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Table 2 QTNs consistently identified for grain weight and grain shape in at least two years by GWAS

From: Identification and allele mining of new candidate genes underlying rice grain weight and grain shape by genome-wide association study

Trait a QTN b Chr. Lead SNP c Allele d P-value Population/Subgroup Year of QTN detected Known gene
TGW (g) qTGW3.1 3 rs3_4504988 C/T 2.59E-08 Whole 2015, 2016  
qTGW3.2 3 rs3_16733441 T/G 2.25E-08 Whole 2015–2017 GS3 [33]
  3 rs3_16733441 T/G 1.78E-11 Xian 2015–2017  
qTGW5 5 rs5_5371529 C/A 7.22E-10 Whole 2015–2017 qSW5/GW5 [34]
  5 rs5_5361877 T/A 1.38E-10 Xian 2015–2017  
qTGW7 7 rs7_28305040 A/G 8.12E-18 Whole 2015–2017 FZP [35]
  7 rs7_28362557 G/A 7.37E-08 Xian 2015–2017  
  7 rs7_28322588 T/C 1.04E-09 Basmati 2015–2017  
  7 rs7_28287280 A/G 9.14E-12 Aus 2015–2017  
qTGW9 9 rs9_21404841 C/T 2.47E-08 Whole 2015, 2017  
qTGW11 11 rs11_3019935 T/C 5.17E-07 Xian 2016, 2017  
GL (mm) qGL3 3 rs3_16733441 T/G 1.97E-73 Whole 2015–2017 GS3 [33]
  3 rs3_16733441 T/G 8.65E-59 Xian 2015–2017  
  3 rs3_16733441 T/G 2.54E-15 Temperate geng 2016, 2017  
  3 rs3_16733441 T/G 5.16E-09 Tropical geng 2015–2017  
  3 rs3_16728308 C/T 4.75E-09 Aus 2016, 2017  
qGL4 4 rs4_29308534 C/T 1.79E-06 Whole 2015, 2017  
qGL5 5 rs5_5373491 A/G 2.49E-21 Whole 2015–2017 qSW5/GW5 [34]
  5 rs5_5361894 A/G 2.09E-18 Xian 2015–2017  
  5 rs5_5351264 T/A 3.44E-08 Tropical geng 2016, 2017  
  5 rs5_5288638 G/A 2.58E-07 Aus 2015–2017  
qGL7 7 rs7_28289869 T/C 4.62E-19 Whole 2015–2017 FZP [35]
  7 rs7_28287400 C/G 7.12E-07 Xian 2016, 2017  
  7 rs7_28290297 G/A 1.40E-10 Tropical geng 2015–2017  
  7 rs7_28287280 A/G 7.82E-08 Basmati 2016, 2017  
qGL10 10 rs10_13616240 A/C 1.19E-07 Whole 2015–2017  
GW (mm) qGW3 3 rs3_16733441 T/G 6.82E-09 Whole 2015–2017 GS3 [33]
  3 rs3_16717406 G/A 2.21E-08 Xian 2015–2017  
qGW5 5 rs5_5371772 G/A 1.84E-77 Whole 2015–2017 qSW5/GW5 [34]
  5 rs5_5361894 A/G 1.96E-71 Xian 2015–2017  
  5 rs5_5364791 T/C 3.73E-10 Temperate geng 2015–2017  
  5 rs5_5375786 G/A 2.07E-25 Tropical geng 2015–2017  
  5 rs5_5346606 T/A 2.16E-19 Aus 2015–2017  
qGW7 7 rs7_24898274 A/T 2.59E-16 Whole 2015–2017 GL7/GW7 [11, 12]
  7 rs7_24902815 A/G 3.17E-07 Tropical geng 2015–2017  
qGW8 8 rs8_26504638 A/G 3.58E-10 Aus 2016, 2017 GW8 [13]
RLW qRLW1 1 rs1_3657795 A/G 1.42E-07 Aus 2015, 2017  
qRLW3 3 rs3_16733441 T/G 2.50E-55 Whole 2015–2017 GS3 [33]
  3 rs3_16733441 T/G 4.00E-43 Xian 2015–2017  
  3 rs3_16733441 T/G 4.11E-07 Temperate geng 2015–2017  
  3 rs3_16728485 G/C 6.65E-11 Tropical geng 2016, 2017  
  3 rs3_16686074 G/A 7.33E-08 Basmati 2015–2017  
qRLW4 4 rs4_29317460 C/A 3.68E-09 Whole 2015–2017  
  4 rs4_29309086 C/G 1.14E-08 Aus 2015–2017  
qRLW5 5 rs5_5371609 A/G 3.59E-69 Whole 2015–2017 qSW5/GW5 [34]
  5 rs5_5361894 A/G 1.25E-67 Xian 2015–2017  
  5 rs5_5364791 T/C 9.49E-12 Temperate geng 2015–2017  
  5 rs5_5375793 G/A 5.48E-25 Tropical geng 2016, 2017  
  5 rs5_5375764 A/G 5.56E-15 Aus 2015–2017  
qRLW7 7 rs7_24533303 T/C 4.89E-13 Whole 2015–2017 GL7/GW7 [11, 12]
  7 rs7_24537476 C/T 3.67E-07 Xian 2015–2017  
  7 rs7_24902815 A/G 8.02E-07 Tropical geng 2016, 2017  
qRLW8 8 rs8_26504638 A/G 1.17E-14 Aus 2015–2017 GW8 [13]
  1. aTrait abbreviations are as given in the legend to Fig. 1
  2. bA QTN was considered as a local LD block region where the significant trait-associated SNPs were located
  3. cThe SNP with the minimum P-value
  4. dMajor/Minor allele