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Table 1 Sixteen QTLs for the GNC, GCC, and C/N ratio of milled rice identified in a single-locus GWAS

From: Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice

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   
GCC qCC-1.1 1 18,333,711 18,405,691 1 rs1_18390016 3.95E-06 LOC_Os01g33410 GJ   
qCC-2.1 2 32,773,074 32,956,207 3 rs2_32881022 2.32E-07 LOC_Os02g53710-LOC_Os02g53720 GJ   
qCC-2.2 2 33,160,172 33,274,475 4 rs2_33,160,172 1.00E-06 LOC_Os02g54120 GJ   
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   NRR; CRCT
qCC-7.1 7 127,781 283,670 23 rs7_144536 3.42E-07 LOC_Os07g01240 GJ   
C/N ratio qCN-1.1 1 1,942,481 1,952,710 2 rs1_1952292 3.05E-07 LOC_Os01g04380 Whole   
qCN-1.2 1 1,959,903 2,123,819 2 rs1_2023817 1.57E-06 LOC_Os01g04540 GJ   
qCN-3.1 3 34,300,375 34,309,240 2 rs3_34300823 1.66E-06 LOC_Os03g60310-LOC_Os03g60340 XI   
qCN-4.1 4 31,985,258 32,185,258 1 rs4_32085258 1.93E-06 LOC_Os04g53850 XI   
qCN-5.1 5 19,481,277 19,681,277 1 rs5_19565967 1.14E-06 LOC_Os05g33340 Whole   OsPPDKB
qCN-5.2 5 25,421,042 25,621,042 1 rs5_25521042 1.52E-06 LOC_Os05g43880-LOC_Os05g43890 XI XI  
qCN-7.1 7 23,515,915 23,515,983 1 rs7_23515974 2.99E-06 LOC_Os07g39280 GJ   OsBZR1
qCN-9.1 9 9,221,280 9,230,703 1 rs9_9222530 5.93E-06 LOC_Os09g15190-LOC_Os09g15200 GJ   
qCN-11.1 11 25,603,546 25,604,997 1 rs11_25,603,546 9.05E-07 LOC_Os11g42510-LOC_Os11g42520 GJ GJ  
  1. aXI and GJ represent Xian/Indica and Geng/Japonica, respectively