Table 3 Key candidate genes in Oryza longistaminata to be targeted for introducing mutations in the cis region of the promoter
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 | MOC1 | MONOCULM 1 | Os06g0610300 | LOC_Os06g40780 | GRAS protein 33 | 97.75% (434/444), 1.13% (5/444) | Li et al. (2003) |
Seed quality | GluA2 | GLUTELIN SUBFAMILY A2 FROM WILD RICE SPECIES | Os10g0400200 | LOC_Os10g26060 | Seed storage protein GLUTELIN | 99.60% (498/500), 0% (0/500) | Yang et al. (2019) |
Seed quality | GIF1 (CIN2) | GRAIN INCOMPLETE FILLING 1 (cell-wall invertase 2) | Os04g0413500 | LOC_Os04g33740 | Cell-wall invertase | 98.17% (590/601), 0.50% (3/601) | Wang et al. (2008) |
Grain shape | PGL1 (ILI6) | POSITIVE REGULATOR OF GRAIN LENGTH 1 (INCREASED LEAF INCLINATION 6) | Os03g0171300 | LOC_Os03g07510 | Atypical non-DNA-binding bHLH protein | 100% (92/92), 0% (0/92) | |
Grain shape | GS2 | GRAIN SIZE 2 | Os02g0701300 | LOC_Os02g47280 | Growth-Regulating Factor 4 (GRF4) | 98.41% (309/314), 0% (0/314) | Li et al. (2018) |
Grain shape | BG1 | BIG GRAIN1 | Os03g0175800 | LOC_Os03g07920 | Positive regulator of auxin response and transport | 98.08% (307/313), 1.28% (4/313) | Liu et al. (2015) |
Grain shape | LG1 | LARGE GRAIN 1 | Os02g0244300 | LOC_Os02g14730 | Ubiquitin-specific protease 15, deubiquitination enzyme | 99.69% (972/975), 0% (0/975) | Shi et al. (2019) |
Grain shape | GLW7 | GRAIN LENGTH AND WEIGHT ON CHROMOSOME 7 | Os07g0505200 | LOC_Os07g32170 | SBP (SQUAMOSA promoter Binding Protein) DNA binding protein 13 | 95.50% (212/222), 2.70% (6/222) | Si et al. (2016) |
Panicle architecture | NOG1 | NUMBER OF GRAINS 1 | Os01g0752200 | LOC_Os01g54860 | Enoyl-CoA hydratase/isomerase | 99.74% (382/383), 0% (0/383) | Huo et al. (2017) |
Panicle architecture | DEP1 | DENSE AND ERECT PANICLE 1 | Os09g0441900 | LOC_Os09g26999 | Unknown phosphatidylethanolamine-binding protein (PEBP) like domain protein | 96.56% (421/436), 2.29% (10/436) | |
Panicle architecture | GGC2 | - | Os08g0456600 | - | G Protein gamma subunit | 97.33% (328/337), 0.59% (2/337) | Sun et al. (2018) |
Nutrient uptake and photosynthesis | AHA1 (OSA1) | H + -ATPASE 1 | Os03g0689300 | LOC_Os03g48310 | Plasma membrane H+-ATPase 1, regulation of ammonium (NH4+) uptake | 99.58% (952/956), 0% (0/956) | Zhang et al. (2021) |