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Table 3 Percentage explained variance (%Var), phenotypic means of SNP alleles, and significant (P < 0.05) marker-trait associations

From: DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits

Candidate gene

Site position1

%Var

P-value

Means of SNP alleles2

(accession classes)

BLZ1

Flowering time [days after sowing]

 

1733

6.46

0.0033

A: 67.96

C: 69.87

 

1825

7.38

0.0031

G: 67.96

A: 69.91

 

1888

6.46

0.0033

C: 67.96

T: 69.87

 

1890

7.10

0.0017

G: 67.50

A: 69.54

 

2038

7.52

0.0011

Del: 67.62

AT: 69.68

 

2520

7.10

0.0017

G: 67.50

A: 69.54

 

2562

6.46

0.0033

C: 67.96

T: 69.87

 

2774

7.10

0.0017

T: 67.50

C: 69.54

BPBF

Crude protein content [%]

 

-368

6.65

0.0003

G: 14.85

A: 15.63

 

-315

5.40

0.0003

T: 14.85

C: 15.63

 

-303

6.50

0.0003

T: 14.87

A: 15.63

 

-215

6.86

0.0002

C: 14.86

G: 15.63

 

-209

6.19

0.0004

A: 14.88

G: 15.63

 

-166

6.07

0.0003

A: 14.87

G: 15.64

 

-101

5.38

0.0004

T: 14.88

C: 15.64

 

-27

4.94

0.0003

C: 14.88

T: 15.65

 

-3

6.76

0.0002

T: 14.82

C: 15.64

 

62

4.02

<.0001

T: 14.79

C: 15.66

 

579

12.40

0.0003

T: 14.90

C: 15.66

 

586

3.34

0.0025

G: 14.93

A: 15.58

 

618

3.42

0.0019

A: 14.91

G: 15.58

 

713

5.45

0.0008

A: 14.88

G: 15.60

 

797

4.06

0.0029

G: 14.94

T: 15.58

 

972

4.40

0.0016

G: 14.91

A: 15.59

 

1026

7.91

0.0019

T: 14.98

G: 15.62

 

1075

3.51

0.0007

A: 14.91

G: 15.63

 

1129

5.57

0.0007

C: 14.92

A: 15.63

 

Starch content [%]

 

-368

4.44

0.0004

A: 55.58

G: 56.74

 

-315

7.30

0.0007

C: 55.57

T: 56.66

 

-303

5.39

0.0002

A: 55.56

T: 56.77

 

-215

4.41

0.0004

G: 55.58

C: 56.73

 

-209

4.84

0.0003

G: 55.57

A: 56.74

 

-166

5.12

0.0001

G: 55.55

A: 56.78

 

-101

4.79

0.0001

C: 55.53

T: 56.78

 

-27

4.22

0.0001

T: 55.55

C: 56.79

 

-3

3.27

0.0008

C: 55.61

T: 56.72

 

62

0.16

0.0009

C: 55.56

T. 56.70

  1. 1: Positions refer to the sequence alignment given in additional file 3
  2. 2: All differences between classes for a given site position are significant at P = 0.05