title: Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations.
abstract: The identification of signals left by recent positive selection provides a feasible approach for targeting genomic variants that underlie complex traits and fitness. A better understanding of the selection mechanisms that occurred during the evolution of species can also be gained. In this study, we simultaneously detected the genome-wide footprints of recent positive selection that occurred within and between Chinese Holstein and Simmental populations, which have been subjected to artificial selection for distinct purposes. We conducted analyses using various complementary approaches, including LRH, XP-EHH and FST, based on the Illumina 770K high-density single nucleotide polymorphism (SNP) array, to enable more comprehensive detection.
  
  
  
  We successfully constructed profiles of selective signals in both cattle populations. To further annotate these regions, we identified a set of novel functional genes related to growth, reproduction, immune response and milk production. There were no overlapping candidate windows between the two breeds. Finally, we investigated the distribution of SNPs that had low FSTvalues across five distinct functional regions in the genome. In the low-minor allele frequency bin, we found a higher proportion of low-FSTSNPs in the exons of the bovine genome, which indicates strong purifying selection of the exons.
  
  
  
  The selection signatures identified in these two populations demonstrated positive selection pressure on a set of important genes with potential functions that are involved in many biological processes. We also demonstrated that in the bovine genome, exons were under strong purifying selection. Our findings provide insight into the mechanisms of artificial selection and will facilitate follow-up functional studies of potential candidate genes that are related to various economically important traits in cattle.
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, 100193, China.|Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, AU-Foulum, 8830, Tjele, Denmark.
authors.forename: Minhui
authors.initials: M
authors.lastname: Chen
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, 100193, China.
authors.forename: Dunfei
authors.initials: D
authors.lastname: Pan
authors.affiliation: National Natural Science Foundation of China, Beijing, 100085, China.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Ren
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, 100193, China.
authors.forename: Jinluan
authors.initials: J
authors.lastname: Fu
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China.
authors.forename: Junya
authors.initials: J
authors.lastname: Li
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, AU-Foulum, 8830, Tjele, Denmark.
authors.forename: Guosheng
authors.initials: G
authors.lastname: Su
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, 100193, China.
authors.forename: Aiguo
authors.initials: A
authors.lastname: Wang
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, 100193, China.
authors.forename: Li
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, 100193, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, China Agricultural University, Beijing, 100193, China. liujf@cau.edu.cn.
authors.forename: Jian-Feng
authors.initials: JF
authors.lastname: Liu
mesh_terms: D000483:Alleles; D000818:Animals; D002417:Cattle / Q000235:genetics*; D005787:Gene Frequency; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D000068618:Selective Breeding / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods