Abstract
BackgroundMeat 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.ResultsA 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.ConclusionsIn 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.
Highlights
Meat and egg-type chickens have been selected for several generations for different traits
Polymorphism identification The initial variant call resulted in 15,944,063 Single Nucleotide Polymorphism (SNP) and 1,997,771 Insertions and Deletions (INDEL) from 28 individuals analyzed, including autosomes 1–28 and 32, two linkage groups, mitochondrial, sex chromosomes (W/Z), and unplaced scaffolds
Most of the variants were located in noncoding regions, we identified 7255 intolerant nonsynonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions
Summary
Meat and egg-type chickens have been selected for several generations for different traits. Chickens are one of the most important animals in the world, because of the intensive production of meat and eggs, and because they are a model for developmental and genomic studies. The domestic chicken has hundreds of different breeds, but commercial chickens can be divided into two main groups – broilers (meat-type) and layers (eggtype), which have been artificially selected for centuries. These two types have different phenotypic and genotypic profiles as a consequence of distinct genetic backgrounds and intensive genetic selection for different traits [2]. Selection of layer chickens is focused mainly on reproductive traits, e.g. egg production and egg quality
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