Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip
Ver/Abrir
Autor/a
Ramayo-Caldas, Yuliaxis
Castelló, Anna
Alves, Estefania
Mercadé, Anna
Souza, Carla A
Fernández, Ana I
Perez-Enciso, Miguel
Folch, Josep M
Fecha de publicación
2010-10-22ISSN
1471-2164
Resumen
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.
Tipo de documento
Artículo
Versión del documento
Versión publicada
Lengua
English
Materias (CDU)
575 - Genética general. Citogenética general. Inmunogenética. Evolución. Filogenia
Páginas
10
Publicado por
BMC
Publicado en
BMC Genomics
Citación
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
Número del acuerdo de la subvención
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
Este ítem aparece en la(s) siguiente(s) colección(ones)
- ARTICLES CIENTÍFICS [2831]
Excepto si se señala otra cosa, la licencia del ítem se describe como http://creativecommons.org/licenses/by/4.0/