Table 1. Summary of candidate genes and local linkage disequilibrium region underlying the most significant using the interaction model.
| Chr. | Pop. | Time interval for days after treatment | QTL region (bp) | SNP ID | P-value | Candidate gene |
|---|---|---|---|---|---|---|
| 3 | aus | 2-6 | 8857549 | SNP-3.8856486. | 1.42 × 10-8 | Os03g16070 (expressed protein) |
| 8878386..8907753 | in LD region | Os03g16334 (fringe-related protein) | ||||
| 8891188..8907753 | in LD region | Os03g16120 (myosin heavy chain-related)Os03g16130 (calcium/Calmodulin dependent kinase)Os03g16140 (digalactosyldiacylglycerol synthase, chloroplast precursor) | ||||
| 8907753..9120385 | in LD region | Region with several candidate genes | ||||
| 8994756..9034370 | in LD region | Region with several candidate genesOs03g16350 (DNA-binding protein) | ||||
| 5 | aus | 2-6 | 3243210..3280158 | in LD region | Region with several candidate genes | |
| 3280158..3307505 | in LD region | Region with several candidate genes Os05g06430 (OsPDIL2-1 protein disulfide isomerase PDIL2-1) | ||||
| 8122862.. 8307465 | in LD region | Region with several candidate genes | ||||
| 8917080..9056046 | in LD region | Region with several candidate genesOs05g15890 (SNF2 family N-terminal domain containing protein)Os05g15920 and Os05g15880(glycosyl hydrolase, putative expressed) | ||||
| 5 | aus | 2-6 | 23407227..23536238 | in LD region | Region with several candidate genesOs05g39850 (MCM3 - Putative minichromosome maintenance MCM complex subunit 3)Os05g39870 (CAMK_KIN1 calcium/calmodulin dependent protein kinase)Os05g39900 (CBL-interacting serine/threonine-protein kinase 15) | |
| 23626677..24249943 | in LD region | Region with several candidate genes | ||||
| 2-9 and 6-9 | 26826818..26934016 | in LD region | Region with several candidate genesOs05g46320 (OsFBX173 - F-box domain containing protein)Os05g46290 (T-complex protein, putative)Os05g46350 (IQ calmodulin-binding motif domain containing protein)Os05g46490 (hydrolase, alpha/beta fold family domain containing protein) | |||
| 27319587 | SNP-5.27256942. | 7.15 × 10-7 | Os05g47670 (zinc finger, C3HC4 type domain containing protein) | |||
| 28178747 | SNP-5.28116101. | 4.16 × 10-7 | Os05g49120 (NLI interacting factor-like phosphatase) | |||
| 8 | INDAUS | 2-6 | 10911095..11107666 | in LD region | Region with several candidate genes | |
| Os08g18920 (protein kinase) | ||||||
| Os08g18740 (zinc knuckle-family protein) | ||||||
| 10745000..10844000 | in LD region | Region with several candidate genes | ||||
| 13032730..13630347 | SNP-8.13627631. | 1.36 × 10-6 | ||||
| 20997000..21064000 | in LD region | |||||
| 11 | Indica | 2-6 and 2-9 | 2789940..2795848 | SNP-11.2785843 | 3.54 × 10-6 | Os11g05930 (response regulator receiver domain containing protein, expressed) |
| SNP-11.2791751 | 3.22 × 10-7 | - | ||||
| 2-6 | 3629008..3765215 | in LD region | Region with several candidate genes | |||
| SNP-11.3631311. | 3.03 × 10-7 | Os11g07230 (receptor kinase) | ||||
| SNP-11.3637597. | 3.03 × 10-7 | Os11g07240 (serine/threonine-protein kinase BRI1-like 2 precursor) | ||||
| in LD region | Os11g05930 (response regulator receiver domain) | |||||
| Os11g05935 (mucin) |
Chr., chromosome; GWAS, genome-wide association study; LD, linkage disequilibrium; MLM, mixed linear model; Pop,, population QTL, quantitative trait loci; SNP, single-nucleotide polymorphism. All the significant associations are presented for the three diversity panels (indica, aus and INDAUS) and intervals (2-9; 2-6; 6-9; 9-13 days after treatment). Statistical significance of the GWAS associations were determined using the Bonferroni-adjusted threshold of α=0.05, which corresponded to P=8.99 × 10−6, 2.57 × 10−6 and 3.02 × 10−6 for the INDAUS, indica and aus sub-populations respectively.