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

Yuliaxis Ramayo-Caldas (1) , Anna Castello (1) , Romi N Pena (2, 3) , Estefania Alves (4) , Anna Mercadé (1) , Carla A Souza (1, 5) , Ana I Fernández (4) , Miguel Perez-Enciso (1, 6) , Josep M Folch (1)

1 UAB - Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
2 IRTA - Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology
3 Department of Animal Production
4 Departamento de Mejora Animal
5 UCB - Universidade Católica de Brasília=Catholic University of Brasília
6 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies

Recent 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. We 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. Our 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.

Domaines: Sciences du Vivant [q-bio]

Yuliaxis Ramayo-Caldas, Anna Castello, Romi N Pena, Estefania Alves, Anna Mercadé, et al.. Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip. BMC Genomics, 2010, 11, pp.1-10. ⟨10.1186/1471-2164-11-593⟩. ⟨hal-02668605⟩