Abstract
BackgroundThe central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility.ResultsIn total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952) of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612) were intronic and 9% (n = 464) were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS). Significant (P < 0.01) mean allele frequency differentials between the low and high fertility groups were observed for 720 SNPs (58 NSS). Allele frequencies for 43 of the SNPs were also determined by genotyping the 150 individual animals (Sequenom® MassARRAY). No significant differences (P > 0.1) were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total).ConclusionsThe results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post-natal growth and development and subsequent lactogenesis and fertility. We have identified a large number of variants segregating at significantly different frequencies between cattle groups divergent for calving interval plausibly harbouring causative variants contributing to heritable variation. To our knowledge, this is the first report describing sequencing of targeted genomic regions in any livestock species using groups with divergent phenotypes for an economically important trait.
Highlights
The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established
With the exception of F279Y, a non-synonymous SNP in exon 8 of growth hormone receptor (GHR) [8] strongly associated with milk yield and composition in dairy cattle, there is a dearth of information on candidate causal polymorphisms affecting performance in genes of this axis and its regulators
Of the approximate 1.5 Mb of sequence targeted for enrichment, 1.2 Mb was sequenced with an average of 44-fold coverage per base across both pools (Table 1)
Summary
The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility. The identification of putative genetic variants, including rare variants, underlying complex traits requires the analysis of large numbers of individual samples [18] and even with the rapid development of high-throughput sequencing technology and associated decreasing costs [19], sequencing of large numbers of individual genomes remains prohibitively expensive. The pooling of DNA from subsets of samples prior to high-throughout sequencing to reduce sequencing costs is a viable alternative and has been successfully used to identify variants associated with complex traits in humans [23,24]
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