Table 5.
Categorization of 53 candidate genes with known biological function that included or were within a 100 kb window of a significant single nucleotide polymorphisms (SNPs) detected in a genome-wide association study (GWAS) for a panel of 470 Oryza sativa accessions, composed of rice diversity panel 1 (RDP1, n = 379) (Eizenga et al., 2014) and the aus subset (n = 91) of the 3,000 rice genome project (Li et al., 2014a).
| # | Gene category | Candidate genes | Total number of genes |
|---|---|---|---|
| 1 | Phytohormone biosynthesis/signaling | Os01g0938900, Os01g0939200, OsNPC2, OsCPT1, OsIAA18, FSM, OsCKX1, CKX4, OsCKX5, VLN4, OsWRKY72 | 11 |
| 2 | Cell wall biosynthesis and defense response | UGT703A1, Os01g0938600, OsWAK43, OsGT43E, OsCCR34, OsXTH27, Os09g0510000 | 7 |
| 3 | Abiotic stress response | Os02g0796000, Os04g0177400, OsSWAP70B, HSP101, Os10g0334500, OsFTIP1 | 6 |
| 4 | Biotic stress response | GPDH2, OsPR2, Os11g0129000, OsWRKY77, ZRP4, Os08g0170700 | 6 |
| 5 | Detoxification | Os02g0584800, Os02g0585100, Os01g0684900, Os01g0939700 | 4 |
| 6 | Nutrient uptake | Os07g0519100, Os07g0519300, OsHAK6 | 3 |
| 7 | Protein synthesis | tRNA-Gln, Os05g0519900, Os05g0520200 | 3 |
| 8 | Sugar transport/metabolism | OsMST7, OsHXK3, Os12g0192500 | 3 |
| 9 | Cellular development | OsSPL19, Os04g0177300 | 2 |
| 10 | DNA damage response/DNA repair | Os01g0939300, OsMUS81 | 2 |
| 11 | Metabolite modification | Os11g0141100, OsCYP93F1 | 2 |
| 12 | mRNA splicing | Os02g0586500 | 1 |
| 13 | Transcription | Os04g0492300 | 1 |
| 14 | Lipid biosynthesis | Os08g0200100 | 1 |
| 15 | rRNA processing | OsRH5 | 1 |
| Total | 53 |
Traits included emergence (%), speed of emergence measured and shoot dry weight measured in a field trial at Los Baños, Philippines in which seed were planted 8 cm deep, and mesocotyl length (ML, cm) measured in a test tube experiment after five days incubation in the dark at 30°C in a controlled environment chamber.