Web of Science: 32 citations, Scopus: 32 citations, Google Scholar: citations
Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs
Esteve Codina, Anna (Centre de Recerca en Agrigenòmica)
Paudel, Yogesh (Wageningen University. Animal Breeding and Genomics Centre)
Ferretti, Luca (Centre de Recerca en Agrigenòmica)
Raineri, Emanuele (Centre Nacional d'Anàlisi Genòmica)
Megens, Hendrik-Jan (Wageningen University. Animal Breeding and Genomics Centre)
Silió, Luis (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Departamento de Mejora Genética Animal)
Rodríguez, María C (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Departamento de Mejora Genética Animal)
Groenen, Martein AM (Wageningen University. Animal Breeding and Genomics Centre)
Ramos-Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica)
Pérez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)

Date: 2013
Abstract: 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. 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. 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.
Note: Número d'acord de subvenció EC/FP7/249894
Note: Número d'acord de subvenció MINECO/AGL2010-14822
Note: Número d'acord de subvenció MICINN/CGL2009-09346
Note: Número d'acord de subvenció MICINN/CSD2007-00036
Rights: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Language: Anglès.
Document: article ; recerca ; publishedVersion
Subject: Iberian pig ; Next generation sequencing ; Pig ; Selection tests ; Structural variation
Published in: BMC Genomics, Vol. 14 (March 2013) , art. 148, ISSN 1471-2164

PMID: 23497037
DOI: 10.1186/1471-2164-14-148


14 p, 1.6 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (scientific output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles

 Record created 2018-01-27, last modified 2019-07-30



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