Table 1 Summary of reported GWAS on domestic animals

1

Milk yield

50K

62,343 Holstein Friesian cows sired by 798 sires

Mixed linear models

P < 0.001

Identified 362 significant SNPs

[4]

2

Milk yield

50K

767 Holstein bulls

Single and Multiple trait regression analysis

P < 0.001

Identified 169 significant SNPs

[5]

3

Milk yield

50K

2,093 Chinese Holstein from the Holstein cattle farms in Beijing, China

Single locus regression analysis

Bonferroni P < 0.05 level

Identified 105 significant SNPs including two SNPs located close to the DGAT1 gene (160bp apart) and within the GHR gene, respectively

[6]

4

Milk yield

50K

1,039 bulls with pedigree information from Danish Jersey cattle

Regression analysis

Bonferroni correction P < 1.5e⁻⁶

Identified 98 significant SNPs

[7]

5

Milk quality traits

50K

780 Holstein sons of 142 sires

Bayesian analysis (BayesA)

P ≤ 0.001

Identified 73-461 significant SNPs (depending on trait)

[8]

6

Milk quality traits

50K

3,356 Japanese Black cattle from Yamagata Prefecture

GRAMMAR-CG method

Bonferroni correction P < 1.28e^-6 (5%); P < 2.57e^-7 (1%)

Identified 32 significant SNPs mainly in region of 49-55 Mb on BTA19 containing FASN gene

[9]

7

Milk quality traits

50K

1,905 Dutch Holstein Friesian cows from 398 commercial farms throughout the Netherlands

Two step single SNP association analysis using general linear model and animal model

FDR < 0.05

Identified 54 significant regions mainly on BTA14, 19, and 26 containing ABCG2, PPARGC1A, ACSS2, DGAT1, ACLY, SREBF1, STAT5A, GH, FASN, SCD1 and AGPAT6

[10]

8

Milk quality traits

50K

1,912 Holstein-Friesian cows from 398 commercial herds throughout the Netherlands

General linear model

FDR <0.01

Identified several important regions mainly on BTA5, 6, 11 and 14

[11]

9

Fertility trait

10K

10 low-fertility and 10 high-fertility bulls of Pure Holstein

Regression analysis

P < 0.01

Identified 97 significant SNPs including one SNP in Integrin beta 5 gene

[12]

10

Fertility trait

50K

267 Holstein cows

Generalized linear mixed model

P < 0.05

Identified 27 significant SNPs

[13]

11

Fertility trait

50K

2,531 Danish and Swedish Holstein bulls

Mixed model analysis

Bonferroni correction P < 2.16e^-5 (BTA1); P < 7.41e^-5 (BTA28)

Identified 74 significant SNPs mainly on BTA 3, 5, 10, 13, 19, 20, and 24

[14]

12

Fertility trait

50K

2,062 Danish and Swedish Holstein bulls

Mixed model analysis

Bonferroni correction P < 2.16e^-5 (BTA1); P < 7.41e^-5 (BTA28)

Identified several important regions on BTA4, 6, 12, 18, 20, and 25

[15]

13

Growth trait

50K

150 sires representing 7 breeds including Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus and Simmental

ANOVA test

FDR < 0.01

Identified 231 significant SNPs

[16]

14

Growth trait

10K; 50K

852 steers from 7 different pure breeds including Angus, Murray Grey, Shorthorn, Hereford, Brahman, Santa Gertrudis and Belmont Red

Regression analysis

P <0.001

Identified 75 significant SNPs mainly on BTA3, 5, 7, and 8

[17]

15

Meat quality and carcass traits

50K

940 Beef cattle

Regression analysis

P <0.001

Identified 87 significant SNPs for meat quality traits and 127 significant SNPs for carcass traits

[18]

16

Classical bovine spongiform encephalopathy (BSE)

50K

Holstein cows including 143 BSE affected (case) and 173 unaffected (control) collected in Southern England

Chi-square test

P < 5e^-5

Identified one SNP on chromosome 1 at 29.15 Mb and another locus on chromosome 14

[19]

17

Bovine Tuberculosis (TB)

50K

14,013 Irish Holstein- Friesian cows

Regression analysis

Bonferroni correction P < 1.21e^-6

Identified 3 significant SNPs in a 65kb genomic region on BTA 22 containing SLC6A6 gene

[20]

18

Bovine Paratuberculosis

50K

Italian and American Holstein cows including Group A with 590 cases vs 600 controls and Group B with 590 cases vs 117 controls

GRAMMAR-CG method

P < 5e^-5

Identified 6 significant SNPs on BTA 1, 12 and 15 and several other significant SNPs on BTA 1, 6, 7, 13, 16, 21, 23 and 25

[21]

19

Dominant White Phenotype and Bilateral Deafness

770K

Seven white and 79 spotted German Fleckvieh

General Linear Model (GLM)

-log₁₀P_raw = 254.4; -log₁₀P_{Bonferroni-adjusted} = 248.6

Identified a most significant region on BTA 22 containing MITF gene

[22]

20

Androstenone

60K

987 pigs divergent for androstenone concentration from a commercial Duroc- based sire line

QFAM test

FDR of q-value ≤ 0.05

Identified 37 significant SNPs mainly on SSC1 and SSC6

[23]

21

skatole levels

60K

891 pigs from a composite Duroc sire line

QFAM test

FDR of q-value ≤ 0.05

Identified 16 significant SNPs on SSC6: 0-6Mb

[24]

22

Boar taint and related sex steroids

60K

1,251 purebred Norwegian Landrace and 918 purebred Duroc male pigs

ANOVA test

P < 0.05

Identified g 28 regions related to boar taint

[25]

23

Boar taint and fertility traits

60K

1,533 purebred Landrace and 1,027 purebred Duroc male pigs

ANOVA test

P < 0.05

Identified 34 significant regions mainly on SSC1, 2, 3, 4, 7, 13, 14 and 15

[26]

24

Knobbed acrosome defect

60K

14 Finnish Yorkshire boars affected with KAD and 21 controls

Chi-square test

Permutation correction P < 0.0002

Identified a significant 0.7 Mb region on SSC15 containing STK17b and HECW2 genes

[27]

25

Body Composition and Structural Soundness Traits

60K

412 Large White line pigs and 408 pigs from a Large White ×  Landrace cross

Bayes C

Bootstrap correction 0.001 < P < 0.002

Identified several important genes including MC4R, IGF2, CHCHD3, BMP2 and HOXA

[28]

26

Fat area

60K

150 crossbred pigs [Pietrain × (German Large White ×  German Landrace)]

ANOVA test

P < 1.0e^-5

Identified 663 important genes

[29]

27

Brown coat colour

60K

Brown pigs (n = 121) vs non-brown-coated pigs (n = 745)

Chi-square test

Permutation test

Identified TYRP1 gene

[30]

28

Racing distance

50K

118 elite Thoroughbred racehorses divergent for race distance aptitude

Chi-square test

Bonferroni correction P_unadj. = 1.61e^-9; P_Bonf. = 6.58e^-5

Identified a significant 690 kb region on ECA18 containing MSTN gene

[31]

29

Dwarfism

50K

Ten Friesian dwarf horses vs ten controls

Chi-square test

Bonferroni correction P < 1.72e^-6

Identified a significant region on ECA14: 3.8-5.4 Mb containing PROP1 gene

[33]

30

Lavender Foal Syndrome (LFS)

50K

Egyptian Arabian including 7 affected foals, their 31 relatives, as well as 114 controls

Fisher’s exact test

P < 0.05

Identified a significant region containing RAB27A and MYO5A genes

[34]

31

Recurrent laryngeal neuropathy (RLN)

50K

234 cases (196 Warmbloods, 20 Trotters, 14 Thoroughbreds, and 4 Draft horses), 228 breed-matched controls

Chi-square test

Bonferroni correction P < 1.09e^-6 (significant); P < 2.11e^-5 (suggestive)

Identified two significant SNPs on ECA21 and ECA31

[35]

32

Horn morphology

50K

107 Soay sheep from

the neighbouring island of Soay

Chi-square test

K_eff correction of P < 1.859e^-6

Identified a significant region on Chr10 including RXFP2 gene

[36]

33

Inherited Rickets

50K

Corriedale sheep including 17 affected and 3 carriers

IBD analysis

P < 0.05

Identified a 6Mb region on Chr6 including DMP1 gene

[40]

34

Degenerative myelopathy (DM)

50K

Pembroke Welsh corgi including 38 DM-affected cases and 17 controls

Chi-square test

P < 0.01

Identified a region of 28.91-29.67 Mb on CFA31 including SOD1 gene

[43]

35

Canine atopic

dermatitis (cAD)

20K

48 Golden Retrievers including 25 with atopic dermatitis and 23 healthy controls

Chi-square test

P < 0.001

Identified 35 significant SNPs

[46]

36

Arrhythmogenic right ventricular cardiomyopathy (ARVC)

50K

65 ARVC-affected boxer dogs vs 100 controls

Chi-square test

P < 0.05

Identified a region of CFA17: 32,256,760-32, 388,077bp containing STRN gene

[47]

37

Intervertebral Disc Calcification

20K

Dachshund dogs including 48 cases and 46 controls

Chi-square test

Permutation test using 100,000 permutations

Identified a region of CFA12: 36.8-38.6Mb with 36 significant SNPs

[48]

38

Fatness

3K

720 birds from two populations including F₂: Broiler ×  Fayoumi and F₂: Broiler × Leghorn

One-way ANOVA test

P < 0.01

Identified 39 significant SNPs mainly on GGA1, 2, 3, 4, 7, 8, 10, 12, 15 and 27

[49]

39

Body weight

60K

278 individuals from F₂ population crossed by Silky Fowl × White Plymouth Rock

Linear regression analyses

Bonferroni correction P < 1.92e^-6 (significant); P < 3.85e^-5 (suggestive)

Identified 9 significant SNPs on GGA4: 71.6-80.2 Mb including LDB2 gene

[50]

40

Growth traits

60K

489 birds from F₂ population crossed by WRR × XH

Generalized least square analysis

Bonferroni correction P < 4.08e^-8 (highly significant); P < 2.04e^-6 (significant); P < 4.08e^-5 (suggestive)

Identified 68 significant SNPs and 23 genes for 18 growth traits

[51]

41

Egg production and quality

60K

385 White leghorn and 361 brown-egg dwarf layers

Fisher’s combined probability method

Bonferroni correction P < 1.5 e^-6,

Identified 8 significant SNPs and two genes including GRB14 and GALNT1

[52]