Genome-Wide Patterns of Genetic Variation in Two Domestic Chickens

Abstract

Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ∼23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ∼7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

“…However, some previous CNV studies in chickens based on aCGH and SNP platforms mainly suffered from low resolution and sensitivity [9,[32][33][34][35]. A latest study exhibited the detection of four main types of genetic variation from whole genome sequencing data using two chickens [36], suggesting the efficiency of CNV detection via deep sequencing. Considering that a great number of CNVs appears to be segregating in distinct breeds, we selected 12 chickens from multiple breeds with extensive genetic diversity, including seven Chinese indigenous breeds [37], four commercial breeds and one Red Jungle Fowl.…”

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication

“…For example, using different analyses, we identified two genes, TSHR and TBC1D1, both of which were previously reported to regulate seasonal reproduction and growth among domestic chickens [1,25]. IG-F2BP3 was identified by its high score in the 10-kb grid size XP-CLR test (Figure 1), and further supported by the 5-kb and 2-kb grid size analyses (Supplementary information, Figure S2).…”

Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

“…Recently, population genomics studies, which search for genetic signatures of selection in the genome (Akey, 2009), have been conducted using high density SNPs genotyping and whole genome sequencing techniques in the livestock genome (e.g., Rubin et al, 2010;Elferink et al, 2012;Fan et al, 2013;Qanbari et al, 2015). This population genomics approach has allowed gene-level resolution mapping of loci that have been positively selected for, without any phenotypic information (Qanbari et al, 2014).…”