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Copy number variation in F ayoumi and L eghorn chickens analyzed using array comparative genomic hybridization
Author(s) -
Abernathy J.,
Li X.,
Jia X.,
Chou W.,
Lamont S. J.,
Crooijmans R.,
Zhou H.
Publication year - 2014
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12141
Subject(s) - biology , copy number variation , comparative genomic hybridization , genetics , inbreeding , genome , copy number analysis , gene , population , demography , sociology
Summary Copy number variation refers to regions along chromosomes that harbor a type of structural variation, such as duplications or deletions. Copy number variants ( CNV s) play a role in many important traits as well as in genetic diversity. Previous analyses of chickens using array comparative genomic hybridizations or single‐nucleotide polymorphism chip assays have been performed on various breeds and genetic lines to discover CNV s. In this study, we assessed individuals from two highly inbred (inbreeding coefficiency > 99.99%) lines, L eghorn G ‐ B 2 and F ayoumi M 15.2, to discover novel CNV s in chickens. These lines have been previously studied for disease resistance, and to our knowledge, this represents the first global assessment of CNV s in the Fayoumi breed. Genomic DNA from individuals was examined using the Agilent chicken 244 K comparative genomic hybridization array and quantitative PCR . We identified a total of 273 CNV s overall, with 112 CNV s being novel and not previously reported. Quantitative PCR using the standard curve method validated a subset of our array data. Through enrichment analysis of genes within CNV regions, we observed multiple chromosomes, terms and pathways that were significantly enriched, largely dealing with the major histocompatibility complex and immune responsiveness. Using an additional round of computational and statistical analysis with a different bioinformatic pipeline, we identified 43 CNV s among these as high‐confidence regions, 14 of which were found to be novel. We further compared and contrasted individuals of the two inbred lines to discover regions that have a significant difference in copy number between lines. A total of 40 regions had significant deletions or duplications between the lines. Gene Ontology analysis of genomic regions containing CNV s between lines also was performed. This between‐line candidate CNV list will be useful in studies with these two unique genetic lines, which may harbor variations that underlie quantitative trait loci for disease resistance and other important traits. Through the global discovery of novel CNV s in chicken, these data also provide resources for further genetic and functional genomics studies.