Abstract
BackgroundCopy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs.ResultsThe Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix). The mapped CNVs comprised 1538 gains and 386 losses, resulting at population level in 1216 CNV regions (CNVRs), of which 959 gains, 226 losses and 31 complex (i.e. containing both losses and gains). The CNVRs covered a total of 47 Mb of the whole genome sequence length, corresponding to 5.12% of the chicken galGal4 autosome assembly.ConclusionsThis study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been genetically characterized. The genomic study disclosed that the population, even if presenting extreme morphological variation, cannot be organized in differentiated genetic subpopulations. Finally this study provides a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native unselected for more than 500 years chicken population.
Highlights
Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations
Copy Number Variants (CNV) are genomic structural variations distributed over the whole genome in all species and refers to genomic segments of at least 50 bp in size [1], for which copy number differences have been observed in comparison to reference genome assemblies [2, 3]
CNV and Copy number variant region (CNVR) detection The Table 1 reports the descriptive statistics of identified CNVs and CNVRs
Summary
Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs. Copy Number Variants (CNV) are genomic structural variations distributed over the whole genome in all species and refers to genomic segments of at least 50 bp in size [1], for which copy number differences have been observed in comparison to reference genome assemblies (insertions, deletions and more complex changes) [2, 3]. In Mexico the poultry population, even if it shows large morphological variability, is not divided into breeds or strains and, possibly, can be considered as a unique widespread Creole chicken population (Gallus gallus domesticus), as the result of undefined crosses among different breeds imported into Mexico from Europe for almost 500 years [15, 16]. A wide variety of biotypes with different colors of
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
