.03553.x |
| Oil content | A03_VARUNA_g3061.t1 | AT3G01570 | OLE4 | Negatively regulate the size of oil body | https://doi.org/10.1186/s12870-019-1891-y |
| Oil content | B01_VARUNA_g2620.t1 | AT3G01570 | OLE4 | Negatively regulate the size of oil body | https://doi.org/10.1186/s12870-019-1891-y |
| Oil content | B01_VARUNA_g4359.t1 | AT5G35550 | TT2 | Mutant seeds resulted in enhanced seed FA accumulation and altered FA composition | https://doi.org/10.1104/pp.112.202945 |
| Oil content | B03_VARUNA_g5220.t1 | AT4G09820 | TT8, BHLH42 | Double mutants of BnTT8 produce seeds with elevated seed oil and protein content and altered FA composition | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | B01_VARUNA_g1437.t1 | AT1G61720 | BAN | Negative regulator of flavonoid biosynthesis that prevents pigments accumulation | https://doi.org/10.1046/j.1365-313X.1997.11020289.x |
| Seed coat color | A01_VARUNA_g2946.t1 | AT1G61720 | BAN | Negative regulator of flavonoid biosynthesis that prevents pigments accumulation | https://doi.org/10.1046/j.1365-313X.1997.11020289.x |
| Seed coat color | A01_VARUNA_g3406.t1 | AT1G61720 | BAN | Negative regulator of flavonoid biosynthesis that prevents pigments accumulation | https://doi.org/10.1046/j.1365-313X.1997.11020289.x |
| Seed coat color | B05_VARUNA_g3917.t1 | AT1G53500 | MUM4 | Mucilage synthesis or secretion in the seed coat | https://doi.org/10.1093/jxb/erp102 |
| Seed coat color | A05_VARUNA_g1704.t1 | AT1G53500 | MUM4 | Mucilage synthesis or secretion in the seed coat | https://doi.org/10.1093/jxb/erp102 |
| Seed coat color | A06_VARUNA_g104.t1 | AT1G53500 | MUM4 | Mucilage synthesis or secretion in the seed coat | https://doi.org/10.1093/jxb/erp102 |
| Seed coat color | A06_VARUNA_g613.t1 | AT1G09540 | MYB61 | Mutant seeds lack mucilage extrusion and deposition | https://doi.org/10.1105/tpc.010265 |
| Seed coat color | B06_VARUNA_g5004.t1 | AT1G34790 | TT1 | Mutants display yellow color due to lack of tannin pigments in the seed coat | https://doi.org/10.1101/gad.212702 |
| Seed coat color | A09_VARUNA_g2999.t1 | AT1G34790 | TT1 | Mutants display yellow color due to lack of tannin pigments in the seed coat | https://doi.org/10.1101/gad.212702 |
| Seed coat color | A02_VARUNA_g4188.t1 | AT5G48100 | TT10 | Mutants exhibit delay in seed coat browning due to the oxidation of flavonoids | https://doi.org/10.1105%2Ftpc.105.035154 |
| Seed coat color | A06_VARUNA_g3597.t1 | AT5G48100 | TT10 | Mutants exhibit delay in seed coat browning due to the oxidation of flavonoids | https://doi.org/10.1105%2Ftpc.105.035154 |
| Seed coat color | B05_VARUNA_g1350.t1 | AT3G59030 | 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 | A07_VARUNA_g2393.t1 | AT3G59030 | 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 | MSTRG.4757.2 | AT5G23260 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/tpc.004127 |
| Seed coat color | B08_VARUNA_g1307.t1 | AT5G23260 | TT16 | Accumulates proanthocyanidin in the endothelium | https://doi.org/10.1105/tpc.004127 |
| Seed coat color | B02_VARUNA_g2630.t1 | AT5G17220 | 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 | A02_VARUNA_g716.t1 | AT5G17220 | 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 | B01_VARUNA_g4359.t1 | AT5G35550 | TT2 | Accumulate proanthocyanidins in the endothelium during early seed development | https://doi.org/10.1105/tpc.010098 |
| Seed coat color | B06_VARUNA_g1751.t1 | AT5G42800 | TT3 | Mutants show increased anthocyanin accumulation and have yellow seed coat | https://doi.org/10.1371/journal.pone.0232090 |
| Seed coat color | A10_VARUNA_g2403.t1 | AT5G13930 | TT4 | Involved in the biosynthesis of flavonoids | https://doi.org/10.1046/j.1365-313X.1995.08050659.x |
| Seed coat color | A03_VARUNA_g575.t1 | AT5G13930 | TT4 | Involved in the biosynthesis of flavonoids | https://doi.org/10.1046/j.1365-313X.1995.08050659.x |
| Seed coat color | A02_VARUNA_g536.t1 | AT5G13930 | TT4 | Involved in the biosynthesis of flavonoids | https://doi.org/10.1046/j.1365-313X.1995.08050659.x |
| Seed coat color | B02_VARUNA_g2406.t1 | AT5G13930 | TT4 | Involved in the biosynthesis of flavonoids | https://doi.org/10.1046/j.1365-313X.1995.08050659.x |
| Seed coat color | B08_VARUNA_g4097.t1 | AT5G13930 | TT4 | Involved in the biosynthesis of flavonoids | https://doi.org/10.1046/j.1365-313X.1995.08050659.x |
| Seed coat color | A02_VARUNA_g4226.t1 | AT5G13930 | TT4 | Involved in the biosynthesis of flavonoids | https://doi.org/10.1046/j.1365-313X.1995.08050659.x |
| Seed coat color | B03_VARUNA_g623.t1 | AT5G13930 | TT4 | Involved in the biosynthesis of flavonoids | https://doi.org/10.1046/j.1365-313X.1995.08050659.x |
| Seed coat color | B06_VARUNA_g557.t1 | AT5G13930 | TT4 | Involved in the biosynthesis of flavonoids | https://doi.org/10.1046/j.1365-313X.1995.08050659.x |
| Seed coat color | MSTRG.49249.1 | AT5G07990 | TT7 | Mutants show altered level and patterns of proanthocyanidin deposition in the cell | https://doi.org/10.1104/pp.006189 |
| Seed coat color | B03_VARUNA_g5220.t1 | AT4G09820 | TT8 | Regulates phenylpropanoid synthesis in seed coat | https://doi.org/10.1111/pbi.13281 |
| Seed coat color | A05_VARUNA_g828.t1 | AT2G37260 | TTG2 | Control the production of proanthocyanidin in the inner testa layer | https://doi.org/10.1016/j.ydbio.2016.03.031 |