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Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics

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Abstract

Genetical genomics approaches aim at identifying quantitative trait loci for molecular traits, also known as intermediate phenotypes, such as gene expression, that could link variation in genetic information to physiological traits. In the current study, an expression GWAS has been carried out on an experimental Iberian × Landrace backcross in order to identify the genomic regions regulating the gene expression of those genes whose expression is correlated with growth, fat deposition, and premium cut yield measures in pig. The analyses were conducted exploiting Porcine 60K SNP BeadChip genotypes and Porcine Expression Microarray data hybridized on mRNA from Longissimus dorsi muscle. In order to focus the analysis on productive traits and reduce the number of analyses, only those probesets whose expression showed significant correlation with at least one of the seven phenotypes of interest were selected for the eGWAS. A total of 63 eQTL regions were identified with effects on 36 different transcripts. Those eQTLs overlapping with phenotypic QTLs on SSC4, SSC9, SSC13, and SSC17 chromosomes previously detected in the same animal material were further analyzed. Moreover, candidate genes and SNPs were analyzed. Among the most promising results, a long non-coding RNA, ALDBSSCG0000001928, was identified, whose expression is correlated with premium cut yield. Association analysis and in silico sequence domain annotation support TXNRD3 polymorphisms as candidate to regulate ALDBSSCG0000001928 expression, which can be involved in the transcriptional regulation of surrounding genes, affecting productive and meat quality traits.

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Acknowledgements

This work was funded by Ministerio de Economía y Competitividad (MINECO) project AGL2011-29821-C02 and AGL2014-56369-C2. Ángel Martínez-Montes was funded by a (FPI) PhD grant from the Spanish Ministerio de Ciencia e Innovación. We want to thank Fabián Garcia, Anna Mercadé, and Anna Castelló for technical assistance. We would like to thank all the members of the INIA, IRTA, and UAB institutions who contributed to the generation and sample recollection of the animal materials used in this work.

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Authors and Affiliations

  1. Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain

    Angel M. Martínez-Montes, Anixa Muiños-Bühl, Almudena Fernández & Ana I. Fernández

  2. Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain

    Josep M. Folch

  3. Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain

    Josep M. Folch

  4. Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 25198, Lleida, Spain

    Noelia Ibáñez-Escriche

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  1. Angel M. Martínez-Montes
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  2. Anixa Muiños-Bühl
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  3. Almudena Fernández
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  6. Ana I. Fernández
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Correspondence to Angel M. Martínez-Montes.

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Martínez-Montes, A.M., Muiños-Bühl, A., Fernández, A. et al. Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics. Mamm Genome 28, 130–142 (2017). https://doi.org/10.1007/s00335-016-9674-3

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