Study On The Copy Number Variation Of The CHKB,KLF6,GPC1 And CHRM3 Genes Associated With Growth Traits And Gene Expression In Chinese Domestic Yak(Bos Grunniens)

Copy number variation?CNV?is a significant marker of the genetic and phenotypic diversity among individuals that accounts for complex quantitative traits of phenotype and diseases via modulating gene dosage,position effects,alteration of downstream pathways,modification of chromosome structure and position within the nucleus and disrupting coding regions in the genome.Associating copy number variations?CNVs?with growth and gene expression are a powerful approach for identifying genomic characteristics that contribute to phenotypic and genotypic variation.A previous study using next-generation sequencing illustrated that the choline kinase beta?CHKB?,Krüpple-like factor 6?KLF6?,glypican 1?GPC1?and cholinergic receptor muscarinic 3?CHRM3?genes reside within copy number variable regions?CNVRs?of yak populations that overlap with quantitative trait loci?QTLs?of meat quality and growth.The aim of this study was to detect the distributions of CNVs of the KLF6,CHKB,GPC1,and CHRM3 genes in five breeds of domestic yak?Datong,Polled,Gannan,Tianzhu white and Plateau yaks?and to explore their effect on growth traits and gene expression.The data was analyzed by real-time quantitative PCR?qPCR?,Pearson product-moment correlation?R?,and one-way analysis of variance?ANOVA?using SPSS software?IBM SPSS 20?.These results indicated that the normal CNV types of the CHKB and GPC1,the loss CNV types of the KLF6,and the gain CNV types of the CHRM3 genes were significantly?P<0.05?associated with high body length,height and weight and chest girth in six-month-old and five-year-old Datong yaks.The association study between CNVs and growth traits suggested that CNVs of the CHKB,KLF6,GPC1 and CHRM3 genes might be important for yak breeding programs,particularly to improve the growth traits.The results showed that the distribution CNVs of the CHKB,KLF6,and GPC1 genes presented more copy number losses in Tianzhu,Gannan and Plateau yak populations compared with the Datong and polled yak having relatively more copy number gains.However,the CHRM3 CNV showed more copy number gains in five yak populations.Therefore,these results indicate that there are relatively more copy number losses?deletion?in the yak populations;supporting the hypothesis that log₂ ratio is more powerful at detecting loss than gain in copy number types.The expression levels of CHKB,KLF6,GPC1 and CHRM3 were mostly high during fetal development?embryo?and low in adult tissues but these followed the same patterns at both developmental ages,supporting a biological role for these genes in cell proliferation and differentiation and development,particularly during fetal development.These observations underscored that the DNA copy number and mRNA transcription levels of the CHKB,KLF6,GPC1 and CHRM3 genes were negatively correlated owing to the influence of gene expression.These results confirmed the significant function of CHKB,KLF6,GPC1 and CHRM3 CNVRs in determining the mRNA expression levels of these genes in Bos grunniens skeletal muscles and the expression of these genes affects quantitative growth traits in yak populations through the negative relationship between DNA copy numbers and gene expression.This work provides the first observation of the biological role of CNVs of the CHKB,KLF6,GPC1 and CHRM3 genes in Datong yak breed and might,therefore,provide a novel opportunity to utilize data on CNVs in designing molecular markers for the selection of animal breeding programs for larger populations of various yak breeds.Therefore,we hypothesized that this study provided inclusive information on the application of CNVs of the CHKB,KLF6,GPC1 and CHRM3 genes in growth traits in Datong yaks and its possible function in bovine species.