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Table 2 Most significant SNP marker for FTI and the underlying female fertility traits

From: Genome-wide association study for female fertility in Nordic Red cattle

Trait namea

Marker name

rsname

−log10(P)

Annotationb

Ensemble

Gene name

Gene description

Proportion of additive genetic variance explained by the SNP

BTA1

 

FTI

Chr1:128614529

rs137748444

11.49

intergenic_variant

   

1.17

AISC

Chr1:127295226

rs43271631

9.89

intron_variant

ENSBTAG00000002232

TRPC1

Bos taurus transient receptor potential cation channel, subfamily C, member 1

0.89

AISH

Chr1:128189301

rs136231770

11.75

upstream_gene_variant

ENSBTAG00000021886

GRK7

Bos taurus G protein-coupled receptor kinase 7

1.21

ICF

Chr1:128663781

Chr1:128663781c

7.32

intergenic_variant

   

0.67

IFLC

Chr1:127295226

rs43271631

12.24

intron_variant

ENSBTAG00000002232

TRPC1

Bos taurus transient receptor potential cation channel, subfamily C, member 1

1.26

IFLH

Chr1:128189301

rs136231770

12.49

upstream_gene_variant

ENSBTAG00000021886

GRK7

Bos taurus G protein-coupled receptor kinase 7

1.32

NRRC

Chr1:127295226

rs43271631

7.37

intron_variant

ENSBTAG00000002232

TRPC1

Bos taurus transient receptor potential cation channel, subfamily C, member 1

0.72

NRRH

Chr1:128106801

rs43262199

8.36

intergenic_variant

   

0.93

BTA2

 

FTI

Chr2:133075293

rs42761190

8.51

intergenic_variant

   

0.90

AISC

Chr2:133079214

rs42761183

6.17

intergenic_variant

   

0.57

AISH

Chr2:132321329

rs209242168

13.30

intron_variant

ENSBTAG00000040215

EIF4G3

Uncharacterized protein

1.44

ICF

Chr2:133126588

rs109245794

9.98

upstream_gene_variant

ENSBTAG00000012217

PLA2G2F

Bos taurus phospholipase A2, group IIF

0.95

IFLC

Chr2:133077462

rs42761186

6.00

intergenic_variant

   

0.57

IFLH

Chr2:132321329

rs209242168

10.50

intron_variant

ENSBTAG00000040215

EIF4G3

Uncharacterized protein

1.13

NRRC

Chr2:131498393

rs110082997

6.92

intergenic_variant

   

0.74

NRRH

Chr2:132321329

rs209242168

13.01

intron_variant

ENSBTAG00000040215

EIF4G3

Uncharacterized protein

1.51

BTA3

 

FTI

Chr3:33388881

rs43336559

14.22

intergenic_variant

   

1.56

AISC

Chr3:33388881

rs43336559

15.78

intergenic_variant

   

1.47

AISH

Chr3:30770425

rs134664378

23.07

intron_variant

ENSBTAG00000014299

RHOC

Bos taurus ras homolog gene family, member C

2.48

ICF

Chr3:31574900

rs43334971

8.05

intron_variant

   

0.80

IFLC

Chr3:33388881

rs43336559

11.99

intergenic_variant

   

1.24

IFLH

Chr3:35629755

rs109158850

15.86

intron_variant

ENSBTAG00000031575

VAV3

vav 3 guanine nucleotide exchange factor

1.69

NRRC

Chr3:33388483

rs381207703

18.34

intergenic_variant

   

1.87

NRRH

Chr3:32024752

rs43332934

21.55

upstream_gene_variant

ENSBTAG00000014102

WDR77

Bos taurus WD repeat domain 77

2.41

BTA5

 

FTI

Chr5:62781359

rs135099682

10.79

intergenic_variant

   

1.15

AISC

Chr5:62781359

rs135099682

9.99

intergenic_variant

   

0.89

AISH

Chr5:62781359

rs135099682

13.87

intergenic_variant

   

1.37

ICF

Chr5:61879166

rs207754946

8.01

intergenic_variant

   

0.76

IFLC

Chr5:61625072

rs434505378

10.16

intergenic_variant

   

0.97

IFLH

Chr5:62781359

rs135099682

13.45

intergenic_variant

   

1.34

NRRC

Chr5:64863598

rs383102267

6.74

intergenic_variant

   

0.59

NRRH

Chr5:61836879

rs211681535

6.95

intergenic_variant

   

0.69

BTA6

 

FTI

Chr6:43511992

rs41983284

13.59

intron_variant

ENSBTAG00000004653

GPR125

G protein-coupled receptor 125

1.54

AISC

Chr6:43223916

rs133258175

12.17

intergenic_variant

   

1.15

AISH

Chr6:44642153

rs209918674

20.98

intergenic_variant

   

1.99

ICF

Chr6:42542483

rs110363606

7.77

intron_variant

ENSBTAG00000047743

KCNIP4

Bos taurus Kv channel interacting protein 4

0.71

IFLC

Chr6:45794025

rs109808198

12.17

intergenic_variant

   

1.26

IFLH

Chr6:41455222

rs43610453

16.21

intron_variant

ENSBTAG00000005108

SLIT2

Slit homolog 2 (Drosophila)

1.59

NRRC

Chr6:42245672

rs109518200

12.48

intron_variant

ENSBTAG00000047743

KCNIP4

Bos taurus Kv channel interacting protein 4

1.27

NRRH

Chr6:44642153

rs209918674

17.63

intergenic_variant

   

1.80

BTA6

 

FTI

Chr6:98115824

rs208894094

11.29

intergenic_variant

   

1.26

AISC

Chr6:98115824

rs208894094

6.38

intergenic_variant

   

0.58

AISH

Chr6:99400480

rs379908987

14.72

intron_variant

ENSBTAG00000022449

SCD5

Bos taurus stearoyl-CoA desaturase 5

1.51

ICF

Chr6:98048673

rs133357086

10.91

intergenic_variant

   

1.06

IFLC

Chr6:98115824

rs208894094

8.88

intergenic_variant

   

0.92

IFLH

Chr6:99400480

rs379908987

13.58

intron_variant

ENSBTAG00000022449

SCD5

Bos taurus stearoyl-CoA desaturase 5

1.42

NRRC

Chr6:98385129

rs210763629

4.43

intergenic_variant

   

0.45

NRRH

Chr6:96953202

rs110379023

12.73

intron_variant

ENSBTAG00000035776

C4orf22

Chromosome 4 open reading frame 22

1.19

BTA13

 

FTI

Chr13:58664049

rs378998625

14.85

intron_variant

ENSBTAG00000013574

ANKRD60

Ankyrin repeat domain 60

1.75

AISC

Chr13:56125951

rs109185706

12.69

intergenic_variant

   

1.18

AISH

Chr13:59923876

rs41700956

16.72

intergenic_variant

   

2.28

ICF

Chr13:59112800

rs42555672

12.19

downstream_gene_variant

ENSBTAG00000013574

ANKRD60

Ankyrin repeat domain 60

1.26

IFLC

Chr13:57020976

rs109484180

13.17

intergenic_variant

   

1.37

IFLH

Chr13:59923876

rs41700956

16.77

intergenic_variant

   

2.29

NRRC

Chr13:60559073

rs41699546

6.44

intergenic_variant

   

0.60

NRRH

Chr13:57048934

rs110280398

12.14

intergenic_variant

   

1.23

BTA15

 

FTI

Chr15:34677367

rs41763261

15.90

intron_variant

ENSBTAG00000001410

GRAMD1B

GRAM domain containing 1B

1.68

AISC

Chr15:34737376

rs110670590

10.87

intron_variant

ENSBTAG00000001410

GRAMD1B

GRAM domain containing 1B

0.99

AISH

Chr15:33428419

rs382278362

9.99

intergenic_variant

   

0.97

ICF

Chr15:34702074

rs41763326

9.86

intron_variant

ENSBTAG00000001410

GRAMD1B

GRAM domain containing 1B

0.89

IFLC

Chr15:34677367

rs41763261

15.55

intron_variant

ENSBTAG00000001410

GRAMD1B

GRAM domain containing 1B

1.55

IFLH

Chr15:33428419

rs382278362

10.81

intergenic_variant

   

1.08

NRRC

Chr15:34829707

rs378927222

11.19

intergenic_variant

   

1.67

NRRH

Chr15:34802991

rs208575577

11.65

intergenic_variant

   

1.50

BTA20

 

FTI

Chr20:67116858

rs133488500

11.44

intergenic_variant

   

1.39

AISC

Chr20:67623217

rs110045690

13.52

intergenic_variant

   

1.22

AISH

Chr20:68086468

rs208936479

15.87

intergenic_variant

   

1.68

ICF

Chr20:66806800

rs384363430

10.20

intergenic_variant

   

0.93

IFLC

Chr20:67124570

rs42467155

13.09

intergenic_variant

   

1.50

IFLH

Chr20:68084517

rs383590013

15.71

intergenic_variant

   

1.71

NRRC

Chr20:67623217

rs110045690

10.79

intergenic_variant

   

1.05

NRRH

Chr20:68086468

rs208936479

12.82

intergenic_variant

   

1.46

BTA24

 

FTI

Chr24:31820659

rs137134841

18.50

intron_variant

ENSBTAG00000007383

ZNF521

Zinc finger protein 521

2.17

AISC

Chr24:31820659

rs137134841

15.00

intron_variant

ENSBTAG00000007383

ZNF521

Zinc finger protein 521

1.48

AISH

Chr24:31817915

rs381174897

25.32

intron_variant

ENSBTAG00000007383

ZNF521

Zinc finger protein 521

2.80

ICF

Chr24:31442858

rs43737972

7.94

intergenic_variant

   

0.70

IFLC

Chr24:31820659

rs137134841

14.49

intron_variant

ENSBTAG00000007383

ZNF521

Zinc finger protein 521

1.58

IFLH

Chr24:31817915

rs381174897

22.20

intron_variant

ENSBTAG00000007383

ZNF521

Zinc finger protein 521

2.50

NRRC

Chr24:30565598

rs42446963

11.49

intergenic_variant

   

1.16

NRRH

Chr24:31817915

rs381174897

18.03

intron_variant

ENSBTAG00000007383

ZNF521

Zinc finger protein 521

2.13

  1. A marker is significant if the –log10(P) > 8.25
  2. aFTI: fertility index, AIS: number of inseminations per conception, ICF: length in days of the interval from calving to first insemination, IFL: days from first to last insemination, and NRR: 56-day non-return rate (Suffix h: heifers and suffix c: cows)
  3. bIn case the SNP marker is annotated as a downstream_gene_variant or an upstream_gene_variant the gene closest located to this SNP is mentioned
  4. cSNP marker did not have an rs id
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