Table 3.
Quantitative trait loci (QTL; n = 21) for emergence (EMERG, %), speed of emergence (SOE) and shoot dry weight (SDW, g) were measured in a field trial at Los Baños, Philippines, in which seeds were planted 8 cm deep, and for 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.
| QTL | Lead SNP | Chr. | Pos. (Mb) | FDR adjusted P-value | PVE | Candidate gene | Reported Locus |
|---|---|---|---|---|---|---|---|
| qSDW-1.1 | mlid0006464909 | 1 | 28.2–28.2 | 0.05 | 2.9–3.1 | Os01g0684900 | |
| qSDW-IND-1.1 | mlid0006467086 | 1 | 28.2–28.2 | 0.08 | 8.7–8.9 | Os01g0684900 | |
| qEMERG-AUS-1.1 | mlid0007349026 | 1 | 32.8–33.3 | 0.05 | 13.6–15.9 | OsCKX5, Os01g0775500 | |
| qSOE-1.1 | mlid0008395331 | 1 | 37.6–38.4 | 0.05 | 2.7–2.8 | FSM | qML1.4 (Xiong et al., 2017; Wang et al., 2021b) |
| qEMERG-AUS-1.2 | mlid0008927838 | 1 | 40.9–41.7 | 0.03 | 13.2–17.8 | OsHAK6, Os01g0938600, Os01g0938900, Os01g0939200, Os01g0939300, GPDH2, Os01g0939700, CKX4, OsHXK3, OsPR2, OsMUS81, OsNPC2 | qMel-1 (Cao et al., 2002; Wu et al., 2015a), and seq-rs609 (for shoot length) (Dang et al., 2014; Lu et al., 2016) |
| qEMERG-AUS-2.1 | mlid0014164785 | 2 | 20.9–22.6 | 0.05 | 3.0–14.0 | Os02g0556100, OsCPT1, Os02g0586500 | |
| qEMERG-2.1 | mlid0014379250 | 2 | 22.4–22.6 | 0.04 | 2.6–3.9 | Os02g0584800, Os02g0585100 | |
| qSOE-2.1 | mlid0014379250 | 2 | 22.5–22.6 | 0.04 | 2.6–3.7 | Os02g0584800, Os02g0585100 | |
| qSDW-2.1 | mlid0016678899 | 2 | 33.8–33.9 | 0.07 | 2.8–3.0 | Os02g0796000 | |
| qSDW-IND-4.1 | mlid0026230401 | 4 | 5.3–5.3 | 0.04 | 8.8–10.0 | Os04g0177300, Os04g0177400 | |
| qSDW-IND-4.2 | mlid0030902086 | 4 | 24.5–24.7 | 0.09 | 9.0–9.0 | Os04g0492300 | |
| qEMERG-AUS-5.1 | mlid0038926320 | 5 | 25.8–27.9 | 0.05 | 13.1–16.0 | HSP101, Os05g0519900, Os05g0520200, OsIAA18, OsGT43E | seq-rs2638 (Lu et al., 2016) |
| qEMERG-AUS-6.1 | mlid0045621374 | 6 | 24.5–24.6 | 0.05 | 14.4–16.2 | OsCYP93F1, OsFTIP1 | |
| qEMERG-AUS-7.1 | mlid0049755165 | 7 | 11.9–12.6 | 0.05 | 13.4–14.6 | Os07g0300900-OsRH5 | qFML7.1 (Zhao et al., 2018; Liu et al., 2020) |
| qEMERG-7.1 | mlid0051610551 | 7 | 19.0–20.0 | 0.05 | 2.6–2.9 | Os07g0519100, Os07g0519300 | |
| qML-9.1 | mlid0065562882 | 9 | 19.7–19.8 | 0.05 | 3.0–3.0 | Os09g0510000, Os09g0510200, OsCCR3, HMGR3 | |
| qEMERG-AUS-10.1 | mlid0066458929 | 10 | 1.1–1.2 | 0.05 | 15.3–16.2 | OsXTH27, Os10g0117400, ZRP4, Os10g0118800 | |
| qEMERG-AUS-11.1 | mlid0072207246 | 11 | 1.4–1.9 | 0.05 | 15.0–15.0 | Os11g0141100 | |
| qEMERG-AUS-11.2 | mlid0076143945 | 11 | 17.4–17.4 | 0.05 | 14.5–15.2 | OsWRKY72 | |
| qSDW-11.1 | mlid0076168099 | 11 | 17.0–17.6 | 0.01 | 3.0–15.0 | OsSPL19, OsWRKY72, OsENODL22, Os11g0491600, Os11g0492300 | |
| qSDW-IND-11.1 | mlid0076168461 | 11 | 17.3–17.6 | 0.02 | 8.6–14.3 | OsSPL19, OsWRKY72, OsENODL22, Os11g0491600, Os11g0492300 |
QTL, quantitative trait loci; Chr, chromosome; pos, position (Mb); PVE, phenotypic variance explained (%).
Significant single nucleotide polymorphisms (SNPs) identified by genome-wide association study (GWAS) analyses based on mixed linear modelsimplemented 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. A genomic region was defined as a QTL if two or more significant marker-trait association (SNPs) were found in a 100 kb window around the lead SNP. 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. QTL without a suffix were identified from analysis of the whole panel, whereas those with the AUS suffix were identified from the aus genetic group subset (n = 145) and ‘IND’ from the aus + indica (INDICA varietal group) subset (n = 224). The candidate genes in each QTL region were identified using annotations on lead SNP of the QTL, considering the genes that falls under 100 kb window of lead SNP.