Table 1 Key candidate genes to be knocked out in Oryza longistaminata in order to construct phenotypes with high agronomic value
Trait | Gene name | CGSNL1 gene name or gene name synonym(s) | RAP2 ID | MSU3 ID | Description | Similarity and gaps to O. sativa [or haplotype] | References |
|---|---|---|---|---|---|---|---|
Plant architecture | SD1 | SEMI DWARF 1 | Os01g0883800 | LOC_Os01g66100 | GA 20-oxidase2 Highly active GR type (Kuroha et al. 2018) | 98.23% (388/395), 1.52% (6/395) | |
Plant architecture | PROG1 | PROSTRATE GROWTH 1 | Os07g0153600 | LOC_Os07g05900 | Zinc-finger nuclear transcription factor. Deletion of tandem repeat genes (7/8) promoted erect growth and high yield of Asian cultivated rice | [O. longistaminata possesses 10 zinc-finger genes] | |
Plant architecture | TAC1 (SPK) | Tiller angle control 1 (SPREADING STUB of “Kasalath”) | Os09g0529300 | LOC_Os09g35980 | Unknown functionSplicing site of 3'UTR of O. longistaminata is indica TAC1 type (high expression type) | 98.84% (256/259), 0% | |
Plant architecture | D10 (OsCCD8) | DWARF10 (carotenoid cleavage dioxygenase 8) | Os01g0746400 | LOC_Os01g54270 | Carotenoid cleavage dioxygenase 8, strigoractone (SL) biosynthesis | 98.07% (559/570), 0.53% (3/570) | Minakuchi et al. (2010) |
Plant architecture | OsFC1 (TB1) | FINE CULM 1 (teosinte-branching 1) | Os03g0706500 | LOC_Os03g49880 | TCP family transcription factor. FC1 function is required for SL to exert its effect of inhibiting bud outgrowth | 97.55% (318/326), 1.53% (5/326) | Minakuchi et al. (2010) |
Plant architecture and yield | OsPDCD5 | Programmed cell death 5 | Os05g0547850 | LOC_Os05g47446 | Homolog of the mammalian programmed cell death protein 5 | 99.22% (128/129), 0% | Dong et al. (2021) |
Shattering | qSH1 | Shattering (QTL)-1 | Os01g0848400 | LOC_Os01g62920 | BEL1-type homeobox family | 98.37% (605/615), 0.98% (6/615) | |
Shattering | Sh4 | SHATTERING 4 | Os04g0670900 | LOC_Os04g57530 | Trihelix transcription factor, Myb/SANT-LIKE 23 | 96.71% (382/395), 1.77% (7/395) | Li et al. (2006) |
Shattering | Sh5 | SHATTERING 5 | Os05g0455200 | LOC_Os05g38120 | BELL1-type homeodomain transcription factor | 97.94% (570/582), 1.20% (7/582) | Yoon et al. (2014) |
Shattering | SHAT1 | SHATTERING ABORTION 1 | Os04g0649100 | LOC_Os04g55560 | APETALA2 transcription factor | 97.01% (455/469), 1.71% (8/469) | Zhou et al. (2012) |
Seed dormancy | Sdr4 | SEED DORMANCY 4 | Os07g0585700 | LOC_Os07g39700 | Zinc finger protein | 96.73 (325/336), 1.79% (6/336) | Sugimoto et al. (2010) |
Awn | LABA1 (LOGL6/An-2) | LONG AND BARBED AWN 1 (LOG-like 6/Awn-2) | Os04g0518800 | LOC_Os04g43840 | Cytokinin synthesis enzyme | 100% (251/251), 0% (0/251) | Hua et al. (2015) |
Awn | RAE2 (OsEPFL1) | REGULATOR OF AWN ELONGATION 2 (EPIDERMAL PATTERNING FACTOR-LIKE 1) | Os08g0485500 | LOC_Os08g37890 | Epidermal patterning factor-like 1 (EPFL1) protein, small secretary signal peptide O. longistaminata possesses O. glaberrima type (6C) | (vs. O. glaberrima) 90.77% (118/130), 6.92% (9/130) | Bessho-Uehara et al. (2018) |
Seed colouration | Phr1 (BHC) | Phenol reaction 1 (BLACK HULL C) | Os04g0624500 | LOC_Os04g53300 | Polyphenol oxidase | 95.59% (563/589), 3.23% (19/589) | Yu et al. (2008) |
Seed coat colouration | Rc | - | Os07g0211500 | LOC_Os07g11020 | Basic helix-loop-helix (bHLH) protein, proanthocyanidin synthesis | (vs O. rufipogon) 96.76% (656/678), 1.92% (12/678) | |
Seed coat colouration | Rd | RED PERICARP AND SEED COAT | Os01g0633500 | LOC_Os01g44260 | Dihydroflavonol-4-reductase (DFR), proanthocyanidin synthesis | 98.25% (280/285), 1.95% (3/285) | Konishi et al. (2008) |
Seed quality | Chalk5 | - | Os05g0156900 | LOC_Os05g06480 | Vacuolar H+-translocating pyrophosphatase | 98.19% (760/774), 1.29% (10/774) | Li et al. (2014) |
Grain shape | GW2 | GRAIN WEIGHT 2 | Os02g0244100 | LOC_Os02g14720 | RING-type E3 ubiquitin ligase | 99.76% (423/424), 0% (0/424) | Song et al. (2007) |
Grain shape | GL3.1 | GRAIN LENGTH 3.1 | Os03g0646900 | LOC_Os03g44500 | Protein phosphatase with Kelch-like repeat domain | 100% (1004/1004), 0% (0/1004) | Zhang et al. (2012) |
Grain shape | TGW3 | THOUSAND GRAIN WEIGHT 3 | Os03g0841800 | LOC_Os03g62500 | GLYCOGEN SYNTHASE KINASE 3/SHAGGY-like family | 99.76% (423/424), 0% (0/424) | Ying et al. (2018) |
Grain shape | TGW6 | TOTAL GRAIN WEIGHT6 | Os06g0623700 | LOC_Os06g41850 | Indole-3-acetic acid (IAA)-glucose hydrolase activity | 98/86% (346/350), 0% (0/350) | Ishimaru et al. (2013) |
Grain shape | LK3 (GS3/qGL3a) | LONG KERNEL 3 (GRAIN SIZE 3) | Os03g0407400 | - | Plant-specific organ size regulation (OSR) domain, transmembrane region | 92.50% (222/240), 5% (12/240) | Mao et al. (2010) |
Grain shape | APG (PIL16) | ANTAGONIST OF PGL1 (PHYTOCHROME INTERACTING FACTOR-LIKE 16) | Os05g0139100 | LOC_Os05g04740 | Typical DNA-binding bHLH protein | 88.27% (444/503), 3.38% (17/503) | |
Grain shape and panicle architecture | SG1 | SHORT GRAIN 1 | Os09g0459200 | LOC_Os09g28520 | Unknown product, brassinosteroid signalling | 98.10% (155/158), 0.63% (1/158) | Nakagawa et al. (2012) |
Panicle architecture | LG1 | LIGULELESS 1 | Os04g0656500 | LOC_Os04g56170 | SBP (SQUAMOSA promoter Binding Protein) DNA binding protein 8 | 98.90% (411/416), 0% (0/416) | |
Panicle architecture | Gn1a | GRAIN NUMBER 1A | Os01g0197700 | LOC_Os01g10110 | Cytokinin oxidase/dehydrogenase 2 | 97.89% (557/569), 1.23% (7/569) | Ashikari et al. (2005) |
Panicle architecture | EP2 (DEP2) | ERECT PANICLE 2 (DENSE AND ERECT PANICLE 2) | Os07g0616000 | LOC_Os07g42410 | Transcriptional regulator | 99.05% (1354/1367), 0.15% (2/1367) | Zhu et al. (2010) |
Cadmium ion tolerance | OsCd1 | - | Os03g0114800 | LOC_Os03g02380 | Major facilitator superfamily protein, Cd uptake | 100% (457/457), 0% (0/457) | Yan et al. (2019) |
Cadmium ion tolerance | CAL1 | CADMIUM ACCUMULATION IN LEAF 1 | Os02g0629800 | LOC_Os02g41904 | Defensin-like protein, positive regulation of Cd accumulation in rice leaves | 100% (80/80), 0% (0/80) | Luo et al. (2018) |
Flooding tolerance | OsCBL10 | calcineurin B-like protein10 | Os01g0711500 | LOC_Os01g51420 | Calcineurin B-like protein, calcium sensor, flooding response during seed germination | 99.62% (265/266), 0% (0/266) | Ye et al. (2018) |
Salt tolerance | SIT1 | SALT INTOLERANCE1 | Os02g0640500 | LOC_Os02g42780 | Lectin receptor-like kinase, mediation of salt sensitivity, regulation of ethylene homeostasis | 98.37% (663/674), 0.15% (1/674) | Li et al. (2014) |
Drought and salt tolerance | DST | DROUGHT AND SALT TOLERANCE | Os03g0786400 | LOC_Os03g57240 | C2H2 zinc finger transcription factor | 93.57% (291/311), 4.50% (14/311) | Santosh Kumar et al. (2020) |
Drought and salt tolerance | DCA1 | DST CO-ACTIVATOR 1 | Os10g0456800 | LOC_Os10g31850 | CHY zinc finger protein, transcriptional co-activator of DST | 98.87% (263/266), 0% (0/266) | Cui et al. (2015) |