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Table 1 Significant (-lod10 p ≥ 3) marker-trait associations identified by genome-wide association scans in elite barley germplasm

From: A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys

 

Peak

Peak (i-select) marker

i-select peak cM

MxBk peak cM

IBSC peak cM

-LOG (10)P

Candidate annotation

Barley gene id/transcript (MLOC)

cM (MxBk)

Morex contig

Car 5 DPA FPKM

Car 15 DPA FPKM

CAZY

1H

QBgn.S-1H1

11_11484

51.2

48.4

48.4

3.2

CslF9

MLOC_59327

48.1

contig_43489

13.6

9.1

GT2

       

GlbI

MLOC_62746

54.4

contig_46926

0.5

30.7

GH17

2H

QBgn.W-2H1

11_21265

28.4

26.2

n/a

3.0

HvXTH_5607

MLOC_5607

23.5

contig_136449

0.2

0.2

GH16

 

QBgn.SW-2H1**

11_10498

49.1

50.9

50.9

4.5

CslF3

MLOC_59289

55.6

contig_43435

0.1

0.1

GT2

  

12_31408

n/a

55.4

53.4

4.9

CslF4

-

55.6

contig_6524

0.0

0.0

GT2

       

CslF8

MLOC_52692

55.6

contig_37718

1.5

1.9

GT2

       

CslF10

MLOC_13463

55.6

contig_1565725

0.0

0.0

GT2

       

CslF12

MLOC_7825

55.6

contig_140266

0.1

0.0

GT2

       

CslH

MLOC_53007

55.6

contig_37984

0.8

1.8

GT2

 

QBgn.W-2H2

11_10651

68.2

n/a

62.8

3.0

Glycoside hydrolase, family 9

MLOC_34376

65.4

contig_243681

64.1

30.0

GH9

 

QBgn.W-2H3

12_31180

155.3

144.3

n/a

3.2

-

-

-

-

-

-

-

3H

QBgn.S-3H1

SCRI_RS_222102

54.8

54.8

54.8

3.3

Glycosyl transferase, family 48

MLOC_501

51.3

contig_103522

7.9

9.9

GT48

       

HvGT48_13377

MLOC_13377

51.3

contig_1565486

8.4

11.1

GT48

        

MLOC_72705

51.6

contig_6218

15.8

11.6

GH1

 

QBgn.SW-3H1

SCRI_RS_237939

63.0

63.0

63.7

3.2

HvGSL7

MLOC_11267

63.3

contig_1560726

43.3

54.7

GT48

  

11_11314

70.2

63.7

61.9

3.3

Glycoside hydrolase, family 5

MLOC_74852

61.9

contig_66652

31.1

4.9

GH5

 

QBgn.W-3H1**

SCRI_RS_166119

86.2

86.2

86.3

4.8

Glycoside hydrolase, family 17

MLOC_5621

88.5

contig_136464

15.2

6.5

GH17

  

11_20628

98.5

87.4

87.4

4.8

-

-

-

-

-

-

-

5H

QBgn.W-5H1

11_21365

21.3

13.1

9.3

3.2

-

-

-

-

-

-

-

 

QBgn.W-5H2

SCRI_RS_3280

n/a

93.0

n/a

3.1

HvCel3

MLOC_44777

96.3

contig_275346

41.2

9.7

GH9

 

QBgn.S-5H1

12_30377

128.7

118.0

118.0

3.2

Cellulose synthase

MLOC_65914

114.0

contig_50865

3.0

0.3

GT2

6H

QBgn.W-6H1

SCRI_RS_207174

54.9

54.9

55.2

3.5

Glycoside hydrolase, family 9

MLOC_37664

51.0

contig_2548837

0.3

0.0

GH9

 

QBgn.S-6H1

SCRI_RS_189619

102.1

102.1

102.1

4.4

Myb, DNA-binding

MLOC_76165

n/a

contig_70355

0.6

4.4

n/a

7H

QBgn.S-7H1

SCRI_RS_230261

140.9

140.9

140.9

3.4

HvGSL5

MLOC_64106

140.4

contig_48373

93.4

38.0

GT48

       

GlbII

MLOC_73214 and MLOC_73215

138.2

contig_6317

N/A

N/A

GT17

       

HvSuSyII

MLOC_10031

140.6

contig_1558277

10.1

17.7

GT1

  1. Germplasm included in the analysis was a subset of 2-row Spring and Winter accessions from the UK and Northern Europe described in [27]. Peaks with adjusted p values < 0.025 indicated by **. Barley Gene id/transcipt (MLOC), Morex Contig, Developing grain without bracts 5 days post anthesis (CAR 5 DPA FPKM) and CAR 15 DPA FPKM from ([31] IBGS). Barley Gene id/ transcipt (MLOC). FPKM - fragments per kilobase of exon per million fragments mapped. QTL names including S represent associations identified in the Spring population, W in the Winter population and SW in both populations. EII on 7H is represented by two gene models and therefore transcript expression data is not available. Dashes represent those regions were no obvious candidate has been identified for that region based on the available annotations.