Abstract
BackgroundIdentification of genomic regions that have been targets of selection for phenotypic traits is one of the most challenging areas of research in animal genetics, particularly in livestock where few annotated genes are available. In this study a genome-wide scan using the Illumina SNP50K Beadchip was performed in the attempt to identify genomic regions associated with milk productivity in sheep. The ovine genomic regions encoding putative candidate genes were compared with the corresponding areas in Bos taurus, as the taurine genome is better annotated.ResultsA total of 100 dairy sheep were genotyped on the Illumina OvineSNP50K Beadchip. The Fisher’s exact test of significance of differences of allele frequency between each pair of the two tails of the distribution of top/worse milk yielders was performed for each marker. The genomic regions where highly divergent milk yielders showed different allele frequencies at consecutive markers was extracted from the OAR v3.1 Ovine (Texel) Genome Assembly, and was compared to the corresponding areas in Bos taurus, allowing the detection of two genes, the Palmdelphin and the Ring finger protein 145. These genes encoded non-synonymous mutations correlated with the marker alleles.ConclusionThe innovation of this study was to show that the DNA genotyping with the Illumina SNP50K Beadchip allowed to detect genes, and mutations in the genes, which have not yet been annotated in the livestock under investigation.
Highlights
Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most challenging areas of research in animal genetics, in livestock where few annotated genes are available
With the aim to identify regions of the ovine genome that potentially affect milk productivity, we genotyped with the Illumina SNP50K Beadchip a population of dairy sheep, extremely variable as regards to milk traits; to the selective genotyping strategy, we examined the variation in SNP allele frequencies between the two tails of the distribution; the genomic regions surrounding or encoding the markers mostly differing in allele frequency between the distribution tails were checked for the presence of expressed genes either in sheep or other mammals, being sheep provided by many less annotated genes than cattle
Milk yield is an extremely complex trait, affected by a huge number of genes; in this work, milk yield was chosen as a target trait because a population showing an extremely high variability for milk traits was available
Summary
Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most challenging areas of research in animal genetics, in livestock where few annotated genes are available. With the aim to identify regions of the ovine genome that potentially affect milk productivity, we genotyped with the Illumina SNP50K Beadchip a population of dairy sheep, extremely variable as regards to milk traits; to the selective genotyping strategy, we examined the variation in SNP allele frequencies between the two tails of the distribution; the genomic regions surrounding or encoding the markers mostly differing in allele frequency between the distribution tails were checked for the presence of expressed genes either in sheep or other mammals, being sheep provided by many less annotated genes than cattle
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