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Table 4 Loci detected for eating and cooking qualities in indica and japonica panels

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

Trait    indica panel japonica panel
Chr. Position P value MAFa R squareb P value MAFa R squareb
AAC 6 1529682 2.15 × 10−7 0.331 0.079    
6 1765761     1.69 × 10−13 0.146 0.279
PRO 2 3118861     1.87 × 10−5 0.098 0.076
4 6536977     1.37 × 10−5 0.055 0.079
5 6814906     3.10 × 10−5 0.122 0.072
6 2576841 2.23 × 10−5 0.458 -    
7 1631971     9.32 × 10−7 0.073 0.102
8 2755270 4.39 × 10−5 0.280 -    
10 9032827     4.38 × 10−6 0.207 0.089
11 22240707 3.60 × 10−5 0.093 -    
11 22563596     2.89 × 10−5 0.064 0.073
PV 6 1665483 2.96 × 10−5 0.322 0.127    
6 1765761     6.42 × 10−6 0.145 0.110
8 2885700     6.78 × 10−5 0.087 0.085
11 5061851     1.46 × 10−5 0.084 0.101
HPV 3 26688241 7.17 × 10−5 0.449 0.625    
5 7944999     6.99 × 10−5 0.096 0.089
6 1750498 1.50 × 10−6 0.280 0.387    
9 18431810     6.09 × 10−5 0.142 0.090
9 18729438 6.47 × 10−5 0.203 0.250    
11 3161548     2.46 × 10−5 0.078 0.101
11 27792076     3.84 × 10−5 0.229 0.096
CPV 6 1750498 1.24 × 10−6 0.280 0.402    
9 18443016     1.28 × 10−6 0.054 0.133
BD 6 1721792 9.99 × 10−5 0.339 0.097    
7 1118122     1.51 × 10−5 0.054 0.111
7 26540950 6.68 × 10−5 0.339 0.103    
11 3735389 4.38 × 10−5 0.398 0.109    
11 20805844     1.84 × 10-5 0.160 0.109
SB 1 31774927     4.37 × 10−5 0.205 0.092
3 8987316     2.53 × 10−5 0.075 0.098
6 1617418 6.01 × 10−6 0.339 0.133    
6 1765761     1.82 × 10−8 0.145 0.183
7 25312126 9.18 × 10−5 0.297 0.095    
11 3781133 9.23 × 10−5 0.356 0.095    
CS 1 31668474     5.17 × 10−6 0.202 0.085
6 1759451     6.46 × 10−7 0.120 0.102
PeT 1 23829740 5.22 × 10−5 0.322 0.323    
2 4054094     1.84 × 10−6 0.111 0.093
3 33737410     3.27 × 10−7 0.060 0.107
5 7996572     1.96 × 10−5 0.057 0.073
PTemp 1 2609442     2.80 × 10−6 0.084 0.055
4 33873772     5.72 × 10−6 0.051 0.052
6 6722646 1.29 × 10−7 0.356 0.295    
6 6747298     3.71 × 10−6 0.482 0.054
9 8085354     1.09 × 10−5 0.090 0.049
  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