A catalogue of validated single nucleotide polymorphisms in bovine orthologs of mammalian imprinted genes and associations with beef production traits

Abstract

Genetic (or 'genomic') imprinting, a feature of approximately 100 mammalian genes, results in monoallelic expression from one of the two parentally inherited chromosomes. To date, most studies have been directed on imprinted genes in murine or human models; however, there is burgeoning interest in the effects of imprinted genes in domestic livestock species. In particular, attention has focused on imprinted genes that influence foetal growth and development and that are associated with several economically important production traits in cattle, sheep and pigs. We have re-sequenced regions in 20 candidate bovine imprinted genes in order to validate single nucleotide polymorphisms (SNPs) that may influence important production traits in cattle. Putative SNPs detected via re-sequencing were subsequently re-formatted for high-throughput SNP genotyping in 185 cattle samples comprising 138 performance-tested European Bos taurus (all Limousin bulls), 29 African B. taurus and 18 Indian B. indicus samples. Analysis of the resulting genotypic data identified 117 validated SNPs. Preliminary genotype-phenotype association analyses using 83 SNPs that were polymorphic in the Limousin samples with minor allele frequencies >0.05 revealed significant associations between two candidate bovine imprinted genes and a range of important beef production traits: average daily gain, average feed intake, live weight, feed conversion ratio, residual feed intake and residual gain. These genes were the Ras proteinspecific guanine nucleotide releasing factor gene ( RASGRF1) and the zinc finger, imprinted 2 gene ( ZIM2). Despite the relatively small sample size used in these analyses, the observed associations with production traits are supported by the purported biological function of the RASGRF1 and ZIM2 gene products. These results support the hypothesis that imprinted genes contribute significantly to important complex production traits in cattle. Furthermore, these SNPs may be usefully incorporated into future marker-assisted and genomic selection breeding schemes.

Single nucleotide polymorphisms in the imprinted bovine insulin‐like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein‐Friesian cattle

“…While most studies of imprinted genes have focussed on mouse and human disease models, there is accumulating evidence suggesting that imprinted loci underlie performance in domesticated animals and hence may serve as molecular targets for artificial selection and animal breeding strategies (Ruvinsky 1999; de Koning et al. 2002; Magee et al. 2010).…”

“…At the time of laboratory analysis, 11 putative B. taurus IGF2R SNPs (all intronic) were deposited in the Ensembl database (Build 3.1 of the B. taurus genome assembly, Ensembl release 46, August 2007; http://aug2007.archive.ensembl.org/Bos_taurus). For SNP validation purposes, high‐fidelity polymerase chain reaction (PCR) amplicons spanning six of these putative IGF2R SNPs, distributed across 90 592 base pairs (bp) of the IGF2R gene, were generated and sequenced in a panel of 17 European B. taurus animals (six Limousin, five Simmental and six Aberdeen Angus samples) (Magee et al. 2010).…”

Variability in Candidate Genes Revealed Associations with Meat Traits in the Piemontese Cattle Breed

“…One of these genes, IGF2, is imprinted in cattle (Dindot et al, 2004), as in other mammalian species, but undergoes a postnatal loss of imprinting (Goodall and Schmutz, 2007), so that only the paternal allele is expressed during the foetal life, while both alleles are expressed after birth. Recently, imprinted genes, including IGF2, were confirmed as candidates for beef production traits in Limousin breed, supporting their role in animal growth and development (Magee et al, 2010). Associations of the IGF2 polymorphism here considered with birth weight were reported in different beef populations and crossbreds, and selection for CC sires was proposed to ensure lower birth weight in order to reduce dystocia risks (Schmutz and Goodall, 2005;Goodall and Schmutz, 2007).…”

“…However, as many of the genotyped SNPs are located in anonymous regions, the detection of associations with traits of interest does not directly lead to the identification of the underlying genes (Magee et al, 2010). For these reasons the candidate gene approach, which aims at identifying specific polymorphisms responsible for the observed effects in genes biologically related to the traits of interest, is still a valuable strategy (Ron and Weller, 2007).…”

Genomic characterisation and conservation genetics of the indigenous Irish Kerry cattle breed

“…This Kerry population sample group is coded as KY12. Genomic DNA was purified from nasal swabs using the Promega Maxwell ® 16 DNA automated DNA extraction platform (Promega UK, Southampton, United Kingdom) and established methods developed at the UCD Animal Genomics Laboratory (Magee et al, 2010; Magee et al, 2011).…”