DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle

Table 2 Information for the SNPs genotyped in this study and summary statistics for the 848 genotyped Irish Holstein-Friesian AI sires

Gene/Expressed allele	BTA	SNP ID¹	Nucleotide position of SNP	SNP gene position	Alleles (1/2)²	Frequency allele 1 (p)³	Heterozygosity	Deviation from HWE
CALCR/maternal	4	rs42940189	11,049,538	Exonic (non-syn)	G/A	0.90	0.15	< 0.001
	4	rs42940187	11,039,296	Exonic (syn)	C/T	0.86	0.23	0.03
GRB10/ isoform-dependent	4	GRB10_p.A5394141C	5,394,141	Intronic	C/A	0.95	0.09	0.11
	4	rs43375833	5,334,910	Intronic	C/T	0.67	0.42	0.14
ZNF215/ maternal	15	rs42575466	44,945,003	Exonic (syn)	G/A	0.95	0.09	< 0.00001
	15	rs42575474	44,934,196	Intronic	G/A	0.67	0.43	0.46
PEG3/ paternal	18	PEG3_p.A64370595G	64,370,595	Upstream	G/A	0.69	0.44	0.36
	18	PEG3_p.C64367437T	64,367,437	Upstream	C/T	0.66	0.45	0.81
	18	rs17871322	64,362,259	Exonic (syn)	G/A	0.66	0.46	0.43
ZIM2/ paternal expression in humans; polymorphic expression in mice	18	rs41899915	64,234,488	Exonic (syn)	C/G	0.80	0.32	0.43
	18	rs41899913	64,233,519	3'UTR	G/C	0.83	0.28	0.85
	18	rs41899911	64,232,216	3'UTR	C/T	0.80	0.32	0.41
	18	rs41899910	64,231,503	3'UTR	T/C	0.70	0.40	0.28
RASGRF1/ paternal	21	RASGRF1_p.C25039690T	25,039,690	Intronic	A/G	0.59	0.42	< 0.001
PHLDA2/ maternal	29	rs42194502	50,555,723	3'UTR	A/T	0.90	0.18	0.17
TSPAN32/ maternal	29	rs42637579	51,123,847	Intronic	G/A	0.63	0.42	< 0.01
	29	rs42637578	51,123,729	Exonic (syn)	T/C	0.94	0.11	0.32

Genotype and allele frequencies and the significance of deviations from Hardy-Weinberg equilibrium (HWE) based on P-values obtained from χ²-test results are shown for all 17 SNPs. All SNP nucleotide positions were obtained from the Build 4.0 of the B. taurus genome sequence on the ENSEMBL database (http://www.ensembl.org) or the UCSC genome browser (http://genome.ucsc.edu). The ORF gene model positions for each SNP are given. For exonic SNPs, amino acid sequence changing SNPs (i.e. non-synonymous SNPs, denoted 'non-syn') and non-amino acid sequence changing SNPs (i.e. synonymous SNPs, denoted 'syn') are shown. The imprinting status of each gene is based on data from human and mice and, where possible, cattle, sheep and pigs [14, 16].
¹ Where possible, SNP identities (IDs) are given as per their entry in the dbSNP database [43]; [http://www.ncbi.nlm.nih.gov/projects/SNP]. Where no dbSNP ID was available, SNPs were labelled as per nomenclature used by Magee et al. [8] as detailed in the main body text of the manuscript.
² Alleles 1 and 2 represent the major and minor alleles, respectively, at a given SNP
³ The frequency of allele 1 (p), the major allele at a SNP locus

ISSN: 2730-6844