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

• DOI: 10.1186/s12864-018-4444-0
• Publication Date: 2018-01-25T11:59:57Z
• Authors: Clarissa Boschiero; Gabriel Costa Mon...; Almas Ara Gheyas; Thaís Fernanda Godoy; Gustavo Gasparin; Pilar Drummond Sa...; Marcela Paduan; Aline Silva Mello...; Mônica Corrêa Ledur; Luiz Lehmann Cout...
• Keywords: 0301 basic medicine; 570; Genetic variants; Meat; [SDV]Life Sciences [q-bio]; Eggs; Quantitative Trait Loci; SNP; QH426-470; Polymorphism, Single Nucleotide; 630; Poultry; Fat deposition; Avian Proteins; 03 medical and health sciences; INDEL Mutation; Next generation sequencing; Genetics; Animals; Fst; Selection, Genetic; 2. Zero hunger; Selection signatures; Genome; High-Throughput Nucleotide Sequencing; INDEL; Genomics; Phenotype; Chickens; TP248.13-248.65; Brazil; Biotechnology; Research Article

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 throghtout 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.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.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.