Genome-Wide Patterns of Genetic Variation in Two Domestic Chickens
| Autor: | Chih-Kuan Chen, Yu-Ting Lai, Chi-Tang Mao, Chih-Feng Chen, Mei-Yeh Jade Lu, Wei-Hua Chang, Wen-Lang Fan, Siao-Man Wu, Wen-Hsiung Li, Jiun-Jie Chen, Chia-Jung Liu, Chen Siang Ng, Wen-Sui Lo, Yu-Hsiang Chen |
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| Rok vydání: | 2013 |
| Předmět: |
DNA Copy Number Variations
chicken Quantitative Trait Loci Single-nucleotide polymorphism Breeding Quantitative trait locus Biology Polymorphism Single Nucleotide Genome INDEL Mutation single nucleotide polymorphism Genetic variation Genetics Animals Copy-number variation Gene Ecology Evolution Behavior and Systematics CNVs Genetic Variation Sequence Analysis DNA Phenotypic trait whole genome resequencing Phenotype Chickens Sequence Alignment Research Article Reference genome |
| Zdroj: | Genome Biology and Evolution |
| ISSN: | 1759-6653 |
| DOI: | 10.1093/gbe/evt097 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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