Table 1 Sixteen QTLs for the GNC, GCC, and C/N ratio of milled rice identified in a single-locus GWAS
Traits | QTL | Chromosome | Start (bp) | End (bp) | No. of significant SNP | Lead SNP | P value of lead SNP | Lead SNP located/flanking genes | Detected panelsa | Detected panels by multiple-locus GWAS | Known related genes |
|---|---|---|---|---|---|---|---|---|---|---|---|
GNC | qNC-1.1 | 1 | 2,931,216 | 2,967,102 | 3 | rs1_2956867 | 1.38E-06 | LOC_Os01g06210-LOC_Os01g06220 | Whole | Â | Â |
GCC | qCC-1.1 | 1 | 18,333,711 | 18,405,691 | 1 | rs1_18390016 | 3.95E-06 | LOC_Os01g33410 | GJ | Â | Â |
qCC-2.1 | 2 | 32,773,074 | 32,956,207 | 3 | rs2_32881022 | 2.32E-07 | LOC_Os02g53710-LOC_Os02g53720 | GJ | Â | Â | |
qCC-2.2 | 2 | 33,160,172 | 33,274,475 | 4 | rs2_33,160,172 | 1.00E-06 | LOC_Os02g54120 | GJ | Â | Â | |
qCC-5.1 | 5 | 19,481,277 | 19,681,277 | 1 | rs5_19566944 | 1.44E-06 | LOC_Os05g33340 | XI | Whole | OsPPDKB | |
qCC-5.2 | 5 | 29,438,881 | 29,580,663 | 8 | rs5_29562689 | 7.43E-08 | LOC_Os05g51550-LOC_Os05g51560 | Whole | Â | NRR; CRCT | |
qCC-7.1 | 7 | 127,781 | 283,670 | 23 | rs7_144536 | 3.42E-07 | LOC_Os07g01240 | GJ | Â | Â | |
C/N ratio | qCN-1.1 | 1 | 1,942,481 | 1,952,710 | 2 | rs1_1952292 | 3.05E-07 | LOC_Os01g04380 | Whole | Â | Â |
qCN-1.2 | 1 | 1,959,903 | 2,123,819 | 2 | rs1_2023817 | 1.57E-06 | LOC_Os01g04540 | GJ | Â | Â | |
qCN-3.1 | 3 | 34,300,375 | 34,309,240 | 2 | rs3_34300823 | 1.66E-06 | LOC_Os03g60310-LOC_Os03g60340 | XI | Â | Â | |
qCN-4.1 | 4 | 31,985,258 | 32,185,258 | 1 | rs4_32085258 | 1.93E-06 | LOC_Os04g53850 | XI | Â | Â | |
qCN-5.1 | 5 | 19,481,277 | 19,681,277 | 1 | rs5_19565967 | 1.14E-06 | LOC_Os05g33340 | Whole | Â | OsPPDKB | |
qCN-5.2 | 5 | 25,421,042 | 25,621,042 | 1 | rs5_25521042 | 1.52E-06 | LOC_Os05g43880-LOC_Os05g43890 | XI | XI | Â | |
qCN-7.1 | 7 | 23,515,915 | 23,515,983 | 1 | rs7_23515974 | 2.99E-06 | LOC_Os07g39280 | GJ | Â | OsBZR1 | |
qCN-9.1 | 9 | 9,221,280 | 9,230,703 | 1 | rs9_9222530 | 5.93E-06 | LOC_Os09g15190-LOC_Os09g15200 | GJ | Â | Â | |
qCN-11.1 | 11 | 25,603,546 | 25,604,997 | 1 | rs11_25,603,546 | 9.05E-07 | LOC_Os11g42510-LOC_Os11g42520 | GJ | GJ | Â |