Detection Of Differential CNVs Between Bos Taurus And Bos Indicus To Study The Ancestry Of Hubei Enshi Cattle

Bos taurus and Bos indicus are the two main cattle subspecies in the world.They have significant differences in environmental adaptability and economic traits.They are the main blood source of beef cattle breeds in the central and southern regions of China;In-depth analysis of the differences in genetic resources between them are of great significance for understanding the formation mechanism of beef cattle’s excellent traits and promoting the process of breed improvement in our country.This study used the next-generation high-throughput sequencing data to successfully construct a copy number variation(CNV,Copy Number Variation)database of 83 cattle of 11 breeds.With the help of various bioinformatics methods(quantitative genetics,comparative genomics et al)we identified differences long structure variations between the genomic sequences of Bos taurus and Bos indicus and analyzed the potential formation and regulation mechanisms of key differential genome sequences.Moreover,further analysis about the blood composition of Bos taurus and Bos indicus in Enshi cattle from the perspective of CNV were carried out.The main findings are as follows:(1)Integrating three CNV detection strategies to perform CNV detection on the next-generation high-throughput sequencing data of 73 representative Bos taurus and Bos indicus of the world,a total of 182,823 CNV events were found.We have annotated and performed enrichment analysis to these CNVs.The results show that the CNVs of cattle mainly occur in the pseudogene region and non-coding region.There are relatively fewer cases that genes’intron and exon are affected by CNV and these genes affected by CNV significantly enriched in immune-related GO(Gene Ontology)items.(2)Using Fst statistics,it was found that there are 7 significant differences(top 0.1%)CNVs between Bos taurus and Bos indicus and their corresponding 8 selected genes(CTNNA1,ENSBTAG00000004415,PKN2,BMPER,PDE1C.DNAJC18,MUSK,PLCXD3).Gene function analysis showed that these selected genes mainly regulate processes such as energy metabolism,heat shock,and muscle cell differentiation.At the same time,functional analysis of the 1.74Mb specific sequence of the Bos indicus population revealed that the function of the genes on specific sequence of the Bos indicus are significantly(FDR<0.05)enriched on regulation of signal transduction to Rho protein(Heat shock related).Further analysis proves that the differential sequence of Bos taurus and Bos indicus is related to the selection adaptability of the two.Using multi-omics strategies to analyze the formation time and impact of the most significant difference in CNV,we found that this CNV is a CTH reverse transcription pseudogene region,which may affect the differences in muscle development between Bos taurus and Bos indicus through the variation of CTH and CTNNA1 near the pseudogene.(3)Using the whole genome sequencing data of 10 Enshi cattle,a total of 27,251 CNVs were detected.Analyzing the gene functions affected by CNV in Enshi cattle,it was found that 21 genes related to puberty were significantly enriched,of which 16 genes that advanced the estrus period were destroyed by CNV,which may be responsible for the relatively late estrus period of Enshi cattle.Using the three analysis methods of principal component analysis,clustering and group stratification to analyze the population structure of Enshi cattle and(1)Bos taurus and Bos indicus.it was shown that Enshi cattle have both pedigrees from Bos taurus and Bos indicus.which preliminarily proves that Enshi cattle may be formed by the hybridization of Bos taurus and Bos indicus.Further statistics on the distribution of CNVs related to selection adaptability of Bos taurus and Bos indicus in Enshi cattle populations show that it still has a diverse distribution in Enshi cattle populations,and the selection pressure is relatively small but full of potential for further selection.This study is the first paper to identify the differential genome sequence and related selected genes related to the selection adaptability of Bos taurus and Bos indicus,with the help of which we successfully analyzed the pedigree composition of Enshi cattle.It provides necessary materials and basis for the further selection and breeding of beef cattle in central and southern China,which promotes the further selection and improvement of Enshi cattle.