Skip to main content

Table 3 Significant SNP marker-trait associations tested in the population (n = 300) after a correction for multiple testing [false discovery rate FDR ≤ 0.10]

From: Identification and characterization of nuclear genes involved in photosynthesis in Populus

Trait

Gene symbol

Locus

Missense mutation

P-value

Phenotypic variation (%)

FDR

Frequency (%)

Pn

XET 5′UTR

XET-SNP2

 

< 0.001

5.4

0.0003

0.48

(G)

XET 5′UTR

XET-SNP3

 

< 0.001

7.2

0.0006

0.41

(T)

XET Exon1

XET-SNP5

Leu to Pro

< 0.001

5.2

0.0012

0.41

(C)

XET Exon1

XET-SNP6

Ala to Pro

< 0.001

5.4

0.0009

0.38

(C)

Dabb Exon2

Dabb-SNP2

Ala to Val

0.001

4.8

0.0019

0.45

(T)

GASA 3′UTR

GASA-SNP3

 

< 0.001

8.0

< 0.0001

0.46

(C)

SAUR Exon

SAUR-SNP1

Glu to Gln

0.008

2.3

0.0158

0.26

(G)

CGSS Exon1

CGSS-SNP1

Met* to Val

< 0.001

7.0

< 0.0001

0.15

(G)

Cond

XET 5′UTR

XET-SNP3

 

< 0.001

7.9

< 0.0001

0.41

(T)

XET Exon1

XET-SNP6

Ala to Pro

< 0.001

5.9

0.0005

0.38

(C)

Dabb Exon2

Dabb-SNP2

Ala to Val

< 0.001

7.0

< 0.0001

0.45

(T)

GASA 3′UTR

GASA-SNP3

 

< 0.001

12.6

< 0.0001

0.46

(C)

SAUR Exon

SAUR-SNP1

Glu to Gln

< 0.001

5.8

< 0.0001

0.26

(G)

CGSS Exon1

CGSS-SNP1

Met* to Val

< 0.001

6.8

< 0.0001

0.15

(G)

Ci

XET 5′UTR

XET-SNP3

 

0.003

3.8

0.0073

0.41

(T)

SAUR Exon

SAUR-SNP1

Glu to Gln

0.007

2.4

0.0149

0.26

(G)

Trmmol

XET 5′UTR

XET-SNP3

 

0.002

4.3

0.0040

0.41

(T)

Dabb Exon2

Dabb-SNP2

Ala to Val

0.004

3.6

0.0100

0.45

(T)

CGSS Exon1

CGSS-SNP1

Met* to Val

0.008

2.3

0.0158

0.15

(G)

H

PI 3′UTR

PI-SNP1

 

0.005

2.6

0.0651

0.38

(T)

  1. Pn, photosynthetic rate; Cond, conductance to H2O; Ci, intercellular CO2 concentration; Trmmol, transpiration rate; H, tree height; Frequency, Allele frequency of either the derived or minor allele. Single nucleotide polymorphism (SNP) alleles corresponding to the frequency listed are given in parentheses.