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Savoia, Simone (2018) Innovative tools for phenotypic characterization and genetic improvement of meat quality in piemontese breed. [Ph.D. thesis]

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Abstract (italian or english)

The main objective of this thesis was to perform a comprehensive investigation of the possibilities for the improvement of meat quality traits focusing on the development of innovative tools.
The study was carried out sampling 1,327 Piemontese young bulls. Animals were fattened in 115 farms and slaughtered at the same commercial abattoir. Information about farms fattening system was collected through on field surveys.
After slaughter, the following carcass traits were recorded: carcass weight, carcass conformation, age at slaughter and carcass daily gain. Individual samples of the Longissimus thoracis muscle were collected and transferred to the laboratory for meat quality analyses: muscle pH, colour parameters of lightness (L*), redness (a*), yellowness (b*), hue angle (h*), chroma (C*), purge losses, cooking losses, and Warner Bratzler shear force, all measured at 7 d after slaughter.
On each meat sample, 5 spectra were collected in a reflectance mode at the abattoir with a portable top-ranking visible near-infrared spectrometer and an hand-held spectrometer. Calibration equations were developed after conventional meat quality assessment using Bayesian methods. The ability of spectroscopy in predicting meat quality traits was evaluated comparing the performances of the two spectrometers.
Genetic correlations between carcass and measured meat quality traits were investigated, as well as genetic relations of meat quality traits with predictions obtained by spectral data. All the sampled young bulls were genotyped with the “GeneSeek Genomic Profiler Bovine LD” (GGP Bovine LD) array containing 30,111 SNPs. A combination of Genome-Wide Association and Pathway Analysis was performed to identify the genomic regions and biological pathways contributing to the variability of carcass and meat quality traits. Genomic variance components and SNP effects were estimated with bayesian methodology and a SNP-BLUP model. Genomic heritability and direct genomic breeding values were computed, assessing the possibility of implement genomic selection for meat quality traits.
Six main typologies of fattening system were identified within the Piemontese breed. Carcass traits were deeply affected by production system, while little effects on meat quality, limited to colour traits, were observed. The small effect of beef production system showed that the variability of meat quality traits mainly depends on individual animal factors, shifting the possibilities for their improvement to genetic aspects.
All the meat quality traits showed not negligible heritabilities, allowing their improvement through selection. They also displayed genetic relationships with carcass traits, indicating a possible modification as a correlated response to selection for growth rate and muscularity, traits currently included in the breeding goal of the Piemontese breed. However, the establishment of a direct selection procedure relies on the availability of phenotypes collected within a routine recording scheme. Predictions of colour traits and purge losses were satisfactory, whereas pH, cooking losses and shear force predictabilities were rather poor. However, all the predicted traits except shear force showed moderate heritabilities and were highly correlated with measured traits, allowing their use for selection purposes.
From genetic architecture point of view of carcass and meat quality traits, our investigation highlighted that, besides myostatin, other genes contribute to explain the variability in carcass and growth characteristics. Moreover, association of pathways related to transporter activity (oxygen, calcium, ion and cation) was found with meat color parameters.
Genomic heritabilities were higher than pedigree-based heritabilies for purge losses and all colour traits, while they were similar for the other meta quality traits. The accuracy of prediction of genomic breeding values was satisfactory and allows to consider genomic selection as a valid tool to improve meat quality traits in Piemontese breed.

Abstract (a different language)

La ricerca alla base di questa tesi di dottorato è stata condotta nell'ambito del progetto "QualiPiem" - Strumenti innovativi per la selezione della qualità della carne nella razza bovina Piemontese. Obiettivo principale è stato valutare la possibilità di migliorare la qualità della carne nei bovini di razza Piemontese, ponendo particolare attenzione agli aspetti applicativi oltre che a quelli conoscitivi. Lo studio ha previsto la comprensione delle basi genetiche dei caratteri di qualità della carne, la messa a punto di strumenti innovativi per il rilievo dei fenotipi, potenzialmente applicabili su larga scala a livello operativo, e l'impiego di informazioni genomiche per la selezione.
Operativamente, il progetto ha previsto il campionamento di 1,327 vitelloni registrati nel Libro Genealogico italiano della razza Piemontese. Gli animali sono stati ingrassati in 115 allevamenti e macellati nella stessa struttura commerciale tra aprile 2015 e febbraio 2017. Le informazioni sui sistemi di ingrasso adottati negli allevamenti sono state raccolte attraverso indagini in campo basate sul colloquio con gli allevatori e analizzate per studiare l'effetto del sistema di allevamento sull'efficienza produttiva e sulla qualità della carne.
Dopo la macellazione, sono stati raccolti i seguenti fenotipi: peso della carcassa a caldo, conformazione della carcassa, età al macello ed accrescimento giornaliero in carcassa. Ventiquattro ore dopo la macellazione, sono stati raccolti campioni individuali del muscolo Longissimus thoracis tra la quinta e la sesta vertebra toracica. I campioni sono stati quindi scansionati per effettuare la misura dell'area del muscolo. Inoltre, su ciascun campione di carne, direttamente al macello, sono stati raccolti 5 spettri in riflettanza con due spettrometri portatili: un ASD LabSpec 2500 (range dello spettro tra 350 e 1,830 nm, con acquisizione ogni nm) ed un JDSU (range dello spettro tra 905 e 1,649 nm, con acquisizione ogni 6 nm). Le equazioni di calibrazione sono state sviluppate con metodologie bayesiane e la capacità predittiva della spettroscopia è stata valutata confrontando le prestazioni dei due spettrometri. La valutazione della qualità della carne è stata eseguita con le tradizionali metodologie di analisi in laboratorio 7 giorni dopo la macellazione ed ha incluso il pH, il colore (L *, a *, b *, h *, C *), le perdite di sgocciolamento, le perdite di liquidi in cottura e la tenerezza.
Sono state studiate le relazioni fenotipiche e genetiche tra i caratteri di efficienza produttiva e quelli di qualità della carne. Inoltre, si è provveduto ad indagare le relazioni genetiche tra i tratti di qualità della carne misurati in laboratorio e le loro predizioni ottenute con la spettrometria nel vicino-infrarosso.
Tutti gli animali campionati sono stati genotipizzati utilizzando il supporto “GeneSeek Genomic Profiler Bovine LD” (GGP Bovine LD) contenente 30.111 SNP. E' stato eseguito uno studio combinando Genome-wide Association e Pathway Analysis per identificare le regioni genomiche e i processi biologici che contribuiscono a spiegare la variabilità dei caratteri di qualità della carne. Le componenti di varianza e gli effetti degli SNP sono stati stimati congiuntamente con la metodologia SNP-BLUP. Sono state stimate le ereditabilità genomiche e predetti gli indici genomici, valutando quindi la possibilità di implementare la selezione genomica per migliorare la qualità della carne nella razza Piemontese.
I risultati ottenuti hanno evidenziato la presenza di sei principali tipologie di ingrasso nel contesto della razza piemontese, ognuna caratterizzata da specifiche tecniche gestionali. I caratteri produttivi sono risultati profondamente influenzati dal sistema di produzione, mentre è emerso un effetto minimo sulla qualità della carne, limitato al colore. L'effetto limitato del sistema di produzione ha dimostrato che la variabilità dei caratteri di qualità della carne dipende principalmente da fattori animale-specifici e che i miglioramenti possono essere apportati agendo a livello dei singoli animali, guardando con particolare attenzione all'aspetto genetico.
E' importante, quindi, che i caratteri di qualità abbiano riportato valori di ereditabilità non trascurabili, lasciandone presupporre un possibile miglioramento attraverso la selezione. Tuttavia, l'inserimento di tali caratteri tra gli obiettivi di selezione dipende dalla disponibilità di fenotipi raccolti all'interno di un processo di registrazione routinario.
Da un punto di vista fenotipico, i caratteri del colore e le perdite di sgocciolamento sono stati predetti in modo soddisfacente con con entrambi gli spettrometri utilizzati in questo studio. La capacità predittiva della spettrometria del vicino infrarosso per il pH, le perdite di cottura e la tenerezza è risultata meno favorevole. Tuttavia, i fenotipi predetti a partire dai dati spettrali sono risultati ereditabili e le elevate correlazioni genetiche tra questi ed i fenotipi osservati potrebbero consentire di utilizzare la spettroscopia a fini selettivi.
Per quanto riguarda l'architettura genetica dei caratteri indagati, il presente studio ha evidenziato che oltre alla miostatina sono presenti diversi geni che contribuiscono a spiegare quote della variabilità esistente, soprattutto per quanto riguarda l'accrescimento in carcassa. Inoltre, è stata messa in evidenza un'associazione tra pathway metabolici inerenti all'attività di trasporto cellulare (ossigeno, calcio, ioni e catione) ed i caratteri di qualità della carne relativi al colore.
L'utilizzo delle informazioni genomiche, congiunto alle parentele pedigree, ha prodotto stime di ereditabilità maggiori rispetto a quelle tradizionali per le perdite di sgocciolamento ed il colore della carne, mentre per gli altri caratteri non sono state evidenziate differenze di rilievo. Gli indici genomici che ne sono conseguiti hanno mostrato una capacità predittiva soddisfacente, permettendo di considerare la selezione genomica come un possibile strumento per migliorare i caratteri di qualità della carne nella razza Piemontese.

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EPrint type:Ph.D. thesis
Tutor:Bittante, Giovanni
Supervisor:Albera, Andrea
Ph.D. course:Ciclo 31 > Corsi 31 > ANIMAL AND FOOD SCIENCE
Data di deposito della tesi:29 November 2018
Anno di Pubblicazione:29 November 2018
Key Words:meat quality; carcass traits; genetic parameters; spectroscopy; gwas; genomic;
Settori scientifico-disciplinari MIUR:Area 07 - Scienze agrarie e veterinarie > AGR/17 Zootecnica generale e miglioramento genetico
Struttura di riferimento:Dipartimenti > Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente
Codice ID:11443
Depositato il:15 Nov 2019 14:39
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