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Table 1 Genome-wide significant associations for pollen fertility, BSS and NSS of the F1 population with the background of CMS-WA in year 2013 and 2014 using the linear mixed model

From: Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.)

TraitChr.20132014Known loci
PositionP-LMMAllele1)MAF2)PVE (%)3)PositionP-LMMAlleleMAFPVE (%)
Pollen fertility1     5,631,7782.97E-08A/T0.16819.01Rf3
9     10,301,0518.11E-08G/A0.3612.90 
1018,809,3525.42E-12C/T0.35937.6718,803,7632.33E-20C/T0.35048.46Rf4
BSS4113,5516.54E-10A/G0.24116.90      
4     962,1491.36E-08A/C0.17215.89 
611,935,3711.18E-08T/A0.06111.91      
6     28,616,3422.37E-07G/A0.4952.93 
86,798,1114.27E-08C/T0.07825.48      
9     10,218,0163.38E-08G/A0.3584.45 
1018,826,3783.50E-13T/G0.17633.5418,803,9392.02E-14C/T0.18219.37Rf4
12     23,866,9699.55E-09T/C0.32520.10 
NSS454,4583.07E-08A/C0.32612.51      
1018,807,8154.20E-10C/G0.41341.5218,803,9392.02E-16C/T0.18219.05Rf4
  1. Note: 1) Allele is presented with the format of ‘major allele / minor allele’
  2. 2) MAF minor allele frequency
  3. 3) PVE phenotypic variation explained by each locus