Identifying artificial selection signals in the chicken genome

PLoS One. 2018 Apr 26;13(4):e0196215. doi: 10.1371/journal.pone.0196215. eCollection 2018.

Abstract

Identifying the signals of artificial selection can contribute to further shaping economically important traits. Here, a chicken 600k SNP-array was employed to detect the signals of artificial selection using 331 individuals from 9 breeds, including Jingfen (JF), Jinghong (JH), Araucanas (AR), White Leghorn (WL), Pekin-Bantam (PB), Shamo (SH), Gallus-Gallus-Spadiceus (GA), Rheinlander (RH) and Vorwerkhuhn (VO). Per the population genetic structure, 9 breeds were combined into 5 breed-pools, and a 'two-step' strategy was used to reveal the signals of artificial selection. GA, which has little artificial selection, was defined as the reference population, and a total of 204, 155, 305 and 323 potential artificial selection signals were identified in AR_VO, PB, RH_WL and JH_JF, respectively. We also found signals derived from standing and de-novo genetic variations have contributed to adaptive evolution during artificial selection. Further enrichment analysis suggests that the genomic regions of artificial selection signals harbour genes, including THSR, PTHLH and PMCH, responsible for economic traits, such as fertility, growth and immunization. Overall, this study found a series of genes that contribute to the improvement of chicken breeds and revealed the genetic mechanisms of adaptive evolution, which can be used as fundamental information in future chicken functional genomics study.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breeding
  • Chickens / classification
  • Chickens / genetics*
  • Genetic Variation
  • Genetics, Population
  • Genome*
  • Genotype
  • Haplotypes
  • Hypothalamic Hormones / genetics
  • Linkage Disequilibrium
  • Oligonucleotide Array Sequence Analysis
  • Parathyroid Hormone-Related Protein / genetics
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Principal Component Analysis
  • Selection, Genetic

Substances

  • Hypothalamic Hormones
  • Parathyroid Hormone-Related Protein

Grants and funding

This research was financially supported by the National Natural Science Foundation of China (31772585, 31601916) and the Fundamental Research Funds for the Central Universities (0900202930, 2662015QD018). The funders did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the “author contributions” section.