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Open Access Research article

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

Anna Esteve-Codina124*, Yogesh Paudel3, Luca Ferretti1, Emanuele Raineri4, Hendrik-Jan Megens3, Luis Silió5, María C Rodríguez5, Martein AM Groenen3, Sebastian E Ramos-Onsins1 and Miguel Pérez-Enciso126*

Author affiliations

1 Center for Research in Agricultural Genomics (CRAG), Campus UAB, Bellaterra, 08193, Spain

2 Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain

3 Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, Wageningen, 6708 WD, The Netherlands

4 Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain

5 Departamento de Mejora Genética Animal, INIA, Madrid, 28040, Spain

6 Institut Català de Recerca i Estudis Avançats (ICREA), Carrer de Lluís Companys 23, Barcelona, 08010, Spain

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Citation and License

BMC Genomics 2013, 14:148  doi:10.1186/1471-2164-14-148

Published: 5 March 2013

Abstract

Background

In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besides, Iberian pigs exhibit high meat quality as well as appetite and propensity to obesity. Here we provide a genome wide analysis of nucleotide and structural diversity in a reduced representation library from a pool (n=9 sows) and shotgun genomic sequence from a single sow of the highly inbred Guadyerbas strain. In the pool, we applied newly developed tools to account for the peculiarities of these data.

Results

A total of 254,106 SNPs in the pool (79.6 Mb covered) and 643,783 in the Guadyerbas sow (1.47 Gb covered) were called. The nucleotide diversity (1.31x10-3 per bp in autosomes) is very similar to that reported in wild boar. A much lower than expected diversity in the X chromosome was confirmed (1.79x10-4 per bp in the individual and 5.83x10-4 per bp in the pool). A strong (0.70) correlation between recombination and variability was observed, but not with gene density or GC content. Multicopy regions affected about 4% of annotated pig genes in their entirety, and 2% of the genes partially. Genes within the lowest variability windows comprised interferon genes and, in chromosome X, genes involved in behavior like HTR2C or MCEP2. A modified Hudson-Kreitman-Aguadé test for pools also indicated an accelerated evolution in genes involved in behavior, as well as in spermatogenesis and in lipid metabolism.

Conclusions

This work illustrates the strength of current sequencing technologies to picture a comprehensive landscape of variability in livestock species, and to pinpoint regions containing genes potentially under selection. Among those genes, we report genes involved in behavior, including feeding behavior, and lipid metabolism. The pig X chromosome is an outlier in terms of nucleotide diversity, which suggests selective constraints. Our data further confirm the importance of structural variation in the species, including Iberian pigs, and allowed us to identify new paralogs for known gene families.

Keywords:
Iberian pig; Next generation sequencing; Pig; Selection tests; Structural variation