Table 1 List of genes involved in controlling rice seed structures and grain qualities
From: Genes and Their Molecular Functions Determining Seed Structure, Components, and Quality of Rice
Gene ID | Gene name | Protein category | Effect the quality | References |
|---|---|---|---|---|
Spikelet hull & grain size & grain quality | ||||
G protein pathway | ||||
Os03g0407400 | GS3 | Gγ subunit | Grain length (AQ) | Fan et al. (2006) Mao et al. (2010) Sun et al. (2018a) |
Os09g0441900 | DEP1/qPE9 | Gγ subunit | Grain length (AQ) | Zhou et al. (2009) Huang et al. (2009) |
Os03g0635100 | RGG1 | Gγ subunit | Grain length (AQ) | Tao et al. (2020) |
Os02g0137800 | RGG2 | Gγ subunit | Grain length (AQ) | Miao et al. (2019) |
Os08g0456600 | GGC2 | Gγ subunit | Grain length (AQ) | Sun et al. (2018a) |
Os05g0333200 | D1/RGA1 | Gα subunit | Grain length (AQ) | Fujisawa et al. (1999) Ashikari et al. (1999) Sun et al. (2018a) |
Os03g0669200 | RGB1 | Gβ subunit | Grain length (AQ) | Utsunomiya et al. (2011) Zhang et al. (2021b) |
The ubiquitin–proteasome pathway | ||||
Os02g0244100 | GW2 | E3 ubiquitin ligase | Grain width (AQ) | Song et al. (2007) |
Os02g0244300 | LG1/OsUBP15 | Ubiquitin specific protease | Grain width (AQ) | Shi et al. (2019) |
Os03g0232600 | TUD1 | U-box E3 ubiquitin ligase | Grain length (AQ) | Hu et al. (2013) |
Os02g0512400 | OsGRX8/WG1 | CC-type glutaredoxin | Grain length, grain width (AQ) | Hao et al. (2021) |
Os06g0265400 | OsbZIP47 | bZIP transcription factor | Grain width (AQ) | Hao et al. (2021) |
Os08g0537800 | WTG1/OsOTUB1 | Deubiquitinating enzyme | Grain width, grain thickness (AQ) | Huang et al. (2017) |
Os06g0650300 | GW6a/OslHAT1 | GNAT-like Protein | Grain length (AQ) | Song et al. (2015) Gao et al. (2021) |
Os05g0551000 | CLG1/OsHRZ2 | RING E3 ubiquitin ligase | Grain length (AQ) | Yang et al. (2021b) |
Mitogen-activated protein kinase (MAPK) signaling | ||||
Os02g0787300 | OsMKK4/SMG1 | Mitogen-activated protein kinase kinase | Grain length, grain width (AQ) | Duan et al. (2014) Guo et al. (2018) |
Os06g0154500 | OsMAPK6/DSG1 | Mitogen activated protein kinase | Grain length, grain width (AQ) | Liu et al. (2015b) |
Os04g0559800 | SMG2/OsMKKK10 | Mitogen activated protein kinase kinase kinase | Grain length, grain width (AQ) | Xu et al. (2018) |
Os01g0699500 | OsMKKK70 | Mitogen activated protein kinase kinase kinase | Grain length, grain width (AQ) | Liu et al. (2021) |
Os01g0699600 | OsMKKK62 | Mitogen activated protein kinase kinase kinase | Grain length, grain width (AQ) | Liu et al. (2021) |
Os05g0115800 | OsMKP1/GSN1 | MAPK phosphatase | Grain length, grain width (AQ) | Guo et al. (2018) Xu et al. (2018) |
Phytohormone perception and homeostasis | ||||
Brassinosteroids | ||||
Os03g0602300 | BRD1/OsDWARF | Brassinosteroid biosynthetic enzyme | Grain length (AQ) | Hong et al. (2002) Mori et al. (2002) |
Os10g0397400 | BRD2 | Brassinosteroid biosynthetic enzyme | Grain length (AQ) | Hong et al. (2005) |
Os04g0469800 | D11/ CYP724B1 | Brassinosteroid biosynthetic enzyme | Grain length (AQ) | Tanabe et al. (2005) Zhu et al. (2015) Wu et al. (2016b) Zhou et al. (2017c) |
Os05g0187500 | GW5/GSE5/qGW5 | Calmodulin binding protein | Grain width, chalkiness (AQ) Milled rice rate (MQ) | Weng et al. (2008) Shomura et al. (2008) Liu et al. (2017) Duan et al. (2017) |
Os05g0207500 | OsGSK2 | GSK3/SHAGGY-like kinase | Grain length (AQ) | Tong et al. (2012) |
Os02g0236200 | OsGSK3 | GSK3/SHAGGY-like kinase | Grain length (AQ) | Gao et al. (2019) |
Os07g0580500 | OsBZR1 | Transcription factor in BR pathway | Grain length, grain width, grain thickness (AQ) | Zhu et al. (2015) |
Os02g0517531 | LARGE1/ OML4 | MEI2-like protein | Grain length, grain width (AQ) | Lyu et al. (2020) |
Os06g0127800 | DLT/D62/GS6 | GRAS family protein | Grain width (AQ) | Tong et al. (2009) Sun et al. (2013) |
Os05g0158500 | GS5 | Putative serine carboxypeptidase | Grain width (AQ) | Li et al. (2011) Xu et al. (2015) |
Os05g0343400 | OsWRKY53 | WRKY transcription factor | Grain length, grain width (AQ) | Tian et al. (2017) |
Os08g0174700 | OsBAK1 | BRI1-associated receptor kinase | Grain length, grain width (AQ) | Li et al. (2009) |
Os03g0646900 | GL3.1/GL3-1/qGL3/OsPPKL1 | Ser/Thr phosphatase | Grain width (AQ) | Hu et al. (2012) Qi et al. (2012) Zhang et al. (2012a) Gao et al. (2019) |
Os04g0674500 | OsmiR396d | MicroRNA | Grain length, grain width (AQ) | Miao et al. (2020) |
Os02g0701300 | GS2/GL2/OsGRF4/PT2/ LGS1 | Growth-regulating factor | Grain length, grain width (AQ) | Che et al. (2015) Duan et al. (2015) Hu et al. (2015) Sun et al. (2016) Li et al. (2016) Sun et al. (2016) |
Os05g0458600 | OsLAC | Laccase-like protein | Grain length, grain width (AQ) | Zhang et al. (2013) Zhong et al. (2020) |
Os02g0169400 | OsAGO17 | Argonaute protein | Grain length, grain width (AQ) | Zhong et al. (2020) |
Os09g0448500 | GS9 | Transcriptional activator | Grain width, chalkiness (AQ) | Zhao et al. (2018) |
Os01g0718300 | OsBRI1/D61 | BR receptor kinase | Grain length, grain width (AQ) | Yamamuro et al. (2000) |
Os01g0226700 | OFP1 | OVATE family protein | Grain length, grain width (AQ) | Xiao et al. (2017) |
Os01g0732300 | OFP3 | OVATE family protein | Grain length, grain width (AQ) | Xiao et al. (2020) |
Os01g0864000 | OFP8 | OVATE family protein | Grain length, grain width (AQ) | |
Os05g0324600 | OFP19 | OVATE family protein | Grain length (AQ) | Yang et al. (2018a) |
Os05g0477200 | OFP22 | OVATE family protein | Grain length, grain width (AQ) | Chen et al. (2021) |
Os10g0515400 | GW10 | Cytochrome P450 subfamily protein | Grain length, grain width (AQ) | Zhan et al. (2021) |
Os07g0175100 | POW1 | Homeodomain-like protein | Grain length, grain width (AQ) | Zhang et al. (2021c) |
Auxin | ||||
Os06g0623700 | TGW6 | Protein with IAA-glucose hydrolase activity | Grain length, grain width (AQ) | Ishimaru et al. (2013) Akabane et al. (2021) Kabir and Nonhebel (2021) |
Os03g0175800 | BG1 | Positive regulator of auxin response and transport | Grain length, grain width (AQ) | Liu et al. (2015a) |
Os03g0841800 | qTGW3/GL3.3/qGL6 | GSK3/SHAGGY-like kinase | Grain length, grain width, grain thickness (AQ) | Hu et al. (2018) Xia et al. (2018) Ying et al. (2018) |
Os02g0164900 | OsARF6 | Auxin response factor | Grain length (AQ) | Qiao et al. (2021) |
Os05g0447200 | OsAUX3/qGL5 | Auxin influx carrier | Grain length (AQ) | Qiao et al. (2021) |
GA | ||||
Os06g0266800 | OsGSR1/GW6/OsGASR7 | GA-stimulated protein | Grain length, grain width (AQ) | Shi et al. (2020) |
Cytokinin | ||||
Os01g0680200 | OsPUP4/ BG3 | Purine permease | Grain length, grain width, grain thickness (AQ) | Xiao et al. (2019) Yin et al. (2020) |
Os04g0615700 | OsAGO2 | AGO family protein | Grain length (AQ) | Yin et al. (2020) |
Transcriptional regulatory factors | ||||
SQUAMOSA promoter binding protein-like (SPL) family | ||||
Os07g0505200 | OsSPL13/GLW7 | Squamosa promoter-binding-like protein | Grain length, grain width (AQ) | Si et al. (2016) Segami et al. (2017) |
Os11g0247300 | SRS5/TID1 | Alpha-tubulin protein | Grain length, grain width (AQ) | Sunohara et al. (2009) Segami et al. (2012) Segami et al. (2017) |
Os08g0531600 | qGW8/OsSPL16 | Squamosa promoter binding-like protein | AC, GC (ECQ)) Protein content (NQ) | Wang et al. (2012) Wang et al. (2015a) |
Os07g0603300 | GL7/GW7 | TRM-containing protein | Grain length, grain width, chalkiness (AQ) AC, GC (ECQ)) Protein content (NQ) | Wang et al. (2015c) |
APETALA2-type (AP2) transcription factors | ||||
Os05g0389000 | SMOS1/SHB | AP2-type transcription factor | Grain length, grain width (AQ) | Aya et al. (2014) |
Os07g0235800 | SSH1 | AP2-like transcription factor | Grain length, grain width (AQ) | Jiang et al. (2019) |
Basic helix-loop-helix (bHLH) family | ||||
Os04g0350700 | An-1 | Basic helix-loop-helix protein | Grain length (AQ) | Luo et al. (2013) |
Os03g0171300 | PGL1 | Atypical non-DNA-binding bHLH protein | Grain length (AQ) | Heang and Sassa (2012) |
Other transcription factors | ||||
Os06g0666100 | GL6/SG6 | PLATZ transcription factor | Grain length (AQ) | Wang et al. (2019) Zhou and Xue (2020) |
Os03g0215400 | OsMADS1/qLGY3 | MADS-domain transcription factor | Grain length (AQ) | Yu et al. (2018) |
Os03g0333200 | FLR1 | Receptor-like kinase | Grain width, chalkiness (AQ) | Wang et al. (2021) |
Os01g0769700 | FLR2 | Receptor-like kinase | Grain length (AQ) | Wang et al. (2021) |
Other functional proteins | ||||
Os08g0485500 | GAD1 | Secretory signal peptide | Grain length (AQ) | Jin et al. (2016) |
ORGLA04G0254300 | GL4 | Myb like protein similar to SH4/SHA1 | Grain length (AQ) | Wu et al. (2017) |
Os07g0214300 | RAG2 | 16-kDa α-amylase/trypsin inhibitor | Grain length, grain width (AQ) Protein content, lipid content (NQ) | Zhou et al. (2017b) |
Endosperm components and grain quality | ||||
Starch | ||||
Os06g0133000 | Wx | Granule-bound starch synthase | AC, GC, GT (ECQ) Transparency, chalkiness (AQ) Digestion, RS (NQ) | Wang et al. (2010) Zhang et al. (2019a) Huang et al. (2020) Zhang et al. (2021a) Zhou et al. (2021a) |
Os02g0744700 | OsSSIIb/SSII-2 | Soluble starch synthase | AC, GC, GT (ECQ) Transparency (AQ) Protein content (NQ) | Xu et al. (2020) |
Os06g0229800 | OsSSIIa/SSII-3/ALK | Soluble starch synthase | GT (ECQ) | Umemoto et al. (2002) Gao et al. (2003) Chen et al. (2020) Zhang et al. (2020) |
Os08g0191433 | OsSSIIIa/FLO5 | Soluble starch synthase | Chalkiness (AQ) AC, GC (ECQ) Digestion, RS (NQ) | Fujita et al. (2007) Zhou et al. (2016) |
Os02g0528200 | OsSBEIIb/SBE3 | Starch branching enzyme | Chalkiness (AQ) AC, GC (ECQ) Digestion, RS (NQ) | Zhu et al. (2012) Baysal et al. (2020) Miura et al. (2021) |
Os07g0182000 | OsbZIP58/ RISBZ1 | bZIP transcription factor | Chalkiness (AQ) AC (ECQ) | Yamamoto et al. (2006) Kawakatsu et al. (2009) Wang et al. (2013) |
Os02g0725900 | OsNF-YB1 | Component of the NF-Y/HAP transcription factor complex | Grain length, grain width, chalkiness (AQ) AC (ECQ) Protein content, lipid content (NQ) | Bello et al. (2019) Xu et al. (2021) |
Os10g0191900 | OsNF-YC12/OsNF-YC11 | Nuclear transcription factor Y subunit C | Grain length, grain width, chalkiness (AQ) AC (ECQ) Protein content, lipid content (NQ) | Bello et al. (2019) Xiong et al. (2019) |
Os12g0189500 | OsYUC11 | Flavin-containing monooxygenase | Grain length, grain width, chalkiness (AQ) Protein content, lipid content (NQ) | Xu et al. (2021) |
Os02g0682200 | OsMADS6/AFG1 | MADS-box protein | Grain length, grain width (AQ) AC, GC (ECQ) Protein content (NQ) | Zhang et al. (2010) |
Os02g0170300 | OsMADS29 | MADS-box protein | Shrunken seeds (AQ) AC (ECQ) | Yin and Xue (2012) Nayar et al. (2013) |
Os08g0531700 | OsMADS7/OsMADS45 | MADS-box protein | AC (ECQ) | Zhang et al. (2018a) |
Os01g0104500 | OsNAC20/ONAC020 | NAC transcription factor | Grain width, grain thickness (AQ) Starch content (ECQ) Protein content (NQ) | Wang et al. (2020a) |
Os01g0393100 | OsNAC26/ONAC026 | NAC transcription factor | Grain width, grain thickness (AQ) Starch content (ECQ) Protein content (NQ) | Wang et al. (2020a) |
Os03g0686900 | FLO6 | CBM48 domain-containing protein | Transparency, chalkiness (AQ) Starch content (ECQ) Protein content, lipid content (NQ) | Peng et al. (2014) |
Os07g0688100 | FLO18 | PPR protein | Transparency, chalkiness (AQ) AC, starch content (ECQ) Protein content, lipid content(NQ) | Yu et al. (2021) |
Os03g0168400 | FLO10 | PPR protein | Transparency (AQ) Protein content, lipid content (NQ) | Wu et al. (2019) |
Os08g0290000 | FGR1 | Nuclear-localized PPR protein | Grain thickness, transparency (AQ) AC, starch content (ECQ) | Hao et al. (2019) |
Os03g0728200 | FLO14 | Nuclear-localized PPR protein | Chalkiness (AQ) | Xue et al. (2019) |
Os07g0181000 | OsPK2/PKpα1 | Plastidic pyruvate kinase | Starch content (ECQ) Protein content, lipid content (NQ) | Cai et al. (2018) |
Protein | ||||
Os10g0400200 | OsGluA2/qGPC-10 | Glutelin type-A2 precursor | GC, starch content (ECQ) Protein content (NQ) | Yang et al. (2019) |
Os05g0499100 | Glb1 | 26 kDa α-gloubulin | Seed storage protein (NQ) | Wu et al. (1998) |
Os01g0762500 | GluA1 | Glutelin type-A | Seed storage protein (NQ) | Qu et al. (2008) |
Os02g0249800 | GluB1a | Glutelin type-B | Seed storage protein (NQ) | Wu et al. (1998) |
Os02g0249900 | GluB1b | Glutelin type-B | Seed storage protein (NQ) | Wu et al. (1998) |
Os02g0268300 | GluB4 | Glutelin type-B | Seed storage protein (NQ) | Qu and Takaiwa (2004) |
Os02g0268100 | GluB5 | Glutelin type-B | Seed storage protein (NQ) | Qu et al. (2008) |
Os02g0722400 | OsAAP10 | Amino acid permease | AC, RVA (ECQ) Protein content (NQ) | Wang et al. (2020b) |
Os12g0631100 | OsRab5a/gpa1 | Small GTPase | Chalkiness (AQ) Protein content (NQ) | Ren et al. (2020) |
Os06g0643000 | OsGPA5 | Rab5a effector | Chalkiness (AQ) Protein content (NQ) | Ren et al. (2020) |
Os03g0835800 | GPA3 | Regulator of post-Golgi vesicular Traffic | AC (ECQ) Protein content (NQ) | Ren et al. (2014) |
Os08g0127100 | OsHT/OsLHT1 | Amino acid transporter | AC, GC (ECQ) Protein content (NQ) | Guo et al. (2020a) Guo et al. (2020b) |
Os02g0252400 | RPBF/OsDof3 | Prolamin box binding factor | Starch content (ECQ) Protein content, lipid content (NQ) | Kawakatsu et al. (2009) |
Os07g0668600 | OsGZF1 | CCCH‐type zinc‐finger transcription factor | Glutelin content (NQ) | Chen et al. (2014) |
Lipid/fat | ||||
Os02g0716500 | OsFAD2-1 | Fatty acid desaturase | Lipid content (NQ) | Shi et al. (2012) |
Os12g0104400 | OsFAD3 | Fatty acid desaturase | Lipid content (NQ) | Liu et al. (2012) |
Os03g0369100 | OsLTP36 | Lipid transfer protein | Lipid content (NQ) | Wang et al. (2015b) |
Os04g0436100 | OsACOT | Acyl-CoA thioesterase | Grain length, grain width (AQ) Lipid content (NQ) | Zhao et al. (2019) |
Os08g0110700 | FSE1 | Phospholipase-like protein | Lipid content (NQ) | Long et al. (2018) |
Os01g0172400 | OsPLDα1 | Phospholipase Dα | Phytic acid content (NQ) AC,GT, setback viscosity, viscosity profiles (ECQ) | Khan et al. (2019) Khan et al. (2020) |
Lysine (Amino acids) | ||||
Os01g0927900 | AK2 | Aspartate kinase | Lysine content (NQ) | Yang et al. (2020) |
Os04g0574800 | DHPS | Dihydrodipicolinate synthase | Lysine content (NQ) | Yang et al. (2020) Yang et al. (2021a) |
Os02g0783700 | OsLKR/SDH | Lysine ketoglutarate reductase | Lysine content (NQ) | Yang et al. (2020) |
Fe, Zn (Minerals) | ||||
Os08g0207500 | OsZIP4 | Zinc-regulated transporter | Zinc content (NQ) | Ishimaru et al. (2007b) |
Os05g0472700 | OsZIP5 | Zinc-regulated transporter | Zinc content (NQ) | Lee et al. (2010a) |
Os07g0232800 | OsZIP8 | Zinc-regulated transporter | Zinc content (NQ) | Lee et al. (2010b) |
Os03g0667500 | OsIRT1 | Iron-regulated transporter | Iron content (NQ) | Lee and An (2009) |
Os03g0667300 | OsIRT2 | Iron-regulated transporter | Iron content (NQ) | Nakanishi et al. (2006) |
Os11g0106700 | OsFER1 | Rice ferritin protein | Iron content (NQ) | Stein et al. (2009) |
Os12g0106000 | OsFER2 | Rice ferritin protein | Iron content (NQ) | Stein et al. (2009) |
Os03g0307300 | OsNAS1 | Nicotianamine synthase | Iron content (NQ) | Inoue et al. (2003) |
Os03g0307200 | OsNAS2 | Nicotianamine synthase | Iron content (NQ) | Inoue et al. (2003) |
Os07g0689600 | OsNAS3 | Nicotianamine synthase | Iron content (NQ) | Inoue et al. (2003) |
Os04g0542200 | OsYSL9 | Probable metal-nicotianamine transporter | Iron content (NQ) | Senoura et al. (2017) |
Os04g0463400 | OsVIT1 | Vacuolar membrane transporter | Iron content (NQ) | Zhang et al. (2012b) |
Os09g0396900 | OsVIT2 | Vacuolar membrane transporter | Iron content (NQ) | Zhang et al. (2012b) |
Phytochemicals | ||||
Os08g0424500 | OsBadh2 | Betaine aldehyde dehydrogenasea | 2-AP content (ECQ) | Chen et al. (2006) Chen et al. (2008) Kovach et al. (2009) Bradbury et al. (2010) Hui et al. (2021) |
Embryo and grain quality | ||||
Os07g0603700 | OsGE | Cytochrome P450 | Embryo size (NQ) | Nagasawa et al. (2013) |
Os04g0447800 | OsGAD2 | Glutamate decarboxylase | GABA content (NQ) | Akama and Takaiwa (2007) Akama et al. (2009) |
Os02g0112900 | OsGABA-T | γ-aminobutyrate transaminase | GABA content (NQ) | Shimajiri et al. (2013) |
Os03g0236200 | OsGAD3 | Glutamate decarboxylase | GABA content (NQ) | Akama et al. (2020) |
Aleurone layer and grain quality | ||||
Os05g0509700 | TA1/OsmtSSB1 | Mitochondrion-targeted single-stranded DNA binding protein | Thick aleurone (NQ) | Li et al. (2021) |
Os01g0218032 | TA2-1/OsROS1 | DNA demethylase | Thick aleurone (NQ) | Liu et al. (2018a) |
Seed coat and grain quality | ||||
Os07g0211500 | Rc | bHLH protein | Anthocyanin content (NQ) | Sweeney et al. (2006) |
Os01g0633500 | Rd/OsDFR | Dihydroflavonol reductase | Anthocyanin content (NQ) | Furukawa et al. (2007) |
Os04g0557500 | Kala4/OsB2 | bHLH transcription factor | Anthocyanin content (NQ) | Oikawa et al. (2015) |
Os06g0205100 | OsC1 | MYB transcriptional activator | Anthocyanin content (NQ) | Sun et al. (2018b) |
Os02g0682500 | OsTTG1 | WD40 repeat protein | Anthocyanin content (NQ) | Yang et al. (2021c) |