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Table 1 Loci significantly associated with coleoptile length using two MAF (q < 0.01)

From: Genome-wide association mapping reveals novel genes associated with coleoptile length in a worldwide collection of barley

GLM model MAF > 0.05

SNP ID*

Alleles

MAF†

R2 (%)§

q value¶

Candidate gene IDδ

Annotation

1H500582726

C:T

0.24

6.52

8.75E-03

HORVU1Hr1G073010

unknown function

1H514098702

A:C

0.23

6.68

8.75E-03

HORVU1Hr1G076430

Protein FLOWERING LOCUS T

1H516785422

A:G

0.2

6.28

8.75E-03

HORVU1Hr1G077230

Cellulose-synthase-like C6

2H026308852

A:G

0.25

6.32

8.75E-03

.ζ

.

2H640651652

G:C

0.14

6.45

8.75E-03

.

.

4H015498974

C:G

0.09

6.33

8.75E-03

.

.

5H456061421

A:C

0.06

6.45

8.75E-03

HORVU5Hr1G058300

trehalose-6-phosphate phosphatase

6H071685909

C:T

0.35

6.65

8.75E-03

.

.

6H114729800

T:C

0.32

6.81

8.75E-03

.

.

2H025712787

C:T

0.44

6.14

8.87E-03

.

.

3H159754241

A:G

0.11

6.16

8.87E-03

.

.

5H014097066

A:G

0.08

6.10

8.87E-03

HORVU5Hr1G007340

Leucine-rich repeat receptor-like protein kinase family protein

6H095840955

T:C

0.12

6.12

8.87E-03

.

.

1H510799369

A:C

0.26

6.01

9.48E-03

.

.

3H325190801

T:G

0.05

6.00

9.48E-03

.

.

4H009849212

C:T

0.23

5.91

9.48E-03

.

.

6H060392776

T:C

0.36

5.92

9.48E-03

.

.

6H72969182

G:A

0.37

5.91

9.48E-03

HORVU6Hr1G022770

Protein VERNALIZATION INSENSITIVE 3

6H071745828

A:G

0.36

5.87

9.77E-03

HORVU6Hr1G022500

BTB/POZ domain-containing protein

GLM model MAF > 0.01

SNP ID

Alleles

MAF

R2(%)

q value

Candidate gene ID

Annotation

1H514098702

A:C

0.23

6.71

5.45E-03

HORVU1Hr1G076430

Protein FLOWERING LOCUS T

4H015498974

C:G

0.09

6.42

5.45E-03

.

.

6H53910826

C:T

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53910924

T:A

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53911180

T:A

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53911713

A:C

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53912147

C:T

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53912695

T:C

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53913050

A:C

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53913075

C:T

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53913335

G:A

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53913549

C:T

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H53915124

T:A

0.02

5.54

5.45E-03

HORVU6Hr1G019700

Squamosa promoter-binding-like protein 3

6H071685909

C:T

0.35

6.53

5.45E-03

.

.

6H114729800

T:C

0.32

6.69

5.45E-03

.

.

1H500582726

C:T

0.24

6.37

5.50E-03

HORVU1Hr1G073010

unknown function

2H640651652

G:C

0.14

6.35

5.50E-03

.

.

1H516785422

A:G

0.2

6.29

5.63E-03

HORVU1Hr1G077230

Cellulose-synthase-like C6

2H026308852

A:G

0.25

6.29

5.63E-03

.

.

5H456061421

A:C

0.06

6.25

5.81E-03

HORVU5Hr1G058300

trehalose-6-phosphate phosphatase

6H095840955

T:C

0.12

6.22

5.82E-03

.

.

2H025712787

C:T

0.44

6.20

5.83E-03

.

.

1H510799369

A:C

0.26

6.08

7.09E-03

.

.

3H159754241

A:G

0.11

6.03

7.67E-03

.

.

5H014097066

A:G

0.08

5.99

7.98E-03

HORVU5Hr1G007340

Leucine-rich repeat receptor-like protein kinase family protein

3H325190801

T:G

0.05

5.90

9.17E-03

.

.

  1. *the ID consists of the chromosome number followed by the marker’s physical position
  2. †minor allele frequency
  3. §contribution to phenotypic variation
  4. ¶adjusted P value, significant at q < 0.01; the association list of q < 0.05 see supplementary data
  5. δannotated in barley genome assembly IBSC v
  6. ζintergenic region