TABLE 4.
SNPs in candidate genes between the two parents.
| Gene | Position (bp; HAU) |
CRI36 base |
Hai7124 Base |
Mutation type of gene | Effect of SNP | Annotation |
| GH_D03G0980 | 33,195,805 | A | T | 5 Prime UTR premature start codon gain variant | LOW | Probable starch synthase 4, chloroplastic/amyloplastic |
| 33,196,654 | T | C | Synonymous variant | LOW | ||
| GH D03G1091 | 36,671,507 | C | T | Missense variant | MODERATE | Transcription factor PIF7 |
| GH D03G1237 | 40,735,716 | C | A | Missense variant | MODERATE | Endoglucanase 8 |
| 40,742,329 | T | C | Missense variant | MODERATE | ||
| 40,738,388 | C | A | Synonymous variant | LOW | ||
| GH D03G1448 | 45,225,097 | C | T | Stop gained | HIGH | Heat shock cognate 70 kDa protein |
| 45,224,947 | G | C | Missense variant | MODERATE | ||
| 45,223,335 | C | T | Synonymous variant | LOW | ||
| GH D03G1453 | 45,306,561 | G | A | Stop gained | HIGH | Heat shock cognate 70 kDa protein |
| 45,307,072 | C | T | Splice acceptor variant and intron variant | HIGH | ||
| 45,306,618 | T | C | Missense variant | MODERATE | ||
| 45,306,849 | T | C | Missense variant | MODERATE | ||
| 45,307,043 | C | A | Missense variant | MODERATE | ||
| 45,306,838 | T | C | Synonymous variant | LOW | ||
| GH D03G1458 | 45,427,060 | C | T | Synonymous variant | LOW | Ubiquitin-conjugating enzyme E2 7 |
| GH D03G1466 | 45,532,073 | G | A | Missense variant | MODERATE | THO complex subunit 4A |
| 45,533,079 | A | C | Missense variant | MODERATE | ||
| 45,533,104 | A | T | Synonymous variant | LOW | ||
| GH D12G2619 | 59,308,273 | T | C | Synonymous variant | LOW | Transcription factor MYC4 |