Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip

BMC Genomics

Research Article

Josep M Folch¹  Anna Mercadé¹  Anna Castelló¹  Yuliaxis Ramayo-Caldas¹  Miguel Perez-Enciso²  Carla A Souza³  Estefania Alves⁴  Ana I Fernández⁴  Romi N Pena⁵ 

[1] Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain;Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain;Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain;Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain;Universidade Católica de Brasília, Brazil;Departamento de Mejora Animal SGIT-INIA, 28040, Madrid, Spain;Genètica i Millora Animal, IRTA Lleida, 25198, Lleida, Spain;Department of Animal Production, University of Lleida, 25198, Lleida, Spain;

关键词: Copy Number Variation;    Copy Number Variable Region;    Sparse Bayesian Learning;    Backward Elimination;    Consecutive SNPs;   

DOI  :  10.1186/1471-2164-11-593

 received in 2010-06-15, accepted in 2010-10-22,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundRecent studies in pigs have detected copy number variants (CNVs) using the Comparative Genomic Hybridization technique in arrays designed to cover specific porcine chromosomes. The goal of this study was to identify CNV regions (CNVRs) in swine species based on whole genome SNP genotyping chips.ResultsWe used predictions from three different programs (cnvPartition, PennCNV and GADA) to analyze data from the Porcine SNP60 BeadChip. A total of 49 CNVRs were identified in 55 animals from an Iberian x Landrace cross (IBMAP) according to three criteria: detected in at least two animals, contained three or more consecutive SNPs and recalled by at least two programs. Mendelian inheritance of CNVRs was confirmed in animals belonging to several generations of the IBMAP cross. Subsequently, a segregation analysis of these CNVRs was performed in 372 additional animals from the IBMAP cross and its distribution was studied in 133 unrelated pig samples from different geographical origins. Five out of seven analyzed CNVRs were validated by real time quantitative PCR, some of which coincide with well known examples of CNVs conserved across mammalian species.ConclusionsOur results illustrate the usefulness of Porcine SNP60 BeadChip to detect CNVRs and show that structural variants can not be neglected when studying the genetic variability in this species.

【 授权许可】

CC BY   
© Ramayo-Caldas et al; licensee BioMed Central Ltd. 2010