title: Detection of selection signatures of population-specific genomic regions selected during domestication process in Jinhua pigs.
abstract: Chinese pigs have been undergoing both natural and artificial selection for thousands of years. Jinhua pigs are of great importance, as they can be a valuable model for exploring the genetic mechanisms linked to meat quality and other traits such as disease resistance, reproduction and production. The purpose of this study was to identify distinctive footprints of selection between Jinhua pigs and other breeds utilizing genome-wide SNP data. Genotyping by genome reducing and sequencing was implemented in order to perform cross-population extended haplotype homozygosity to reveal strong signatures of selection for those economically important traits. This work was performed at a 2% genome level, which comprised 152 006 SNPs genotyped in a total of 517 individuals. Population-specific footprints of selective sweeps were searched for in the genome of Jinhua pigs using six native breeds and three European breeds as reference groups. Several candidate genes associated with meat quality, health and reproduction, such as GH1, CRHR2, TRAF4 and CCK, were found to be overlapping with the significantly positive outliers. Additionally, the results revealed that some genomic regions associated with meat quality, immune response and reproduction in Jinhua pigs have evolved directionally under domestication and subsequent selections. The identified genes and biological pathways in Jinhua pigs showed different selection patterns in comparison with the Chinese and European breeds.
authors: College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
authors: Zhengcao
authors: Z
authors: Li
authors: College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
authors: Jiucheng
authors: J
authors: Chen
authors: School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
authors: Zhen
authors: Z
authors: Wang
authors: School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
authors: Yuchun
authors: Y
authors: Pan
authors: School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
authors: Qishan
authors: Q
authors: Wang
authors: College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
authors: Ningying
authors: N
authors: Xu
authors: College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China. wzhguang68@zju.edu.cn.
authors: Zhengguang
authors: Z
authors: Wang
mesh_terms: D000818:Animals; D001947:Breeding; D000071278:Domestication; D005260:Female; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes; D006720:Homozygote; D008297:Male; D008460:Meat; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012098:Reproduction / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000235:genetics*
keywords: 
  QTL
  ; Kyoto Encyclopedia of Genes and Genomes pathway; Polygenetic tree; cross population-extended haplotype homozygosity; selective sweep