Table 2 Key candidate genes to be knocked out in Oryza longistaminata in order to construct phenotypes suited for specific environments and consumer preferences
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 |
|---|---|---|---|---|---|---|---|
Seed quality (fragrance) | BADH2 | betaine-aldehyde dehydrogenase 2 | Os08g0424500 | LOC_Os08g32870 | Betaine aldehyde dehydrogenase For fragrant rice: knockout | 99.80% (500/501), 0% (0/501) | Bradbury et al. (2005), Chen et al. (2008); Kovach et al. (2009); Usman et al. (2020) |
Eating and cooking quality | Wx | WAXY | Os06g0133000 | LOC_Os06g04200 | Granule-bound starch synthase, synthesis of amylose in endosperm. GT to TT mutation at the 5' splice site of 1st intron leds low amylose. For high amylopectin (sticky rice): knockout | [GT type] | |
Eating and cooking quality | SSII-3 (ALK) | SOLUBLE STARCH SYNTHASE 2–3 (ALKALI DEGENERATION) | Os06g0229800 | LOC_Os06g12450 | Soluble starch synthase II-3, endosperm starch synthesis GC/TT polymorphism at exon8 correlates rice varieties with high or intermediate gelatinization temperature (GT) (possessing the GC allele) and low GT (possessing the TT allele), respectively | [GC type] | |
Grain shape | GS9 | GRAIN SHAPE GENE ON CHROMOSOME 9 | Os09g0448500 | LOC_Os09g27590 | Transcriptional activator For slender grains: knockout For round grains: Upregulation of expression | 95.97% (333/347), 2.59% (9/347) | |
Grain shape | GW7 | GRAIN-WIDTH 7 | Os07g0603300 | LOC_Os07g41200 | TON1 RECRUIT MOTIF (TRM)-containing protein For grain width: knockout of GW7 | 94.04% (268/285), 2.81% (8/285) | Wang et al. (2015) |
Grain shape | GW8 | GRAIN-WIDTH 8 | Os08g0531600 | LOC_Os08g41940 | SBP (SQUAMOSA promoter Binding Protein) DNA binding protein 16 For grain length: knockout of GW8 | 98.94% (931/941), 0.21% (2/941) | Wang et al. (2012) |
Root system architecture | DRO1 | DEEPER ROOTING 1 | Os09g0439800 | LOC_Os09g26840 | IGT gene family, unknown function | 99.60% (250/251), 0% (0/251) | |
Root system architecture | qSOR1 (DRL1) | QTL for SOIL SURFACE ROOTING 1 (DRO1-LIKE 1) | Os07g0614400 | LOC_Os07g42290 | Homolog of DRO1 For drought tolerance: upregulation of DRO1 expression and possession of WT qSOR1 For salinity tolerance: knockout of DRO1 and qSOR1 | 91.18% (279/306), 5.56% (17/306) | |
Flowering time | Hd2 (DTH7) | HEADING DATE2 (Days to heading 7) | Os07g0695100 | LOC_Os07g49460 | Pseudo response regulator, similar to two-component response regulator-like PRR37 | 99.19% (736/742), 0% (0/742) | Zhou et al. (2021) |
Flowering time | Hd5 (DTH8/Ghd8) | HEADING DAT5 (Days to heading8/grain number plant height and heading date 8) | Os08g0174500 | LOC_Os08g07740 | Putative HAP3 subunit of the CCAAT box-binding transcription factor, NF-YB11 (NUCLEAR FACTOR-Y subunit B11)) | 95.17% (276/290), 2.07% (6/290) | Zhou et al. (2021) |
Flowering time | Ehd1 (EF1) | EARLY HEADING DATE 1 (EARLINESS 1) | Os10g0463400 | LOC_Os10g32600 | B-type response regulator | 98.24% (335/341), 0% (0/341) | Zhou et al. (2021) |
Flowering time | RFT1 | RICE FLOWERING-LOCUS T 1 | Os06g0157500 | LOC_Os06g06300 | Florigen | 98.88% (176/178), 0% (0/178) | Zhou et al. (2021) |
Flowering time | Hd3a (FT) | HEADING DATE 3A (Flowering locus T) | Os06g0157700 | LOC_Os06g06320 | Florigen | 100% (178/178), 0% (0/178) | Zhou et al. (2021) |
Flowering time | Hd6 | HEADING DATE 6 | Os03g0762000 | LOC_Os03g55389 | Similar to protein kinase casein kinase II alpha subunit O. longistaminata possesses “Kasalath” type (functional) | (vs. “Kasalath”) 100% (333/333), 0% (0/333) | Takahashi et al. (2001) |
Flowering time | FRRP1 | Flowering-Related RING Protein 1 | Os10g0565600 | LOC_Os10g41590 | E3 ligases of H2Bub1, C3HC4-type RING finger protein | 99.41% (839/844), 0% (0/844) | Du et al. (2016) |