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Table 3 Loci detected for eating and cooking qualities in Panel 1 and Panel 2

From: Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.)

Trait    Panel1 Panel 2
Chr. Position P value MAFa R squareb P value MAFa R squareb
AAC 6 1765761 5.29 × 10−11 0.436 0.152    
6 1585864     9.21 × 10−8 0.052 0.231
9 19310549     2.32 × 10−7 0.143 0.214
PRO 5 12559930 1.57 × 10−7 0.110 0.242    
11 22563596 2.47 × 10−6 0.092 0.190    
PV 1 5102566     6.31 × 10−5 0.155 0.118
2 29640874 7.77 × 10−5 0.136 0.118    
5 7944999     4.15 × 10−5 0.086 0.125
6 1666386 2.86 × 10−5 0.177 0.133    
7 16503569     1.62 × 10−5 0.194 0.139
HPV 1 3541593     1.72 × 10−5 0.164 0.169
1 27287504 3.51 × 10−5 0.082 0.127    
2 29640874 5.22 × 10−5 0.136 0.121    
5 7944999     2.88 × 10−5 0.086 0.159
6 1750498 5.19 × 10−6 0.141 0.157    
7 16506178     2.63 × 10−5 0.181 0.161
11 27792076     6.92 × 10−6 0.147 0.186
CPV 1 3541593     4.78 × 10−6 0.164 0.178
4 27772775 1.59 × 10−5 0.336 0.130    
6 1750498 3.78 × 10−5 0.141 0.118    
7 16506178     4.68 × 10−6 0.181 0.178
9 15417525 2.31 × 10−5 0.282 0.125    
11 192690 4.16 × 10−5 0.136 0.116    
BD 2 8596549     5.57 × 10−5 0.138 0.102
6 1765761 1.16 × 10−5 0.441 0.183    
6 1985864     9.85 × 10−5 0.052 0.095
SB 4 24056499     1.09 × 10−6 0.125 0.165
6 1765761 2.39 × 10−8 0.441 0.261    
CS 1 30627943 1.98 × 10−5 0.214 0.111    
6 1765761 2.41 × 10−6 0.441 0.138    
9 15474876 2.19 × 10−5 0.277 0.110    
11 24255295 1.96 × 10−5 0.118 0.111    
PeT 2 24259382     7.68 × 10−5 0.086 0.115
2 27305077 1.11 × 10-5 0.055 0.131    
3 33893179 1.12 × 10−5 0.068 0.131    
6 21443081 8.35 × 10−6 0.059 0.135    
10 23087051 9.69 × 10−6 0.132 0.133    
PTemp 6 6757255 1.54 × 10−8 0.491 0.217    
6 21712093 1.11 × 10−6 0.118 0.155    
8 9459681     4.28 × 10−5 0.233 0.141
  1. a: MAF: minor allele frequency; b: R square was calculated by R square of model with SNP minus R square of model without SNP