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Table 4 Significant SNP based on false discovery rate (FDR) q threshold of 0.05 for beef carcass traits using single locus regression model

From: Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

Trait1

Gene ID2

BTA3

Ref. SNP4

BPPos5

MAF6

n7

Estimate ± SE8

P-value*

LR

539020

1

rs43246339

81372644

0.165

664

1.151 ± 0.266

0.00002

IFR

539020

1

rs43246339

81372644

0.167

687

-0.622 ± 0.172

0.0003

IFR

614882

2

rs43287969

1280728

0.329

648

0.404 ± 0.143

0.005

F3

532545

2

rs43307594

43392336

0.379

847

0.473 ± 0.15

0.0016

IFR

538378

2

rs42315485

58475918

0.035

687

-0.968 ± 0.355

0.0065

Marbling

522946

3

ss914082840

2555332

0.445

851

-0.097 ± 0.028

0.00066

Marbling

522946

3

ss914082841

2557106

0.379

837

-0.092 ± 0.031

0.003

LMA

532836

4

rs41599809

96565402

0.107

848

3.08 ± 0.975

0.0016

LMA

532836

4

ss914082853

96570062

0.37

848

-1.807 ± 0.617

0.0035

Marbling

538086

5

ss914082862

50301829

0.414

851

-0.091 ± 0.03

0.0025

IFR

503621

6

ss914082876

32016672

0.131

687

0.625 ± 0.191

0.001

HCW

616908

6

rs41574929

36099801

0.397

949

5.277 ± 1.916

0.006

Marbling

540329

6

ss914082878

37288379

0.166

851

-0.117 ± 0.038

0.002

IFR

540329

6

ss914082878

37288379

0.14

687

-0.535 ± 0.178

0.0028

HCW

540329

6

ss914082878

37288379

0.162

959

7.16 ± 2.468

0.0038

Marbling

536203

6

ss914082880

37386084

0.174

850

-0.121 ± 0.037

0.001

IFR

536203

6

ss914082880

37386084

0.152

685

-0.511 ± 0.172

0.003

HCW

530393

6

rs29010894

37433382

0.124

958

-7.542 ± 2.706

0.005

IFR

530393

6

rs43702346

37439120

0.276

684

-0.393 ± 0.14

0.005

SQF

616568

7

ss914082884

10135670

0.129

928

-0.022 ± 0.008

0.004

GRF

616568

7

ss914082884

10135670

0.13

819

-0.572 ± 0.206

0.0056

Fat3

541122

9

rs43013785

33837458

0.487

841

0.431 ± 0.148

0.004

IFR

529759

11

ss914082698

80982741

0.066

687

0.928 ± 0.28

0.00097

Marbling

537649

12

ss914082709

13011713

0.294

851

0.125 ± 0.033

0.0002

F3

537649

12

ss914082709

13011713

0.293

847

0.443 ± 0.171

0.0097

IFR

535653

12

rs43694364

15748029

0.483

687

0.379 ± 0.131

0.0039

GRF

509602

12

ss914082715

76885563

0.411

845

0.409 ± 0.137

0.0029

LR

509602

12

ss914082715

76885563

0.425

663

-0.584 ± 0.201

0.0037

F3

509602

12

ss914082715

76885563

0.411

846

0.431 ± 0.15

0.004

IFR

509602

12

ss914082716

76889667

0.413

686

-0.503 ± 0.135

0.0002

LYR

509602

12

ss914082716

76889667

0.413

663

0.748 ± 0.208

0.0003

SQFR

509602

12

ss914082716

76889667

0.414

684

-0.355 ± 0.119

0.003

F3

509602

12

ss914082716

76889667

0.417

846

-0.439 ± 0.153

0.004

GRF

509602

12

ss914082716

76889667

0.418

845

-0.381 ± 0.14

0.0065

F3

512287

15

ss914082741

4101726

0.099

843

0.865 ± 0.254

0.00068

Fat1

521326

16

rs41821600

64875340

0.038

849

-2.099 ± 0.627

0.00085

Marbling

540672

20

rs43006895

54577104

0.479

851

0.1 ± 0.029

0.0006

F2

540672

20

rs43006895

54577104

0.478

850

0.904 ± 0.287

0.0017

BFR

534312

21

rs41980260

33909131

0.282

683

-0.162 ± 0.057

0.0049

BFR

534312

21

rs41980261

33909583

0.282

684

-0.151 ± 0.057

0.008

LMA

512725

23

ss914082809

32192762

0.488

848

1.609 ± 0.611

0.0086

LMA

512725

23

ss914082812

32207295

0.283

848

1.84 ± 0.703

0.009

LMA

504741

24

rs42047790

36412358

0.445

848

2.087 ± 0.625

0.0009

LMA

540050

26

rs42106947

37495213

0.488

848

-1.766 ± 0.611

0.004

BFR

518905

27

ss914082824

39712547

0.015

684

0.714 ± 0.231

0.002

IFR

515895

27

ss914082827

39798548

0.076

687

0.654 ± 0.237

0.006

SQFR

515895

27

ss914082827

39798548

0.077

685

0.569 ± 0.208

0.006

  1. 1F1, subcutaneous fat depth between the 1st and 2nd quarter of the longissimus; F2, subcutaneous fat depth between 2nd and 3rd quarter of the longissimus; F3, subcutaneous fat depth between the 3rd and 4th quarter of the longissimus; Marbling was scored as ≤ 3.0 = devoid; 3.1 to 4.0 = traces; 4.1 to 5.9 = slight; 6.0 to 7.0 = small to moderate; and ≥ 7.0 = slightly abundant to abundant; HCW = Hot carcass weight (kg); LMA = longissimus dorsi muscle area (cm2); LR = lean meat within the rib section (%); LY = Lean yield grade (%); GRF = Grade fat (mm); IFR = Intermuscular fat (%); BFR = Body cavity fat within the rib section (%); SQFR = Proportion of subcutaneous fat from the rib section (%); *is a significant SNP after adjusting for chromosome-wise 5% false discovery rate.
  2. Gene ID2 = Entrez gene identifier; BTA3 = Bos taurus autosome; Ref. SNP4 = (rs#) is a reference SNP ID number and (ss#) ID is the National Center for Biotechnology Information (NCBI) assay ID number assigned by NCBI to submitted SNPs for discovered SNPs using RNA-Seq.
  3. BPPos5 = the SNP’s position in a base pair; MAF6 = minor allele frequency; n7 = Number of animals’ phenotypes and genotypes for testing the association; Estimate ± SE8 = allele substitution effect ± standard error, the minor allele which the phenotypes regressed on its number (0, 1, and 2).