. 2012 Aug 22;3(1):26. doi: 10.1186/2049-1891-3-26

Table 1.

Summary of reported GWAS on domestic animals

No.	Trait	Chip	Animal	Method	Significant level	Result	Ref
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, SCD1and 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]