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Table 4 Candidate genes for promising QTLs

From: Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

TLs Genes in QTL Putative candidate genes Gene annotation SNPs Tolerant hyplotype
qPD18_2.1
qSES18_2.1
15 LOC_Os02g4053 MYB transcription factor 10,224,580,840(A/G) G
10,224,580,869(G/T) G
10,224,581,422(C/T) T
10,224,582,310(C/A) A
LOC_Os02g40730 Ammonium transporter (OsAMT1.3) 10,224,691,455(C/A) A
10,224,691,620(C/T) T
10,224,691,683(T/G) G
10,224,692,377(G/T) G
10,224,692,615(G/A) A
qSKD_3.1
qSNa/K0_3.1
18 LOC_Os03g07450 Homeobox associated leucine zipper 10,303,786,888(C/T) T
LOC_Os03g07480 Sucrose transporter 10,303,802,066(T/G) G
qSNa12_4.1 38 LOC_Os04g33640 Glycosyl hydrolases gene family 10,420,374,274(C/T) T
10,420,376,435(G/A) G
LOC_Os04g33720 Glycosyl hydrolases gene family 10,420,414,566(A/G) G