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Table 2 Significant and suggestive SNPs by trait, with their positions, estimated effect, p-value, and annotation in the Chicken Ensembl release 106—Apr 2022

From: Genetic markers associated with bone composition in Rhode Island Red laying hens

Trait

OM/Min

SNP position

Minor allele

Effect sizea

P-valueb

Sig/Sug

Closest genesc

Gene name

Chr

bp

FTIR cortical lipid

OM

2

2,585,350

A

− 0.27

8.6E−06

Sug

ENSGALG00000042657

WNT3A Wnt family member 3A

OM

3

27,204,115

G

0.30

7.6E−08

Sig

ENSGALG00000010020

TTC7A tetratricopeptide repeat domain 7A, located close to CALM2 calmodulin 2

OM

3

27,351,346

C

0.29

1.9E−07

Sig

ENSGALG00000010026

PPP1CB protein phosphatase 1 catalytic subunit beta

OM

3

27,434,588

G

0.31

4.5E−08

Sig

uncharacterized protein coding

 

OM

3

27,548,492

A

0.29

1.0E−06

Sig

ENSGALG00000010039

BRE brain and reproductive organ-expressed

OM

3

27,648,733

G

0.29

1.7E−06

Sug

ENSGALG00000010039

BRE brain and reproductive organ-expressed

FTIR medullary PO4/Amide I

Min

4

83,057,186

A

0.26

1.3E−06

Sig

Non coding

 

Min

4

83,057,186

A

0.26

3.1E−06

Sug

Non coding

 

Min

4

83,154,195

G

0.23

5.1E−06

Sug

Uncharacterized protein coding

 

FTIR medulla CO3 1450/1415

OM

1

175,454,102

C

0.24

1.5E−06

Sug

ENSGALG00000042339

Uncharacterized protein coding

OM

1

175,547,167

G

0.23

3.2E−06

Sug

ENSGALG00000042339

Uncharacterized protein coding

OM

1

175,579,717

A

0.24

1.6E−06

Sug

non coding

 

OM

1

175,604,918

A

0.24

1.6E−06

Sug

ENSGALG00000017068

Uncharacterized protein coding

OM

1

175,622,214

A

0.24

1.6E−06

Sug

ENSGALG00000017068

Uncharacterized protein coding

OM

1

175,631,230

G

0.24

1.8E−06

Sug

ENSGALG00000017068

Uncharacterized protein coding

OM

1

175,660,267

A

0.24

1,8E−06

Sug

Non coding

 

OM

1

175,680,614

G

0.23

4.3E−06

Sug

Non coding

 

OM

1

175,696,576

A

0.24

1.8E−06

Sug

ENSGALG00000047002

lncRNA

OM

1

175,750,307

G

0.23

5.0E−06

Sug

ENSGALG00000017070

PDS5B PDS5 cohesin associated factor B

OM

1

175,788,839

A

0.24

1.2E−06

Sig

ENSGALG00000017070

PDS5B PDS5 cohesin associated factor B

OM

1

175,799,752

G

0.24

1.2E−06

Sig

ENSGALG00000017070

PDS5B PDS5 cohesin associated factor B

OM

1

175,836,437

G

0.24

1.2E−06

Sig

ENSGALG00000053592

lncRNA

OM

1

175,934,229

A

0.24

1.5E−06

Sug

ENSGALG00000017073

BRCA2 DNA repair associated

OM

1

176,026,352

A

0.24

1.2E–−06

Sig

ENSGALG00000017075

FRY microtubule binding protein

OM

1

176,301,701

A

0.25

3.6E−07

Sig

ENSGALG00000017076

B3GLCT beta 3-glucosyltransferase

OM

1

176,311,780

G

0.26

3.1E−07

Sig

ENSGALG00000017076

B3GLCT beta 3-glucosyltransferase

OM

1

176,597,999

G

0.25

7.6E−07

Sig

ENSGALG00000017083

KATNAL1 katanin catalytic subunit A1 like 1 located close to HSPH1 heat shock protein family H

OM

1

176,670,270

C

0.26

3.6E−07

Sig

ENSGALG00000017084

UBL3 ubiquitin like 3

OM

1

176,699,327

G

0.26

3.8E−07

Sig

ENSGALG00000017084

UBL3 ubiquitin like 3

OM

1

176,773,112

A

0.26

2.9E−07

Sig

non coding

 

Medullary collagen maturity

OM

5

37,871,918

G

− 0.22

8.0E−06

Sug

ENSGALG00000010192

FBXO33 F-box protein 33

Cortical crystal scattering

Min

2

102,786,582

A

− 0.25

2.2E−07

Sig

Non coding

 

Min

2

102,836,922

A

− 0.22

2.1E−06

Sug

ENSGALG00000014982

Protein coding

Min

2

102,886,544

A

− 0.21

1.0E−05

Sug

Non coding

 

Cortical crystal orientations

Min

12

8,004,788

G

− 0.43

5.9E−06

Sug

ENSGALG00000005400

CACNA2D3 calcium voltage-gated channel auxiliary subunit alpha2delta 3

Min

12

8,014,900

A

− 0.44

3.5E−06

Sug

ENSGALG00000005400

CACNA2D3 calcium voltage-gated channel auxiliary subunit alpha2delta 3

Min

12

8,021,298

G

− 0.43

6.4E−06

Sug

ENSGALG00000005400

CACNA2D3 calcium voltage-gated channel auxiliary subunit alpha2delta 3

Min

14

14,169,463

G

− 0.32

7.6E−06

Sug

ENSGALG00000009297

TELO2 telomere maintenance 2

Min

25

2,894,535

G

− 0.52

5.0E−06

Sug

ENSGALG00000024094

UBAP2L ubiquitin associated protein 2 like

  1. OM: Organic matter; Min: Mineral component of bone; Sig: significant with p-value < 1.38*10−6; Sug: suggestive with p-value < 10−5 and > 1.38*10−6
  2. aAll traits were standardized (with zero mean and one standard deviation) to facilitate effect size interpretation; effect here is the effect of the minor allele or the effect of the major allele with an opposite sign
  3. bWald test P-value
  4. cIdentified by annotating marker position to Chicken Ensembl Gene
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Genetics Selection Evolution

ISSN: 1297-9686