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Open Access Highly Accessed Research article

A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes

Luca Fontanesi12*, Giuseppina Schiavo12, Giuliano Galimberti3, Daniela Giovanna Calò3, Emilio Scotti1, Pier Luigi Martelli24, Luca Buttazzoni5, Rita Casadio24 and Vincenzo Russo1

Author Affiliations

1 Department of Agricultural and Food Science and Technology, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy

2 Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy

3 Department of Statistical Sciences “Paolo Fortunati”, University of Bologna, Via delle Belle Arti 41, Bologna, 40126, Italy

4 Biocomputing Group, Department of Biology, Geology and Environmental Science, University of Bologna, Via San Giacomo, Bologna, 40126, Italy

5 Consiglio per la Ricerca e la Sperimentazine in Agricoltura, Centro di Ricerca per la Produzione delle Carni e il Miglioramento Genetico (CRA-PCM), Via Salaria 31, Monterotondo Scalo, Roma, 00015, Italy

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BMC Genomics 2012, 13:583  doi:10.1186/1471-2164-13-583

Published: 15 November 2012

Abstract

Background

Carcass fatness is an important trait in most pig breeding programs. Following market requests, breeding plans for fresh pork consumption are usually designed to reduce carcass fat content and increase lean meat deposition. However, the Italian pig industry is mainly devoted to the production of Protected Designation of Origin dry cured hams: pigs are slaughtered at around 160 kg of live weight and the breeding goal aims at maintaining fat coverage, measured as backfat thickness to avoid excessive desiccation of the hams. This objective has shaped the genetic pool of Italian heavy pig breeds for a few decades. In this study we applied a selective genotyping approach within a population of ~ 12,000 performance tested Italian Large White pigs. Within this population, we selectively genotyped 304 pigs with extreme and divergent backfat thickness estimated breeding value by the Illumina PorcineSNP60 BeadChip and performed a genome wide association study to identify loci associated to this trait.

Results

We identified 4 single nucleotide polymorphisms with P≤5.0E-07 and additional 119 ones with 5.0E-07<P≤5.0E-05. These markers were located throughout all chromosomes. The largest numbers were found on porcine chromosomes 6 and 9 (n=15), 4 (n=13), and 7 (n=12) while the most significant marker was located on chromosome 18. Twenty-two single nucleotide polymorphisms were in intronic regions of genes already recognized by the Pre-Ensembl Sscrofa10.2 assembly. Gene Ontology analysis indicated an enrichment of Gene Ontology terms associated with nervous system development and regulation in concordance with results of large genome wide association studies for human obesity.

Conclusions

Further investigations are needed to evaluate the effects of the identified single nucleotide polymorphisms associated with backfat thickness on other traits as a pre-requisite for practical applications in breeding programs. Reported results could improve our understanding of the biology of fat metabolism and deposition that could also be relevant for other mammalian species including humans, confirming the role of neuronal genes on obesity.

Keywords:
GWA; Backfat; Fatness; Obesity; Heavy pig