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Table 3 Top highest genome-wide significant association signals of agronomic traits using EMMAX

From: Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.)

Trait Chr. Position (IRGSP 1.0) Reference allele Alternative allele Alternative allele frequency -log10(P) R2 (%)a Candidate/known geneb
Grain width 1 11,789,024 C A 0.77 6.29 9.41  
Heading days 2 3,970,385 G A 0.05 6.20 11.54  
3 32,824,935 T A 0.05 6.21 8.57 CK1 [29]
3 32,824,941 C G 0.05 6.08 10.75 CK1 [29]
4 463,322 G A 0.95 7.86 12.86  
4 463,371 G A 0.94 7.41 10.97  
8 15,918,110 G A 0.05 6.21 7.42  
8 15,918,112 C T 0.05 6.10 4.38  
9 18,628,054 T C 0.13 6.04 6.87  
Seed set rate 4 31,539,937 A G 0.18 7.35 9.45 LOC_Os04g52940.1
7 7,918,286 G A 0.07 6.16 5.21  
7 8,178,284 A G 0.12 6.47 3.15  
7 8,299,577 G A 0.07 6.33 14.26  
7 8,390,152 C T 0.07 6.08 5.27  
7 8,390,155 C T 0.07 6.09 8.25  
7 8,447,659 T C 0.09 6.45 9.64 LOC_Os07g14800.1
  1. Note: aR2 represents the genetic variants explained by the significant SNPs. bGene ID of MSU rice genome annotation project (http://rice.plantbiology.msu.edu/)