Copy Number Variations and Expression Levels of Guanylate-Binding Protein 6 Gene Associated with Growth Traits of Chinese Cattle

Xiaogang Wang,Xiao Wang,Dan Hao,Yongzhen Huang,Hong Chen,Xinglei Qi,Haja N. Kadarmideen,Bo Thomsen,Xianyong Lan

doi:10.3390/ani10040566

Abstract

Simple SummaryOur study identified the copy number variations (CNVs) and transcriptional expressions of guanylate-binding protein 6 (GBP6) in Chinese cattle, as well as analyzed the association of CNVs and expressions with the growth traits of Chinese cattle. The results showed Xianan cattle with gain types (Log22−ΔΔCt > 0.5) of CNVs of GBP6 had highest relative gene expression levels in the muscle tissues and displayed superior phenotypic values of body weight, cannon circumference and chest circumference. Our study suggested that CNV gain types of GBP6 could be used as the candidate markers in the cattle-breeding program for growth traits.Association studies have indicated profound effects of copy number variations (CNVs) on various phenotypes in different species. In this study, we identified the CNV distributions and expression levels of guanylate-binding protein 6 (GBP6) associated with the growth traits of Chinese cattle. The results showed that the phenotypic values of body size and weight of Xianan (XN) cattle were higher than those of Nanyang (NY) cattle. The medium CNV types were mostly identified in the XN and NY breeds, but their CNV distributions were significantly different (adjusted p < 0.05). The association analysis revealed that the body weight, cannon circumference and chest circumference of XN cattle had significantly different values in different CNV types (p < 0.05), with CNV gain types (Log22−ΔΔCt > 0.5) displaying superior phenotypic values. We also found that transcription levels varied in different tissues (p < 0.001) and the CNV gain types showed the highest relative gene expression levels in the muscle tissue, consistent with the highest phenotypic values of body weight and cannon circumference among the three CNV types. Consequently, our results suggested that CNV gain types of GBP6 could be used as the candidate markers in the cattle-breeding program for growth traits.

Highlights

Structural variations (SVs) in the genome refer to DNA sequence polymorphisms in the fragment lengths with a dozen or hundreds of bases, which have larger effects on phenotypic variations thanSingle nucleotide polymorphisms (SNPs) [1]
The results showed that phenotypic values of BoW, ChC of XN cattle increased when the copy number variations (CNVs) types were from loss to gain, especially for CaC
Our study identified the CNV distributions of guanylate-binding protein 6 (GBP6) among six beef cattle breeds in China, and associated CNV types and gene expression levels with growth traits in XN, QC and NY cattle

Summary

Introduction

Structural variations (SVs) in the genome refer to DNA sequence polymorphisms in the fragment lengths with a dozen or hundreds of bases, which have larger effects on phenotypic variations thanSNPs [1]. Structural variations (SVs) in the genome refer to DNA sequence polymorphisms in the fragment lengths with a dozen or hundreds of bases, which have larger effects on phenotypic variations than. Single nucleotide polymorphisms (SNPs), the single nucleotide genetic variation in the genome, enable most of the common variations to be captured and genetic changes related to complex traits to be detected by many association studies [4]. A great difference between different individual genomes was caused by CNVs, which cover more base pairs than the per-locus mutations of SNPs and result in dramatic phenotypic consequence [5,6]. Association studies indicate that CNVs have profound effects on various phenotypes including diseases (e.g., neurological and developmental diseases) [7,8] and non-pathogenic traits (e.g., height) [9] in humans. Since the first CNV snapshot analysis identified 37 CNVRs in the pig genome across chromosomes 4, 7, 14, and

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