title: Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds.
abstract: Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression.
authors.affiliation: Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China Key laboratory of adaptation and evolution of plateau biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences.
authors.forename: Liangzhi
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China.
authors.forename: Shangang
authors.initials: S
authors.lastname: Jia
authors.affiliation: Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China.
authors.forename: Martin
authors.initials: M
authors.lastname: Plath
authors.affiliation: Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China.
authors.forename: Yongzhen
authors.initials: Y
authors.lastname: Huang
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, Maryland.
authors.forename: Congjun
authors.initials: C
authors.lastname: Li
authors.affiliation: Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China.
authors.forename: Chuzhao
authors.initials: C
authors.lastname: Lei
authors.affiliation: Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China chenhong1212@263.net.
authors.forename: Hong
authors.initials: H
authors.lastname: Chen
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000145:classification / Q000235:genetics*; D056915:DNA Copy Number Variations; D004272:DNA, Mitochondrial / Q000737:chemistry; D006824:Hybridization, Genetic; D008297:Male; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D014998:Y Chromosome / Q000737:chemistry
chemical_list: D004272:DNA, Mitochondrial
keywords: CNV; Y-chromosomal SNPs; mtDNA D-loop; parental origin