Table 3.
Function annotation, sequence variation and gene expression of candidate genes in the qLTG3a region
| Gene RAP IDa | Gene function b | Indel number* | SNP number* | Gene expression level in seeds c |
|---|---|---|---|---|
| Os03g0213300 | Phosphopantetheine attachment site domain containing protein; Hypothetical conserved gene | 1 | 3 | High |
| Os03g0213400 | Similar to RNA helicase | Medium | ||
| Os03g0213500 | Conserved hypothetical protein | High | ||
| Os03g0213600 | Conserved hypothetical protein | 3 | 3 | Medium |
| Os03g0213700 | DUF647 domain containing protein | 1 | Medium | |
| Os03g0213800 | Mitochondrial substrate carrier family protein | 2 | Medium | |
| Os03g0213900 | Conserved hypothetical protein; ROUGH SHEATH2-interacting KH-domain protein | 3 | 3 | Medium |
| Os03g0214000 | Diphosphonucleotide phosphatase 1 precursor; nucleotide pyrophosphatase | 1 | High | |
| Os03g0214050 | Hypothetical protein | no data | ||
| Os03g0214100 | Replication protein A1 | 1 | Low | |
| Os03g0214200 | Mediator of OsbZIP46 deactivation and degradation, Negative regulation of ABA signaling and drought tolerance; Ninja-family protein 1 | Medium | ||
| Os03g0214400 | Digalactosyldiacylglycerol synthase 2 | 4 | High | |
| Os03g0214600 | 26S proteasome subunit RPN9a; 26S proteasome non-ATPase regulatory subunit 13 | 2 | High | |
| Os03g0214900 | Conserved hypothetical protein | 4 | 2 | Medium |
| Os03g0215000 | Integral membrane family protein | High | ||
| Os03g0215200 | Putative transcription factor, Carpel specification, Midrib formation | Low | ||
| Os03g0215400 | MADS-domain-containing protein, sexual reproduction | 1 | Medium | |
| Os03g0215600 | Zinc finger, CCHC retroviral-type domain containing protein | Very low | ||
| Os03g0215700 | Myosin II heavy chain-like family protein | 3 | 1 | Very low |
| Os03g0215800 | Pyridoxal phosphate-dependent enzyme | 1 | Low | |
| Os03g0215900 | 67kD chloroplastic RNA-binding protein, P67 | Low | ||
| Os03g0216000 | Zinc-finger protein KNUCKLES | Very low | ||
| Os03g0216300 | Pentatricopeptide repeat domain containing protein; Hypothetical conserved gene | 1 | Low | |
| Os03g0216400 | Pentatricopeptide repeat domain containing protein | Low | ||
| Os03g0216500 | Conserved hypothetical protein | 1 | Low | |
| Os03g0216600 | Alpha-glucosidase (EC 3.2.1.20) | High | ||
| Os03g0216700 | Citrate transporter, Efficient translocation of Fe | 1 | Medium | |
| Os03g0216733 | Hypothetical protein | no data | ||
| Os03g0216766 | Hypothetical gene | no data | ||
| Os03g0216800 | Polygalacturonase B (Fragment) | 1 | 1 | Very low |
| Os03g0216900 | Prefoldin domain containing protein | Low | ||
| Os03g0217000 | Inhibin beta B chain precursor | 1 | Low | |
| Os03g0217200 | Cyclin-like F-box domain containing protein | Medium | ||
| Os03g0217400 | Conserved hypothetical protein | Low | ||
| Os03g0217801 | Hypothetical gene | no data | ||
| Os03g0217900 | Hypothetical protein | Medium | ||
| Os03g0218100 | Sec63 domain containing protein | no data | ||
| Os03g0218200 | F-box domain containing protein | 1 | Low | |
| Os03g0218300 | Conserved hypothetical protein | 3 | Medium | |
| Os03g0218400 | Similar to Hexose transporter | Low |
*Sequence variation analysis of candidate genes was derived from BSA sequencing data. The number of InDels was derived from the upstream and exonic regions of the candidate genes, and the number of SNPs was derived from the nonsynonymous SNPs in the exonic regions. The ΔSNP-index and ΔInDel-index were greater than 0.8
a,bRAP ID and gene function are based on the Rice Annotation Project Database (RAP-DB): http://rapdb.dna.affrc.go.jp
cThe expression level of candidate genes in seeds was analyzed by the public tool RiceXPro (http://ricexpro.dna.affrc.go.jp/) and divided into four levels