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Genome-wide association and pathway analysis of carcass and meat quality traits in Piemontese young bulls

Published online by Cambridge University Press:  15 August 2019

S. Pegolo Open the ORCID record for S. Pegolo [Opens in a new window] ,
A. Cecchinato ,
S. Savoia ,
L. Di Stasio ,
A. Pauciullo ,
A. Brugiapaglia ,
G. Bittante  and
A. Albera
S. Pegolo*
Affiliation:
Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’Università 16, 35020 Legnaro, PD, Italy
A. Cecchinato
Affiliation:
Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’Università 16, 35020 Legnaro, PD, Italy
S. Savoia
Affiliation:
Associazione Nazionale Allevatori Bovini di Razza Piemontese, Strada Trinità 32/A, 12061 Carrù, CN, Italy
L. Di Stasio
Affiliation:
Department of Agricultural, Forest and Food Science, Università degli studi di Torino, Via L. Da Vinci 44, 10095 Grugliasco, TO, Italy
A. Pauciullo
Affiliation:
Department of Agricultural, Forest and Food Science, Università degli studi di Torino, Via L. Da Vinci 44, 10095 Grugliasco, TO, Italy
A. Brugiapaglia
Affiliation:
Department of Agricultural, Forest and Food Science, Università degli studi di Torino, Via L. Da Vinci 44, 10095 Grugliasco, TO, Italy
G. Bittante
Affiliation:
Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’Università 16, 35020 Legnaro, PD, Italy
A. Albera
Affiliation:
Associazione Nazionale Allevatori Bovini di Razza Piemontese, Strada Trinità 32/A, 12061 Carrù, CN, Italy
*
†E-mail: sara.pegolo@unipd.it
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Abstract

A key concern in beef production is how to improve carcass and meat quality traits. Identifying the genomic regions and biological pathways that contribute to explaining variability in these traits is of great importance for selection purposes. In this study, genome wide-association (GWAS) and pathway-based analyses of carcass traits (age at slaughter (AS), carcass weight (CW), carcass daily gain (CDG), conformation score and rib-eye muscle area) and meat quality traits (pH, Warner-Bratzler shear force, purge loss, cooking loss and colour parameters (lightness, redness, yellowness, chroma, hue)) were conducted using genotype data from the ‘GeneSeek Genomic Profiler Bovine LD’ array in a cohort of 1166 double-muscled Piemontese beef cattle. The genome wide-association analysis was based on the GRAMMAR-GC approach and identified 37 significant single nucleotide polymorphisms (SNPs), which were associated with 12 traits (P<5 × 10−5). In particular, 14 SNPs associated with CW, CDG and AS were located at 38.57 to 38.94 Mb on Bos taurus autosome 6 and mapped within four genes, that is, Leucine Aminopeptidase 3, Family with Sequence Similarity 184 Member B, Non-SMC Condensin I Complex Subunit G and Ligand-Dependent Nuclear Receptor Corepressor-Like. Strong pairwise linkage disequilibrium was found in this region. For meat quality traits, most associations were 1 SNP per trait, except for a signal on BTA25 (at ~11.96 Mb), which was significant for four of the five meat colour parameters assessed. Gene-set enrichment analyses yielded significant results for six traits (right-sided hypergeometric test, false discovery rate <0.05). In particular, several pathways related to transmembrane transport (i.e., oxygen, calcium, ion and cation) were overrepresented for meat colour parameters. The results obtained provide useful information for genomic selection for beef production and quality in the Piemontese breed.

Keywords

genomic analysisfunctional analysisbeefdouble-muscledPiedmontese
Type
Research Article
Information
animal , Volume 14 , Issue 2 , February 2020 , pp. 243 - 252
Copyright
© The Animal Consortium 2019 

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