Open Access Research article

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

Yuliaxis Ramayo-Caldas1*, Anna Castelló1, Romi N Pena25, Estefania Alves3, Anna Mercadé1, Carla A Souza16, Ana I Fernández3, Miguel Perez-Enciso14 and Josep M Folch1

Author Affiliations

1 Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain

2 Genètica i Millora Animal, IRTA Lleida, 25198 Lleida, Spain

3 Departamento de Mejora Animal SGIT-INIA, 28040 Madrid, Spain

4 Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

5 Department of Animal Production, University of Lleida, 25198 Lleida, Spain

6 Universidade Católica de Brasília, Brazil

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BMC Genomics 2010, 11:593  doi:10.1186/1471-2164-11-593

Published: 22 October 2010

Additional files

Additional file 1:

Table S1. Results of the distribution analysis in American pig populations.

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Additional file 2:

Table S2. Gene annotation within the CNVRs retrieved from the Ensembl Genes 57 Database using the Biomart software.

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Additional file 3:

Fig. S1. Results of quantitative PCR (qPCR) for CNVRs 15 (top), 17 (middle), and 32 (bottom). A total of 17 animals are showed in each plot. Breed abbreviations are: Ib: Iberian; Ld: Landrace; Hib: animals belonging to several generations of the IBMAP cross (F1, F2, and BC); CC: Cuban creole pig; Gu: Guatemala local breed; Yu: Yucatan miniature pig; Pe: Peruvian creole pig.

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Additional file 4:

Table S3. List of pig genes previously reported in the Human Database of Genomic Variants.

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Additional file 5:

Fig. S2. Structure of the IBMAP cross. Abbreviations are: Ib: Iberian; Ld: Landrace; F1: first generation; F2: second generation; F3: third generation; BC: first backcross; BC1_LD: second backcross.

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Additional file 6:

Table S4. Description of samples from American local breeds.

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Additional file 7:

Table S5. Primers and probes used in quantitative PCR validation

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