Detection of copy number variations and their effects in Chinese bulls

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.

Association study and expression analysis of CYP4A11 gene copy number variation in Chinese cattle

“…However, there have been no reports about the function of the CYP4A11 gene in cattle. We previously confirmed that the cattle CYP4A11 gene was located within CNVR44 that encompasses QTLs that alter economic traits like meat quality and milk production21. This location suggests that the copy number of CYP4A11 must be variable, which we hypothesized may have genetic effects that can be conveyed to phenotypes.…”

“…This reflected the positive effect of multiple copies of CYP4A11 on growth, which may be attributed to the location of CYP4A11 in the CNVR44 which includes QTLs that are linked to economic traits21. As previous reports showed, some genes were located within CNVRs that directly overlapped with QTLs for body weight, marbling score, and somatic cell count38, or were partly encompassed by QTLs for body weight, carcass weight, and breast muscle weight3940.…”

“…PLA2G2D , a gene related to milk production and meat quality, was reported to have multiple copies in beef cattle5. Consistently, PLA2G2D was found to be located in CNVR 22, whose number of repeats can significantly reduce the mRNA levels of PLA2G2D and correspondingly cause growth retardation in Chinese cattle21. Yue et al 4142.…”

Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep

“…Although there are numerous breeds of cattle and sheep both within and outside China, and no less than 10 studies report on the genomes of cattle, just two papers investigate CNVs in the sheep genome [9][10][11][12][13]. expressed as a decimal, whose GenCall score is greater than the specified threshold) less than 98% were excluded.…”

Modal Analysis on the Wind Tunnel Test Bed based on Workbench

“…Modal analysis [4,5] is a kind of modern method of studying the dynamic characteristics of the structure. It is mainly used to determine the vibration characteristics of the structure and the parts of the machine, including natural frequency and vibration.…”