Epistatic interactions between at least three loci determine the “rat-tail” phenotype in cattle

Table 4 Summary of genome-wide significant associations from a GWAS for hair conformation and hair dilution traits associated with the RTS in F₁, F₂ and BC individuals with at least one E ^D allele at the extension locus and heterozygous for the PMEL c.64G>A locus

Trait	Model^a	Marker	BTA	Position (bp)	p value	q value^b
Level of coat colour dilution	Case–control	Hapmap44614-BTA-72802	5	21,114,508	8.90E−07	0.033
Level of coat colour dilution	Case–control	Hapmap53597-rs29010787	5	19,015,523	1.15E−06	0.043
Level of coat colour dilution	Case–control	BTA-74302-no-rs	5	18,047,140	1.22E−06	0.046
Hair length variation	Case–control	BTA-74302-no-rs	5	18,047,140	1.74E−07	0.007
Hair length variation	Case–control	Hapmap42402-BTA-103350	5	21,484,201	2.69E−07	0.010
Hair length variation	Case–control	Hapmap44614-BTA-72802	5	21,114,508	1.04E−06	0.039
Hair length variation	Case–control	ARS-BFGL-NGS-26310	5	12,123,561	1.17E−06	0.044
RTS classification phenotype	Case–control	Hapmap44614-BTA-72802	5	21,114,508	9.03E−07	0.033
RTS classification phenotype	Case–control	Hapmap53597-rs29010787	5	19,015,523	1.14E−06	0.043
RTS classification phenotype	Case–control	BTA-74302-no-rs	5	18,047,140	1.17E−06	0.044
Hair length variation	Mixed	BTA-74302-no-rs	5	18,047,140	7.36E−09	0.0003
Hair length variation	Mixed	ARS-BFGL-NGS-26310	5	12,123,561	1.68E−07	0.006
Hair length variation	Mixed	BTA-103542-no-rs	5	16,795,347	1.84E−07	0.007
RTS classification phenotype	Mixed	BTA-74302-no-rs	5	18,047,140	3.43E−08	0.001
RTS classification phenotype	Mixed	Hapmap42402-BTA-103350	5	21,484,201	8.16E−07	0.030

^aCase–control: genotype association study in a case–control design, Mixed: mixed linear models including phenotype scores
^bBonferroni corrected p values to account for multiple testing

ISSN: 1297-9686