Copy Number Variation Of Cattle Genome

Copy number variation(CNV),as the main source of structural variation(SV)of animal genome,shapes the characteristics of phenotype diversity.The complicated origin of domestic cattle and the richness of cattle breed resources provide research materials for the analysis of genomic CNV.In this study,the whole genome re-sequencing data of 295 individuals from 42 domestic cattle breeds were selected(Bos indicus included 142 individuals and Bos taurus included 153 individuals),covering the Americas,Africa and South Asia,southeast Asia and southern China.Based on the latest high-quality bovine genome(ARS-UCD 1.2),CNVR data set of cattle genomes was extracted.We compared CNV in Bos indicus and Bos taurus genomes,and studied the relationship between spotted and white coat color traits with CNV in Pakistani zebu.And the following results were obtained in this study combined with population genetic analysis method:1.A total of 7,542 CNVRs were screened from 295 domestic cattle,including 5,866 Gain,1,436 Loss and 240 Both,with a total length of 47,344,858 bp,accounting for 1.74%of the cattle genome.The distribution of CNVR on chromosomes was not random,but mainly distributed in intergene region and intron region.2.Of the 142 Bos indicus genomes,a total of 10,170 CNVRs were selected,including8,478 Gain CNVRs,1,532 Loss CNVRs,and 160 Both CNVRs.Of the 153 Bos taurus genomes,a total of 4,239 CNVRs were selected,including 2,152 Gain CNVRs,1,877 Loss CNVRs,and 210 Both CNVRs.3.There was a significant difference in CNVR between Bos indicus and Bos taurus,and Bos indicus genomes have more abundant CNVR than Bos taurus genomes.The functional genes of differential CNVRs between Bos indicus and Bos taurus genomes were mainly enriched in immunity,reproduction,and development,and there were significant copy number variations in CATHL1,CATHL4,RASGRF1,and IGF1 R genes between Bos indicus and Bos taurus.4.Significant signals were detected in the KIT gene region for spotted coat color and white coat color traits in Pakistani zebu,and copy number variation in the KIT gene region(Chr6:69975194 – 70467027)was found to be a causative mutation in spotted coat color versus white coat color in Pakistani zebu.This study systematically evaluated the copy number variation of domestic cattle from the genome-wide perspective,and provided a CNV data set for the world’s major cattle breeds.The CNVs of the genome of Bos indicus and Bos taurus were analyzed,and it was found that the CNV of KIT gene was a causative mutation in the spotted coat color and white coat color traits of Pakistani zebu,which provided a scientific basis for the protection and utilization of genetic resources in Bos taurus and Bos indicus and had important theoretical and practical significance.