Discovery, characterization and validation of single nucleotide polymorphisms within 206 bovine genes that may be considered as candidate genes for beef production and quality

Abstract

A large number of putative single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project. However, few of these have been validated and many will turn out to be sequencing artefacts or have low minor allele frequencies. In addition, there is little information available on SNPs within coding regions, which are likely to be responsible for phenotypic variation. Therefore, additional SNP discovery is necessary to identify and validate polymorphisms both in specific genes and genome-wide. Sequence-tagged sites within 286 genes were resequenced from a panel of animals representing a wide range of European cattle breeds. For 80 genes, no polymorphisms were identified, and 672 putative SNPs were identified within 206 genes. Fifteen European cattle breeds (436 individuals plus available parents) were genotyped with these putative SNPs, and 389 SNPs were confirmed to have minor allele frequencies above 10%. The genes containing SNPs were localized on chromosomes by radiation hybrid mapping and on the bovine genome sequence by Blast. Flanking microsatellite loci were identified, to facilitate the alignment of the genes containing the SNPs in relation to mapped quantitative trait loci. Of the 672 putative SNPs discovered in this work, only 11 were found among the validated SNPs and 100 were found among the approximately 2.3 million putative SNPs currently in dbSNP. The genes studied in this work could be considered as candidates for traits associated with beef production and the SNPs reported will help to assess the role of the genes in the genetic control of muscle development and meat quality. The allele frequency data presented allows the general utility of the SNPs to be assessed.

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

“…117/133). The SNP density reported here is comparable to the estimates previously reported by Heaton et al (2001), while the putative SNP-to-validated SNP conversion rate is higher than that reported by Williams et al (2009;56.0%), but lower than the 92.0% conversion rate reported by Van Tassell et al (2008).…”

“…DNA sequence analysis provided a total of 133 putative SNPs detected across 15 of the 20 candidate imprinted genes screened. This data set yielded an estimated SNP discovery rate of one putative SNP for every 333 bp sequenced -a figure that is comparable to other studies involving bovine SNP discovery and validation (Williams et al, 2009).…”

“…Recent mining of this genome sequence identified a total of 2.3 million putative SNPs; however, many of these are unvalidated and a large proportion are expected to be either heterozygous DNA sequence variants in the sequenced heifer, which may SNPs in candidate bovine imprinted genes be present at undetectable frequencies in larger populations, or to represent sequencing artefacts often encountered during genome sequencing projects (Williams et al, 2009). Consequently, there is a strong requirement for validating SNPs before initiating population genetic studies in domestic cattle populations.…”

“…The majority of these exist as single nucleotide polymorphisms -E-mail: david.magee@ucd.ie (SNPs) -single base pair (bp) substitutions in genomic DNA where the least common allele has a frequency of 1% or greater within a population (Kruglyak and Nickerson, 2001). Studies of the bovine genome have estimated an average density of one SNP for every 500 bp to 1 kb sequenced, while recent mining of the complete bovine genome sequence has identified over 2.3 million putative SNPs (Heaton et al, 2001;Van Tassell et al, 2008;Elsik et al, 2009;Gibbs et al, 2009;Williams et al, 2009).…”

Variation in the bovine FABP4 gene affects milk yield and milk protein content in dairy cows

“…Variation in bovine FABP4 has been investigated in both beef cattle101112 and dairy cattle89. Eight single nucleotide polymorphisms (SNPs) have been validated in beef cattle, and of these, five SNPs (one non-synonymous SNP, one splice-site SNP and three intronic SNPs) are located in a small exon 3-intron 3 region11 that would be suitable for polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis analysis.…”