title: A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data.
abstract: Pigs have experienced dramatic selection due to domestication, which has led to many different phenotypes when compared to their wild counterparts, especially in the last several decades. Currently, genome-wide scans in both cattle and humans showing positive selection footprints have been investigated. However, few studies have focused on porcine selection footprints, particularly on a genome-wide scale. Surveying for selection footprints across porcine genomes can be quite valuable for revealing the genetic mechanisms of phenotypic diversity. Here, we employed a medium sequencing depth (5-20x/site per individual, on average) approach called genotyping by genome reducing and sequencing (GGRS) to detect genome-wide selection signatures of two domestic pig breeds (Yorkshire and Landrace) that have been under intensive selection for traits of muscle development, growth and behavior. The relative extended haplotype homozygosity test, which identifies selection signatures by measuring the characteristics of haplotypes' frequency distribution within a single population, was also applied to identify potential positively selected regions. As a result, signatures of positive selection were found in each breed. However, most selection signatures were population specific and related to genomic regions containing genes for biological categories including brain development, metabolism, growth and olfaction. Furthermore, the result of the gene set enrichment analysis indicated that selected regions of the two breeds presented a different over-representation of genes in the Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathways. Our results revealed a genome-wide map of selection footprints in pigs and may help us better understand the mechanisms of selection in pig breeding.
authors.affiliation: Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.forename: Qiang
authors.initials: Q
authors.lastname: Chen
authors.forename: Yumei
authors.initials: Y
authors.lastname: Yang
authors.forename: Hongjie
authors.initials: H
authors.lastname: Yang
authors.forename: Pengfei
authors.initials: P
authors.lastname: He
authors.forename: Zhe
authors.initials: Z
authors.lastname: Zhang
authors.forename: Zhenliang
authors.initials: Z
authors.lastname: Chen
authors.forename: Rongrong
authors.initials: R
authors.lastname: Liao
authors.forename: Yingying
authors.initials: Y
authors.lastname: Tu
authors.forename: Xiangzhe
authors.initials: X
authors.lastname: Zhang
authors.forename: Qishan
authors.initials: Q
authors.lastname: Wang
authors.forename: Yuchun
authors.initials: Y
authors.lastname: Pan
mesh_terms: D000818:Animals; D001947:Breeding; D002874:Chromosome Mapping; D005838:Genotype; D006239:Haplotypes; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000145:classification / Q000235:genetics*
keywords: REHH test; genome reducing and sequencing; pig genome; selective sweep