Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population.

BACKGROUND: International evaluations combine data from different countries allowing breeders to have access to larger panels of elite bulls and to increase the accuracy of estimated breeding values (EBV). However, international and national evaluations can use different sources of information to compute EBV (EBVINT and EBVNAT, respectively), leading to differences between them. Choosing one of these EBV results in losing the information that is contained only in the discarded EBV. Our objectives were to define and validate a procedure to integrate publishable sires' EBVINT and their associated reliabilities computed from pedigree-based or single-step international beef cattle evaluations into national evaluations to obtain "blended" EBV. The Italian (ITA) pedigree-based national evaluation was used as a case study to validate the integration procedure. METHODS: Publishable sires' international information, i.e. EBVINT and their associated reliabilities, was included in the national evaluation as pseudo-records. Data were available for 444,199 individual age-adjusted weaning weights of Limousin cattle from eight countries and 17,607 genotypes from four countries (ITA excluded). To mimic differences between international and national evaluations, international evaluations included phenotypes (and genotypes) of animals born prior to January 2019, while national evaluations included ITA phenotypes of animals born until April 2019. International evaluations using all available information were considered as reference scenarios. Publishable sires were divided into three groups: sires with ≥ 15, < 15 and no recorded offspring in ITA. RESULTS: Overall, for these three groups, integrating either pedigree-based or single-step international information into national pedigree-based evaluations improved the similarity of the blended EBV with the reference EBV compared to national evaluations without integration. For instance, the correlation with the reference EBV for direct (maternal) EBV went from 0.61 (0.79) for a national evaluation without integration to 0.97 (0.88) when integrating single-step international information, on average across all groups of publishable sires. CONCLUSIONS: Our proposed one-animal-at-a-time integration procedure yields blended EBV that are in close agreement with full international EBV for all groups of animals analysed. The procedure can be directly applied by countries since it does not rely on specific software and is computationally inexpensive, allowing straightforward integration of publishable sires' EBVINT from pedigree-based or single-step based international beef cattle evaluations into national evaluations.

International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight.

BACKGROUND: Compared to national evaluations, international collaboration projects further improve accuracies of estimated breeding values (EBV) by building larger reference populations or performing a joint evaluation using data (or proxy of them) from different countries. Genomic selection is increasingly adopted in beef cattle, but, to date, the benefits of including genomic information in international evaluations have not been explored. Our objective was to develop an international beef cattle single-step genomic evaluation and investigate its impact on the accuracy and bias of genomic evaluations compared to current pedigree-based evaluations. METHODS: Weaning weight records were available for 331,593 animals from seven European countries. The pedigree included 519,740 animals. After imputation and quality control, 17,607 genotypes at a density of 57,899 single nucleotide polymorphisms (SNPs) from four countries were available. We implemented two international scenarios where countries were modelled as different correlated traits: an international genomic single-step SNP best linear unbiased prediction (SNPBLUP) evaluation (ssSNPBLUPINT) and an international pedigree-based BLUP evaluation (PBLUPINT). Two national scenarios were implemented for pedigree and genomic evaluations using only nationally submitted phenotypes and genotypes. Accuracies, level and dispersion bias of EBV of animals born from 2014 onwards, and increases in population accuracies were estimated using the linear regression method. RESULTS: On average across countries, 39 and 17% of sires and maternal-grand-sires with recorded (grand-)offspring across two countries were genotyped. ssSNPBLUPINT showed the highest accuracies of EBV and, compared to PBLUPINT, led to increases in population accuracy of 13.7% for direct EBV, and 25.8% for maternal EBV, on average across countries. Increases in population accuracies when moving from national scenarios to ssSNPBLUPINT were observed for all countries. Overall, ssSNPBLUPINT level and dispersion bias remained similar or slightly reduced compared to PBLUPINT and national scenarios. CONCLUSIONS: International single-step SNPBLUP evaluations are feasible and lead to higher population accuracies for both large and small countries compared to current international pedigree-based evaluations and national evaluations. These results are likely related to the larger multi-country reference population and the inclusion of phenotypes from relatives recorded in other countries via single-step international evaluations. The proposed international single-step approach can be applied to other traits and breeds.

Phenotypic and genetic variation of ultraviolet-visible-infrared spectral wavelengths of bovine meat.

Spectroscopic predictions can be used for the genetic improvement of meat quality traits in cattle. No information is however available on the genetics of meat absorbance spectra. This research investigated the phenotypic variation and the heritability of meat absorbance spectra at individual wavelengths in the ultraviolet-visible and near-infrared region (UV-Vis-NIR) obtained with portable spectrometers. Five spectra per instrument were taken on the ribeye surface of 1185 Piemontese young bulls from 93 farms (13,182 Herd-Book pedigree relatives). Linear animal model analyses of 1481 single-wavelengths from UV-Vis-NIRS and 125 from Micro-NIRS were carried out separately. In the overlapping regions, the proportions of phenotypic variance explained by batch/date of slaughter (14 ± 6% and 17 ± 7%,), rearing farm (6 ± 2% and 5 ± 3%), and the residual variances (72 ± 10% and 72 ± 5%) were similar for the UV-Vis-NIRS and Micro-NIRS, but additive genetics (7 ± 2% and 4 ± 2%) and heritability (8.3 ± 2.3% vs 5.1 ± 0.6%) were greater with the Micro-NIRS. Heritability was much greater for the visible fraction (25.2 ± 11.4%), especially the violet, blue and green colors, than for the NIR fraction (5.0 ± 8.0%). These results allow a better understanding of the possibility of using the absorbance of visible and infrared wavelengths correlated with meat quality traits for the genetic improvement in beef cattle.

Prediction of meat quality traits in the abattoir using portable near-infrared spectrometers: heritability of predicted traits and genetic correlations with laboratory-measured traits.

BACKGROUND: The possibility of assessing meat quality traits over the meat chain is strongly limited, especially in the context of selective breeding which requires a large number of phenotypes. The main objective of this study was to investigate the suitability of portable infrared spectrometers for phenotyping beef cattle aiming to genetically improving the quality of their meat. Meat quality traits (pH, color, water holding capacity, tenderness) were appraised on rib eye muscle samples of 1,327 Piemontese young bulls using traditional (i.e., reference/gold standard) laboratory analyses; the same traits were also predicted from spectra acquired at the abattoir on the intact muscle surface of the same animals 1 d after slaughtering. Genetic parameters were estimated for both laboratory measures of meat quality traits and their spectra-based predictions. RESULTS: The prediction performances of the calibration equations, assessed through external validation, were satisfactory for color traits (R2 from 0.52 to 0.80), low for pH and purge losses (R2 around 0.30), and very poor for cooking losses and tenderness (R2 below 0.20). Except for lightness and purge losses, the heritability estimates of most of the predicted traits were lower than those of the measured traits while the genetic correlations between measured and predicted traits were high (average value 0.81). CONCLUSIONS: Results showed that NIRS predictions of color traits, pH, and purge losses could be used as indicator traits for the indirect genetic selection of the reference quality phenotypes. Results for cooking losses were less effective, while the NIR predictions of tenderness were affected by a relatively high uncertainty of estimate. Overall, genetic selection of some meat quality traits, whose direct phenotyping is difficult, can benefit of the application of infrared spectrometers technology.

Prediction of meat quality traits in the abattoir using portable and hand-held near-infrared spectrometers.

The use of near-infrared spectrometers (NIRS) for predicting meat quality traits directly in the abattoir was tested with three trials. For the calibration trial, spectra were acquired from the cross-cut surface of the Longissimus thoracis muscle on 1166 carcasses of Piemontese young bulls with a portable visible-near-infrared spectrometer (Vis-NIRS) and with a small hand-held instrument (Micro-NIRS). A sample of the same muscle was analyzed to provide the reference. Validation statistics of the two instruments were similar. Predictabilities of meat color and purge loss were good, whereas for the other traits they were less promising. The repeatability trial showed that post-slaughter factors, not predictable by NIR spectra collected in the abattoir, affect reference meat quality values. A trial under operative conditions showed that both spectrometers were able to capture the major sources of variation in most of the meat quality traits. Overall, NIRS could be used to predict the animals' "native" characteristics exploitable for genetic improvement of meat quality traits.

Heritability and genetic correlations of carcass and meat quality traits in Piemontese young bulls.

Age at slaughter (AS), carcass weight (CW), carcass daily gain (CDG), conformation (EUS), and rib-eye area (REA) were recorded on 1166 Piemontese young bulls. pH, lightness (L*), redness (a*), yellowness (b*), hue angle (h*), chroma (C*), purge loss (PL), cooking loss (CL) and shear force (WBSF) were assessed on the Longissimus thoracis muscle of the same animals. Heritability of carcass traits ranged from 0.07 (EUS) to 0.32 (CDG), with those of meat quality from 0.12 (PL) to 0.32 (WBSF). Genetically, an increase in AS exerts an unfavourable effect on PL (0.40) and colour traits (L*-0.20, a*-0.32, b* -0.25), whereas CW and CDG have the opposite effect. EUS is correlated favourably with PL (-0.32) and unfavourably with WBSF (0.53), while REA is correlated unfavourably with PL (0.41), CL (0.35), a* (-0.58) and b* (-0.44), and favourably with L* (0.41). Current selection goals of the Piemontese breed can indirectly modify some of the quality traits of beef, particularly colour and tenderness.

Characterisation of beef production systems and their effects on carcass and meat quality traits of Piemontese young bulls.

Using the Piemontese breed as a case study, we characterised beef production systems within the EU classification, and investigated their effects on carcass and meat quality traits. The research involved 1,327 young bulls fattened on 115 farms. The production systems identified by hierarchical cluster analysis were: traditional (restricted feeding and either tie-stalls or loose-housing), modern breeders and fatteners and specialised fatteners (the last two were divided in those using or not using total mixed rations). Despite the large variability in management techniques within production systems, production systems affected (P < 0.05) farm size, animal density, environmental scoring, diet, slaughter age and all carcass traits except weight. Lightness (L*) of Longissimus thoracis was the only meat quality trait affected (P < 0.05), with values greater in the traditional tie-stall system (+0.9 L*). Given the very limited effect of production systems on meat quality traits, factors related to individual animals within farms, such as genetics, should be considered for their improvement.