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Skeletal muscle transcriptional profiles in two Italian beef breeds, Chianina and Maremmana, reveal breed specific variation

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Abstract

Chianina and Maremmana breeds play an important role in the Italian cattle meat market. The Chianina breed is an ancient breed principally raised for draught. Now this breed is the worldwide recognized producer of top quality beef, tasteful and tender, specifically the famous “Florentine steak”. The Maremmana characterized by a massive skeletal structure, is a rustic cattle breed selected for adaptability to the marshy land of the Maremma region. We used a high throughput mRNA sequencing to analyze gene expression in muscle tissues of two Italian cattle breeds, Maremmana (MM) and Chianina (CN) with different selection history. We aim to examine the specific genetic contribution of each breed to meat production and quality, comparing the skeletal muscle tissue from Maremmana and Chianina. Most of the differentially expressed genes were grouped in the Glycolysis/Gluconeogenesis pathways. The rate and the extent of post-mortem energy metabolism have a critical effect on the conversion of muscle to meat. Furthermore, we aim at discovering the differences in nucleotide variation between the two breeds which might be attributable to the different history of selection/divergence. In this work we could emphasize the involvement of pathways of post-mortem energy metabolism. Moreover, we detected a collection of coding SNPs which could offer new genomic resources to improve phenotypic selection in livestock breeding program.

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Abbreviations

MM:

Maremmana

CN:

Chianina

SNP:

Single nucleotide polymorphism

FPKM:

Fragments per kilobase of exon per million fragments mapped

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

DEG:

Differentially expressed gene

ES:

Exon skipping

A5SS:

Alternative 5′ splice site

A3SS:

Alternative 3′ splice site

RI:

Retained intron

OT:

Others

TSS:

Single transcription start site

UTR:

Untraslated region

SIFT:

Sorting intolerant from tolerant

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Acknowledgments

This manuscript is dedicated to the memory of our friend and colleague Lorraine Pariset. Her work and passion on livestock genetics and her inquiring mind will be always an inspiration to us. This work is part of the GENZOOT research program, funded by Italian Ministry of Agricultural, Forestry and Food Policies (MIPAAF).

Author information

Author notes

  1. S. Bongiorni

    Present address: Department of Ecology and Biology, DEB, University of Tuscia, Via San Camillo de Lellis, 01100, Viterbo, Italy

Authors and Affiliations

  1. Department for Innovation in Biological, Agro-food and Forest Systems, DIBAF, University of Tuscia, Via San Camillo de Lellis, 01100, Viterbo, Italy

    S. Bongiorni & A. Valentini

  2. Molecular Digital Diagnostics (MDD), Via San Camillo de Lellis, 01100, Viterbo, Italy

    C. E. M. Gruber

  3. Cineca Supercomputing Center, Via dei Tizi, 6/B, 00185, Roma, Italy

    G. Chillemi & S. Bueno

  4. Consiglio per la Ricerca e la sperimentazione in Agricoltura, Via Salaria, 31, Monterotondo, Rome, 00015, Italy

    S. Failla & B. Moioli

  5. Department of Pharmacy and Biotechnology - FaBiT, University of Bologna, Via Zamboni, 33, Bologna, 40126, Italy

    F. Ferrè

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  1. S. Bongiorni
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  2. C. E. M. Gruber
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  3. G. Chillemi
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Corresponding author

Correspondence to S. Bongiorni.

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This study was carried out in strict accordance with the European Union recommendation directive 2010/63/EU and the Italian low 116/92 about animal care.

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Bongiorni, S., Gruber, C.E.M., Chillemi, G. et al. Skeletal muscle transcriptional profiles in two Italian beef breeds, Chianina and Maremmana, reveal breed specific variation. Mol Biol Rep 43, 253–268 (2016). https://doi.org/10.1007/s11033-016-3957-3

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  • DOI: https://doi.org/10.1007/s11033-016-3957-3

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