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Table 2 Genome-wide significant associations for BSS and NSS of the F1 population with the background of CMS-HL 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.)

Trait

Chr.

2013

2014

Known loci

Position

P-LMM

Allele1)

MAF2)

PVE (%)3)

Position

P-LMM

Allele

MAF

PVE (%)

BSS

2

     

26,741,479

2.24E-07

G/A

0.059

8.18

 

4

     

12,956,620

1.17E-08

T/C

0.359

8.81

 

6

     

21,359,687

1.36E-07

A/T

0.377

11.25

 

10

18,828,056

1.39E-08

G/A

0.492

12.79

18,880,986

1.74E-10

A/G

0.456

18.09

Rf5

12

     

16,744,603

7.69E-08

A/G

0.101

6.35

 

NSS

10

18,804,231

4.08E-15

A/C

0.231

28.25

18,876,148

8.10E-20

A/G

0.129

31.08

Rf5

  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