Genomic variability in Mexican chicken population using copy number variants

BMC Genetics

Research Article

S. I. Román-Ponce¹  F. J. Ruiz López¹  V. E. Vega-Murillo²  A. Bagnato³  M. G. Strillacci³  M. C. Cozzi³  S. Cerolini³  E. Gorla³ 

[1]Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Km.1 Carretera a Colón, Auchitlán, 76280, Querétaro, CP, Mexico

[2]Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Melchor Ocampo # 234 Desp. 313, Col. Centro Veracruz, C.P. 91700, Veracruz, Mexico

[3]Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133, Milan, Italy

关键词: Copy number variant;    Chicken;    Genetic variability;   

DOI  :  10.1186/s12863-017-0524-4

 received in 2017-04-05, accepted in 2017-06-12,  发布年份 2017

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2017