Resequencing diverse Chinese indigenous breeds to enrich the map of genomic variations in swine

Huimin Kang; Haifei Wang; Ziyao Fan; Pengju Zhao; Amjad Khan; Zongjun Yin; Jiafu Wang; Wenbin Bao; Aiguo Wang; Qin Zhang; Jian-Feng Liu

doi:10.1016/j.ygeno.2015.08.002

Resequencing diverse Chinese indigenous breeds to enrich the map of genomic variations in swine

Genomics. 2015 Nov;106(5):286-94. doi: 10.1016/j.ygeno.2015.08.002. Epub 2015 Aug 18.

Authors

Huimin Kang¹, Haifei Wang², Ziyao Fan³, Pengju Zhao⁴, Amjad Khan⁵, Zongjun Yin⁶, Jiafu Wang⁷, Wenbin Bao⁸, Aiguo Wang⁹, Qin Zhang¹⁰, Jian-Feng Liu¹¹

Affiliations

¹ 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: [email protected].
² 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: [email protected].
³ 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: [email protected].
⁴ 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: [email protected].
⁵ 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: [email protected].
⁶ College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China. Electronic address: [email protected].
⁷ School of Animal Science, Guizhou University, Guiyang 550025, China. Electronic address: [email protected].
⁸ College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China. Electronic address: [email protected].
⁹ 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: [email protected].
¹⁰ 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: [email protected].
¹¹ 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: [email protected].

PMID: 26296457
DOI: 10.1016/j.ygeno.2015.08.002

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.

Keywords: INDEL; NGS; Pigs; SNV.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Breeding
DNA Mutational Analysis*
Female
Genetic Variation*
Genome*
Genomics
Male
Swine / genetics*