Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

Clarissa Boschiero (Lead Author), Gabriel Moreira, Almas Gheyas, Thais Godoy, Gustavo Gasparin, Pilar Mariani, Marcela Paduan, Aline Cesar, Mônica Ledur, Luiz Coutinho (Group Leader)

Research output: Contribution to journalArticlepeer-review


Background: Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throughout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection.
Results: A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL
data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development.
Conclusions: In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.
Original languageEnglish
Article number83
Number of pages18
JournalBMC Genomics
Issue number1
Publication statusPublished - 25 Jan 2018


  • Fat deposition
  • Fst
  • Genetic variants
  • Next generation sequencing
  • Selection signatures
  • SNP
  • Poultry


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