title: Resequencing diverse Chinese indigenous breeds to enrich the map of genomic variations in swine.
abstract: To enrich the map of genomic variations in swine, we randomly sequenced 13 domestic and wild individuals from China and Europe. We detected approximately 28.1 million single nucleotide variants (SNVs) and 3.6 million short insertions and deletions (INDELs), of which 2,530,248 SNVs and 3,456,626 INDELs were firstly identified compared with dbSNP 143. Moreover, 208,687 SNVs and 24,161 INDELs were uniquely observed in Chinese pigs, potentially accounting for phenotypic differences between Chinese and European pigs. Furthermore, significantly high correlation between SNV and INDEL was witnessed, which indicated that these two distinct variants may share similar etiologies. We also predicted loss of function genes and found that they were under weaker evolutionary constraints. This study gives interesting insights into the genomic features of the Chinese pig breeds. These data would be useful in the establishment of high-density SNP map and would lay a foundation for facilitating pig functional genomics study.
authors: 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. Electronic address: nongdaxiaokang@126.com.
authors: Huimin
authors: H
authors: Kang
authors: 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. Electronic address: wanghaiffei@126.com.
authors: Haifei
authors: H
authors: Wang
authors: 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. Electronic address: nuclearfan@cau.edu.cn.
authors: Ziyao
authors: Z
authors: Fan
authors: 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. Electronic address: zhaopengju2014@gmail.com.
authors: Pengju
authors: P
authors: Zhao
authors: 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. Electronic address: amjadkhanqau@gmail.com.
authors: Amjad
authors: A
authors: Khan
authors: College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China. Electronic address: yinzongjun@ahau.edu.cn.
authors: Zongjun
authors: Z
authors: Yin
authors: School of Animal Science, Guizhou University, Guiyang 550025, China. Electronic address: jfwang@gzu.edu.cn.
authors: Jiafu
authors: J
authors: Wang
authors: College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China. Electronic address: wbbbao@yzu.edu.cn.
authors: Wenbin
authors: W
authors: Bao
authors: 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. Electronic address: agwang@cau.edu.cn.
authors: Aiguo
authors: A
authors: Wang
authors: 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. Electronic address: qzhang@cau.edu.cn.
authors: Qin
authors: Q
authors: Zhang
authors: 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. Electronic address: liujf@cau.edu.cn.
authors: Jian-Feng
authors: JF
authors: Liu
mesh_terms: D000818:Animals; D001947:Breeding; D004252:DNA Mutational Analysis; D005260:Female; D014644:Genetic Variation; D016678:Genome; D023281:Genomics; D008297:Male; D013552:Swine / Q000235:genetics*
keywords: INDEL; NGS; Pigs; SNV