Abstract
BackgroundCopy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits.ResultsWe identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits.ConclusionsThe results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle’s evolution and breeding researches.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-480) contains supplementary material, which is available to authorized users.
Highlights
Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits
Compared with single nucleotide polymorphisms (SNPs), CNVs seem to have a stronger impact on phenotype and are shown to have effects on changes in gene expression levels [6], which can be explained by disruption of gene dosage, unmasking of recessive alleles, and loss of regulatory elements or regulatory polymorphisms [7,8]
We found that CNVR310 is significantly associated with heart girth (P < 0.05), probably due to the fact that CNVR310 was overlapped with the Quantitative trait loci (QTLs) for production (QTLs 11079 and 5297) and meat and carcass (QTLs 10021, 12174, 1395, and 22873) in beef cattle (Additional file 1: Tables S3 and S7)
Summary
Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. With one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits. CNV and copy number variable regions (CNVRs) have been a hot-spot in cattle genomic variation researches, which may be associated with, or affect, cattle’s health and production traits under recent selection. The next-generation sequencing was used to detect CNVR with more power [22,25,26] In these studies, the researchers focus more on the detection of CNV in different breeds
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