Abstract
BackgroundCopy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. In this study we used the Illunima BovineHD BeadChip to conduct genome-wide detection of CNVs in 215 polled yaks.ResultsA total of 1066 CNV regions (CNVRs) were detected with a total length of 181.6 Mb, comprising ~ 7.2% of the bovine autosomal genome. The size of these CNVRs ranged from 5.53 kb to 1148.45 kb, with an average size of 170.31 kb. Eight out of nine randomly chosen CNVRs were successfully validated by qPCR. A functional enrichment analysis of the CNVR-associated genes indicated their relationship to a number of molecular adaptations that enable yaks to thrive at high altitudes. One third of the detected CNVRs were mapped to QTLs associated with six classes of economically important traits, indicating that these CNVRs may play an important role in variations of these traits.ConclusionsOur genome-wide yak CNV map may thus provide valuable insights into both the molecular mechanisms of high altitude adaptation and the potential genomic basis of economically important traits in yak.
Highlights
Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits
Here, we produced the first genome-wide CNV map of yak based on the Illumina BovineHD BeadChip genotype data from 215 polled yaks
A total of 1066 CNV region (CNVR) were found in the yak genome, with a total length of 181.6 Mb, comprising ~ 7.2% of the bovine autosomal genome
Summary
Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. Genomic variations in terms of both sequence, as in the case of single nucleotide polymorphism base substitutions, and structure, as in instances of insertions, deletions, inversions, and copy number variations, can lead to the development of a diverse range of phenotypes that can be of economic importance when present in livestock. The yak is the primary form of livestock for the inhabitants of QTP, making its economic importance clear Despite this importance, efforts to improve the genetics of the domestic yak lag far behind those in beef cattle, dairy cattle, and other livestock. A comprehensive understanding of yak genetics offers an opportunity to accelerate genetics-based yak breeding efforts, and to understand the molecular basis of high altitude adaptations and other unique traits in these animals
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