Table 4.
Trait-associated single nucleotide polymorphisms (SNPs; n = 14) identified by genome-wide association study (GWAS) analyses based on mixed linear models implemented in GAPIT (Lipka et al., 2012), with principal component (PC) analysis and kinship (K) used to account for population structure and relatedness among individuals, respectively.
| Significant SNP | Chr. | Pos. (Mb) | FDR adjusted P-value | PVE | Trait | Env | Candidate gene | Reported locus |
|---|---|---|---|---|---|---|---|---|
| mlid0000953939 | 1 | 4.7 | 0.07 | 14% | Emergence | Field (8 cm): aus | Cytokinin dehydrogenase 1 (OsCKX1) | |
| mlid0005023858 | 1 | 21.7 | 0.08 | 13% | Emergence | Field (8 cm): aus | OsMST7: sugar transport protein | |
| mlid0005272164 | 1 | 22.7 | 0.05 | 15% | Emergence | Field (8 cm): aus | OsWRKY77: positive regulator of disease resistance in plants | |
| mlid0005934063 | 1 | 25.6 | 0.08 | 3% | Emergence, SOE | Field (8 cm): whole panel | UGT703A1 (Glycosyltransferase (GT): plays essential role in cell wall biosynthesis | |
| mlid0011051684 | 2 | 8.5 | 0.07 | 3% | SDW | Field (8 cm): whole panel | tRNA-Gln: glutamyl-tRNA (Gln) amidotransferase subunit A, chloroplastic/mitochondrial | qML-2 (Huang et al., 2010; Liu et al., 2020) |
| mlid0029436447 | 4 | 17.8 | 0.09 | 3% | Emergence | Field (8 cm): whole panel | OsWAK43: wall associated kinase gene. | |
| mlid0031961058 | 4 | 30.4 | 0.05 | 16% | Emergence | Field (8 cm): aus | VLN4: Villin-4 modulation of polar auxin transport | |
| mlid0047351824 | 7 | 2.0 | 0.09 | 3% | Emergence | Field (8 cm): whole panel | OsSWAP70B: protein serine/threonine kinase activity | |
| mlid0054688205 | 8 | 4.1 | 0.08 | 13% | Emergence | Field (8 cm): aus | Os08g0170700: disease resistance protein (RP) | qLOE-8 (Zhang et al., 2006; Liu et al., 2020) |
| mlid0055075459 | 8 | 5.7 | 0.05 | 15% | Emergence | Field (8 cm): aus | Os08g0200100: fatty acid biosynthesis process | |
| mlid0068889536 | 10 | 9.5 | 0.05 | 14% | Emergence | Field (8 cm): aus | Os10g0334500: dirigent protein | |
| mlid0080165050 | 12 | 4.7 | 0.09 | 3% | Emergence | Field (8 cm): whole panel | Os12g0192500: thiamin-phosphate pyrophosphorylase | |
| mlid0081609259 | 12 | 9.9 | 0.08 | 13% | Emergence | Field (8 cm): aus | NRTP1: necrotic root tip 1 (NRTP1) | |
| mlid0081913997 | 12 | 11.1 | 0.05 | 14% | Emergence | Field (8 cm): aus | Os12g0288600: conserved hypothetical protein |
QTL, quantitative trait loci; Chr, chromosome; pos, position (Mb); PVE, phenotypic variance explained (%).
The annotated gene/genes within the 100 kb window of significant SNP with biological function relevant to deep-sowing adaptation traits are considered as candidate genes. 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), representing all the genetic groups of O. sativa, was studied. Traits included emergence (%), speed of emergence (SOE) and shoot dry weight (SDW, g) measured in a field trial at Los Baños, Philippines in which seed were planted 8 cm deep. ‘Whole panel’ indicates SNPs identified from analysis of the whole panel, whereas ‘aus’ were identified from the aus genetic group subset (n = 145).