Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

Table 4 Significant SNPs and their genes associated with calving and conformation traits in Holstein cattle and causing potential functional consequences

SNP accession number	BTA^a	Position (bp)	Consequence^b	Amino acid change^c	Entrez gene name	Type traits	Calving traits
rs134519015	5	58464570	NSC	F/S	LOC782296	–	CA
rs110862689	5	105933019	NSC	F/L	AKAP3	BQ, ST	CA, SCEc, SCEh
rs109901274	7	93244933	NSC	F/S	ARRDC3	BD, BQ, CW, RAH	CA, SCEc, SCEh, SCSh
rs134432442	14	1736599	NSC	N/S	CPSF1	BQ	–
rs133271979	14	2019390	NSC	I/M	GRINA	BQ	–
rs110073506	18	56740979	NSC	Q/P	LOC511180	–	CA, SCEc, SCEh
rs136766893	18	58494682	NSC	L/P	BOSTAUV1R416	BD, BQ	CA, SCEc, SCEh, SCSc, SCSh
rs43098627	18	58590005	NSC	Y/S	BOSTAUV1R420	–	DCA, SCEc
rs110283226	18	60233963	NSC	I/R	LOC788599	BD	CA, DCA, SCEc, SCEh, SCSh
rs110104114	18	60342959	NSC	V/G	ZNF677	–	CA, SCEh
rs110302968	18	62832344	NSC	S/R	KIR2DL5A	–	CA, SCEc, SCEh, SCSc, SCSh
rs132815594	18	62843699	NSC	E/G	FCAR	–	CA, SCEc, SCEh, SCSh
rs41902720	18	63588968	NSC	H/R	BOSTAUV1R427	–	CA, SCEc, SCEh
rs41898987	18	65754940	NSC	W/G	ZNF274	–	SCEc
rs41892719	18	56183207	SSI	–	LOC785907	–	CA, SCEc, SCEh
rs41852917	17	71314935	SL	*/Q	HORMAD2	–	CA, SCEc, SCEh

Evaluated traits include calving ability (CA), daughter calving ability (DCA), maternal calving ease (heifer; CEh), maternal calf survival at first calving (heifer; CSh), maternal calving ease at later calvings (cow; CEc), maternal calf survival at later calvings (cow; CSc), direct calving ease at first calving (heifer; SCEh), direct calf survival at first calving (heifer; SCSh), direct calving ease at later calvings (cow; SCEc), direct calf survival at later calvings (cow; SCSc) and sire conception rate (SCR)
^aBTA = Bos taurus autosomes
^bConsequence = non-synonymous coding (NSC), splice site intronic (SSI), stop lost (SL)
^cAmino acid change = glutamic acids (E), phenylalanine (F), glycine (G), histidine (H), isoleucine (I), leucine (L), methionine (M), asparagine (N), proline (P), glutamine (Q), arginine (R), serine (S), valine (V), tryptophan (W), tyrosine (Y)

ISSN: 1297-9686