Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip
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Author
Ramayo-Caldas, Yuliaxis
Castelló, Anna
Alves, Estefania
Mercadé, Anna
Souza, Carla A
Fernández, Ana I
Perez-Enciso, Miguel
Folch, Josep M
Publication date
2010-10-22ISSN
1471-2164
Abstract
Background: 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.
Results: 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.
Conclusions: 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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
575 - General genetics. General cytogenetics
Pages
10
Publisher
BMC
Is part of
BMC Genomics
Citation
Ramayo-Caldas, Yuliaxis, Anna Castelló, Ramona N. Pena, Estefania Alves, Anna Mercadé, Carla A. Souza, Ana Isabel Fernández, Miguel Pérez-Enciso, and Josep María Folch. 2010. “Copy Number Variation in the Porcine Genome Inferred From a 60 K SNP BeadChip.” BMC Genomics 11 (1): 593. doi: 10.1186/1471-2164-11-593
Grant agreement number
MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2008-04818-C03/ES/Genes candidatos e identificacion genomica de loci y rutas geneticas que afectan a la calidad de la carne en cerdos/GAN
MEC/Programa nacional de medios de transporte/CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/
Program
Genètica i Millora Animal
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2685]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/