title: Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs.
abstract: In this study, we performed a genome-wide SV detection among the genomes of thirteen pigs from diverse Chinese and European originated breeds by next genetation sequencing, and constrcuted a single-nucleotide resolution map involving 56,930 putative SVs. We firstly identified a SV hotspot spanning 35 Mb region on the X chromosome specifically in the genomes of Chinese originated individuals. Further scrutinizing this region by large-scale sequencing data of extra 111 individuals, we obtained the confirmatory evidence on our initial finding. Moreover, thirty five SV-related genes within the hotspot region, being of importance for reproduction ability, rendered significant different evolution rates between Chinese and European originated breeds. The SV hotspot identified herein offers a novel evidence for assessing phylogenetic relationships, as well as likely explains the genetic difference of corresponding phenotypes and features, among Chinese and European pig breeds. Furthermore, we employed various SVs to infer genetic structure of individuls surveyed. We found SVs can clearly detect the difference of genetic background among individuals. This clues us that genome-wide SVs can capture majority of geneic variation and be applied into cladistic analyses. Characterizing whole genome SVs demonstrated that SVs are significantly enriched/depleted with various genomic features.
authors.affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
authors.forename: Pengju
authors.initials: P
authors.lastname: Zhao
authors.affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
authors.forename: Junhui
authors.initials: J
authors.lastname: Li
authors.affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
authors.forename: Huimin
authors.initials: H
authors.lastname: Kang
authors.affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
authors.forename: Haifei
authors.initials: H
authors.lastname: Wang
authors.affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
authors.forename: Ziyao
authors.initials: Z
authors.lastname: Fan
authors.affiliation: College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: Zongjun
authors.initials: Z
authors.lastname: Yin
authors.affiliation: School of Animal Science, Guizhou University, Guiyang, 550025, China.
authors.forename: Jiafu
authors.initials: J
authors.lastname: Wang
authors.affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Department of Agricultural, Food &Nutritional Science, University of Alberta, Edmonton, T6G 2C8, Canada.
authors.forename: Zhiquan
authors.initials: Z
authors.lastname: Wang
authors.affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
authors.forename: Jian-Feng
authors.initials: JF
authors.lastname: Liu
mesh_terms: D000818:Animals; D001947:Breeding; D056905:Chromosome Breakpoints; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D014644:Genetic Variation; D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D010641:Phenotype; D010802:Phylogeny; D015203:Reproducibility of Results; D017384:Sequence Deletion; D013552:Swine / Q000145:classification* / Q000235:genetics*