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Table 3 A summary of SNP allele substitution effect and additive genetic variance for each functional class based on imputed 7.8 M variant GWAS for RFI and its component traits in a beef cattle multibreed population

From: Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits

Trait1

Class2

no_of_SNP3

class_mean4

Ratio5

Vgf ± SE6

Vgo ± SE7

Vg_total ± SE8

Vgf/SNP9

Vgf_Ratio10

RFI

Intergenic region variants

5,251,680

0.000461

0.997835

0.067 ± 0.015

0.048 ± 0.014

0.12 ± 0.01

0.001283

0.05765900

Downstream gene variants

253,163

0.000478

1.034632

0.01 ± 0.012

0.105 ± 0.015

0.12 ± 0.01

0.004142

0.18608265

Upstream gene variants

285,798

0.000480

1.038961

0.002 ± 0.011

0.114 ± 0.015

0.12 ± 0.01

0.000644

0.02894225

Synonymous variants

32,019

0.000454

0.982684

0.01 ± 0.01

0.106 ± 0.014

0.12 ± 0.01

0.031869

1.43185934

Intron variants

1,987,366

0.000461

0.997835

0.039 ± 0.014

0.077 ± 0.015

0.12 ± 0.01

0.001966

0.08835385

Missense variants

17,654

0.000522

1.129870

0.006 ± 0.008

0.11 ± 0.013

0.12 ± 0.01

0.036643

1.64638613

3′ UTR variants

15,851

0.000490

1.060606

0.011 ± 0.007

0.105 ± 0.012

0.12 ± 0.01

0.070273

3.15738258

5′ UTR variants

3309

0.000515

1.114719

0.002 ± 0.005

0.114 ± 0.011

0.12 ± 0.01

0.053490

2.40333421

Other regulatory regions

6371

0.000501

1.084416

0 ± 0.007

0.119 ± 0.012

0.12 ± 0.01

0.000000

0.0000000

DMI

Intergenic region variants

5,251,680

0.000946

0.998944

0.219 ± 0.032

0.141 ± 0.03

0.36 ± 0.03

0.004173

0.15156143

Downstream gene variants

253,163

0.000970

1.024287

0.011 ± 0.025

0.348 ± 0.033

0.36 ± 0.03

0.004527

0.16439637

Upstream gene variants

285,798

0.000967

1.021119

0.00001 ± 0.024

0.362 ± 0.033

0.36 ± 0.03

0.000000

0.00001300

Synonymous variants

32,019

0.000924

0.975713

0.009 ± 0.021

0.35 ± 0.031

0.36 ± 0.03

0.029379

1.06696756

Intron variants

1,987,366

0.000944

0.996832

0.119 ± 0.029

0.241 ± 0.032

0.36 ± 0.03

0.005984

0.21733452

Missense variants

17,654

0.001038

1.096093

0.00001 ± 0.02

0.362 ± 0.029

0.36 ± 0.02

0.000006

0.00020571

3′ UTR variants

15,851

0.001009

1.065470

0.032 ± 0.016

0.327 ± 0.027

0.36 ± 0.02

0.203703

7.39785415

5' UTR variants

3309

0.000978

1.032735

0.00001 ± 0.011

0.365 ± 0.026

0.37 ± 0.02

0.000030

0.00109752

Other regulatory regions

6371

0.001017

1.073918

0.00001 ± 0.015

0.362 ± 0.028

0.36 ± 0.02

0.000016

0.00057003

ADG

Intergenic region variants

5,251,680

0.000052

1.000000

0.009 ± 0.002

0.004 ± 0.002

0.014 ± 0.002

0.000178

0.05631654

Downstream gene variants

253,163

0.000054

1.038462

0.0004 ± 0.001

0.013 ± 0.002

0.014 ± 0.002

0.000143

0.04529727

Upstream gene variants

285,798

0.000054

1.038462

0 ± 0.001

0.014 ± 0.002

0.014 ± 0.001

0.000000

0.00000000

Synonymous variants

32,019

0.000051

0.980769

0.001 ± 0.001

0.013 ± 0.002

0.014 ± 0.001

0.003891

1.22935097

Intron variants

1,987,366

0.000051

0.980769

0.003 ± 0.002

0.01 ± 0.002

0.014 ± 0.002

0.000176

0.05555651

Missense variants

17,654

0.000058

1.115385

0 ± 0.001

0.014 ± 0.001

0.014 ± 0.001

0.000000

0.00000000

3′ UTR variants

15,851

0.000054

1.038462

0.001 ± 0.001

0.013 ± 0.001

0.014 ± 0.001

0.005924

1.87143409

5' UTR variants

3309

0.000055

1.057692

0 ± 0.001

0.014 ± 0.001

0.014 ± 0.001

0.000000

0.00000000

Other regulatory regions

6371

0.000060

1.153846

0.001 ± 0.001

0.013 ± 0.001

0.014 ± 0.001

0.018176

5.74204463

MWT

Intergenic region variants

5,251,680

0.040609

0.998795

13.14 ± 1.47

7.93 ± 1.38

21.07 ± 1.42

0.250139

0.43808451

Downstream gene variants

253,163

0.041833

1.028900

0.9 ± 1.1

20.14 ± 1.53

21.04 ± 1.34

0.354482

0.62082809

Upstream gene variants

285,798

0.041653

1.024472

0.76 ± 1.09

20.27 ± 1.53

21.03 ± 1.33

0.265853

0.46560607

Synonymous variants

32,019

0.040382

0.993212

0.71 ± 0.97

20.34 ± 1.45

21.05 ± 1.24

2.216215

3.88140336

Intron variants

1,987,366

0.040446

0.994786

6.3 ± 1.32

14.77 ± 1.48

21.07 ± 1.4

0.317024

0.55522447

Missense variants

17,654

0.044912

1.104629

0.00004 ± 0.75

21.14 ± 1.33

21.14 ± 1.08

0.000227

0.00039682

3′ UTR variants

15,851

0.041232

1.014118

0.27 ± 0.63

20.75 ± 1.27

21.03 ± 1.01

1.733070

3.03524000

5' UTR variants

3309

0.041624

1.023759

0.00004 ± 0.45

21.29 ± 1.19

21.29 ± 0.91

0.001209

0.00211709

Other regulatory regions

6371

0.043722

1.075360

0.00004 ± 0.65

21.05 ± 1.28

21.05 ± 1.02

0.000628

0.00109959

  1. 1RFI residual feed intake in kg of DMI per day, DMI daily dry matter intake in kg per day, ADG average daily gain in kg, MWT metabolic body weight in kg
  2. 2Other regulatory regions consisted of splice regions in intron variants, disruptive in-frame deletion, splice region variants, etc. Detail functional class assignments of DNA variants can be found in (Additional file 3: Table S2)
  3. 3Number of DNA variants (or SNPs in text for simplicity)
  4. 4class_mean is the average of squared SNP allele substitution effects (class_mean) for the functional class
  5. 5Ratio is ratio of the class_mean of the functional class over the weighted average of class_means of all functional classes
  6. 6Vgf ± SE is additive genetic variance of the functional class ± standard error (SE)
  7. 7Vgo ± SE is additive genetic variance of the rest of SNPs in other functional classes ± standard error (SE)
  8. 8Vg_total ± SE is total additive genetic variance of all 7.8 M WGS variants ± standard error (SE)
  9. 9Vgf/SNP is additive genetic variance of the functional class per SNP × 105
  10. 10Vgf_Ratio is ratio of additive genetic variance of the functional class per SNP over the average of additive genetic variance per SNP of all functional classes based on the imputed 7.8 M WGS variant GWAS