Effects of slaughter weight and backfat depth on trimming, curing, and deboning losses and quality traits of Italian dry-cured ham.

This study aimed at assessing the effects of two infra-vitam traits, specifically the slaughter weight (SW) and the ultrasound backfat depth (BCKF) on several post-mortem and quality traits of typical Prosciutto Veneto protected designation of origin (PDO) dry-cured ham. The trial was conducted on a population of 423 pigs fed using different strategies to generate a high variation in SW (175 ± 15.5 kg) and BCKF (23.16 ± 4.14 mm). All the left thighs were weighed at slaughter and the ham factory during the different processing phases. The fat cover depth of green trimmed hams was measured. Data were analyzed with a linear model including SW classified in tertiles, BCKF as a covariate, SW × BCKF interaction, sex, batch, and pen nested within batch. Our results highlighted that, for each 10 kg increase in SW, trimmed and seasoned ham weights increased by 0.76 and 0.54 kg, respectively. The increase in SW significantly reduced relative curing and deboning losses but did not affect ham fat cover depth and trimming losses. A rise in BCKF increased the ham fat cover depth and trimming losses and decreased the curing and deboning losses. Increases in SW and BCKF improved quality traits of the seasoned ham including fat cover depth, visible marbling, inner lean firmness, and fat color. These findings confirm the feasibility of increasing SW and BCKF, which will result in a reduction in the relative losses associated with the dry-curing process while improving the quality of the seasoned ham.

Genetic Correlations between Boar Taint Compound Concentrations in Fat of Purebred Boars and Production and Ham Quality Traits in Crossbred Heavy Pigs.

Selecting pigs with reduced ability to accumulate boar taint (BT) compounds in their tissues is an alternative to male surgical castration. As the majority of slaughter pigs are crossbred, before selecting against BT in purebreds, it is essential to consider possible impacts on commercial traits in crossbreds. This study estimated the genetic correlations between BT compound levels measured in 1115 purebred pigs and carcass and ham quality traits collected in 26,577 crossbred Italian heavy pigs. Genetic correlations were estimated in bivariate Bayesian analyses including one BT trait and one production or ham quality trait at a time. Heritability of androstenone, skatole, and indole was 0.41, 0.49, and 0.37, respectively. A moderate negative correlation between skatole and carcass yield (-0.40), and between all BT compounds and backfat (from -0.26 to -0.55) was observed. Conversely, positive correlations (from 0.11 to 0.54) were found between skatole and ham fat thickness traits. Correlations between BT compounds and iodine number ranged from -0.07 (for androstenone) to -0.64 (for skatole), whereas those with PUFA ranged from -0.13 (for indole) to -0.33 (for skatole). Hence, reducing BT could decrease ham fat thickness and increase unsaturated fatty acids, with potential negative impacts on product quality.

Genomic Prediction and Genome-Wide Association Study for Boar Taint Compounds.

With a perspective future ban on surgical castration in Europe, selecting pigs with reduced ability to accumulate boar taint (BT) compounds (androstenone, indole, skatole) in their tissues seems a promising strategy. BT compound concentrations were quantified in the adipose tissue of 1075 boars genotyped at 29,844 SNPs. Traditional and SNP-based breeding values were estimated using pedigree-based BLUP (PBLUP) and genomic BLUP (GBLUP), respectively. Heritabilities for BT compounds were moderate (0.30-0.52). The accuracies of GBLUP and PBLUP were significantly different for androstenone (0.58 and 0.36, respectively), but comparable for indole and skatole (~0.43 and ~0.47, respectively). Several SNP windows, each explaining a small percentage of the variance of BT compound concentrations, were identified in a genome-wide association study (GWAS). A total of 18 candidate genes previously associated with BT (MX1), reproduction traits (TCF21, NME5, PTGFR, KCNQ1, UMODL1), and fat metabolism (CTSD, SYT8, TNNI2, CD81, EGR1, GIPC2, MIGA1, NEGR1, CCSER1, MTMR2, LPL, ERFE) were identified in the post-GWAS analysis. The large number of genes related to fat metabolism might be explained by the relationship between sexual steroid levels and fat deposition and be partially ascribed to the pig line investigated, which is selected for ham quality and not for lean growth.

Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings.

BACKGROUND: The gilthead sea bream (Sparus aurata) has long been considered resistant to viral nervous necrosis (VNN), until recently, when significant mortalities caused by a reassortant nervous necrosis virus (NNV) strain were reported. Selective breeding to enhance resistance against NNV might be a preventive action. In this study, 972 sea bream larvae were subjected to a NNV challenge test and the symptomatology was recorded. All the experimental fish and their parents were genotyped using a genome-wide single nucleotide polymorphism (SNP) array consisting of over 26,000 markers. RESULTS: Estimates of pedigree-based and genomic heritabilities of VNN symptomatology were consistent with each other (0.21, highest posterior density interval at 95% (HPD95%): 0.1-0.4; 0.19, HPD95%: 0.1-0.3, respectively). The genome-wide association study suggested one genomic region, i.e., in linkage group (LG) 23 that might be involved in sea bream VNN resistance, although it was far from the genome-wide significance threshold. The accuracies (r) of the predicted estimated breeding values (EBV) provided by three Bayesian genomic regression models (Bayes B, Bayes C, and Ridge Regression) were consistent and on average were equal to 0.90 when assessed in a set of cross-validation (CV) procedures. When genomic relationships between training and testing sets were minimized, accuracy decreased greatly (r = 0.53 for a validation based on genomic clustering, r = 0.12 for a validation based on a leave-one-family-out approach focused on the parents of the challenged fish). Classification of the phenotype using the genomic predictions of the phenotype or using the genomic predictions of the pedigree-based, all data included, EBV as classifiers was moderately accurate (area under the ROC curve 0.60 and 0.66, respectively). CONCLUSIONS: The estimate of the heritability for VNN symptomatology indicates that it is feasible to implement selective breeding programs for increased resistance to VNN of sea bream larvae/juveniles. Exploiting genomic information offers the opportunity of developing prediction tools for VNN resistance, and genomic models can be trained on EBV using all data or phenotypes, with minimal differences in classification performance of the trait phenotype. In a long-term view, the weakening of the genomic ties between animals in the training and test sets leads to decreased genomic prediction accuracies, thus periodical update of the reference population with new data is mandatory.

Concentrations of Boar Taint Compounds Are Weakly Associated with Sexual Behavior of Young Boars.

Strategies to control boar taint (BT) in meat relies on the reduction of skatole, indole, and androstenone concentration. This might have unfavorable effects on the libido of breeding boars. The association between BT compound concentration in backfat and libido was investigated in 391 commercial breeding boars. Six sexual behavior traits (SBT; sexual arousal, salivation, mounting performance, interest in the dummy sow, penis unsheathing, and overall libido score) were scored during the training of the boars with the dummy sow. Variation in SBT was analyzed by proportional-odds cumulative logistic models. Overall, indole, skatole, and androstenone concentrations were weakly associated with libido. Farm of origin, age at training or body weight, and BT compound levels were poor predictors of boar performance (the area under the ROC curve ranged from 0.60 to 0.69). This indicates that BT compound concentrations were weakly associated with libido, even though the probability of observing good SBT scores increased with high levels of androstenone, intermediate or low levels of skatole, and intermediate to high levels of indole. Hence, practices aiming at reducing androstenone, and controlling the concentrations of skatole and indole to intermediate levels are not expected to impair the libido of young boars.

Infrared Predictions Are a Valuable Alternative to Actual Measures of Dry-Cured Ham Weight Loss in the Training of Genome-Enabled Prediction Models.

Selection to reduce ham weight losses during dry-curing (WL) requires individual traceability of hams throughout dry-curing, with high phenotyping costs and long generation intervals. Infrared spectroscopy enables cost-effective, high-throughput phenotyping for WL 24 h after slaughter. Direct genomic values (DGV) of crossbred pigs and their purebred sires were estimated, for observed (OB) and infrared-predicted WL (IR), through models developed from 640 and 956 crossbred pigs, respectively. Five Bayesian models and two pseudo-phenotypes (estimated breeding value, EBV, and adjusted phenotype) were tested in random cross-validation and leave-one-family-out validation. The use of EBV as pseudo-phenotypes resulted in the highest accuracies. Accuracies in leave-one-family-out validation were much lower than those obtained in random cross-validation but still satisfactory and very similar for both traits. For sires in the leave-one-family-out validation scenario, the correlation between the DGV for IR and EBV for OB was slightly lower (0.32) than the correlation between the DGV for OB and EBV for OB (0.38). While genomic prediction of OB and IR can be equally suggested to be incorporated in future selection programs aiming at reducing WL, the use of IR enables an early, cost-effective phenotyping, favoring the construction of larger reference populations, with accuracies comparable to those achievable using OB phenotype.

Genomic Predictions of Phenotypes and Pseudo-Phenotypes for Viral Nervous Necrosis Resistance, Cortisol Concentration, Antibody Titer and Body Weight in European Sea Bass.

In European sea bass (Dicentrarchus labrax L.), the viral nervous necrosis mortality (MORT), post-stress cortisol concentration (HC), antibody titer (AT) against nervous necrosis virus and body weight (BW) show significant heritability, which makes selective breeding a possible option for their improvement. An experimental population (N = 650) generated by a commercial broodstock was phenotyped for the aforementioned traits and genotyped with a genome-wide SNP panel (16,075 markers). We compared the predictive accuracies of three Bayesian models (Bayes B, Bayes C and Bayesian Ridge Regression) and a machine-learning method (Random Forest). The prediction accuracy of the EBV for MORT was approximately 0.90, whereas the prediction accuracies of the EBV and the phenotype were 0.86 and 0.21 for HC, 0.79 and 0.26 for AT and 0.71 and 0.38 for BW. The genomic prediction of the EBV for MORT used to classify the phenotype for the same trait showed moderate classification performance. Genome-wide association studies confirmed the polygenic nature of MORT and demonstrated a complex genetic structure for HC and AT. Genomic predictions of the EBV for MORT could potentially be used to classify the phenotype of the same trait, though further investigations on a larger experimental population are needed.

Resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax L.): heritability and relationships with body weight, cortisol concentration, and antibody titer.

BACKGROUND: Susceptibility of European sea bass (Dicentrarchus labrax L.) to viral nervous necrosis (VNN) is well-known. Interest towards selective breeding as a tool to enhance genetic resistance in this species has increased sharply due to the major threat represented by VNN for farmed sea bass and limitations concerning specific therapeutical measures. A sea bass experimental population (N = 650) was challenged with nervous necrosis virus (NNV) to investigate genetic variation in VNN mortality. In addition, relationships of this trait with serum cortisol concentration after stress exposure, antibody titer against NNV antigens, and body weight at a fixed age were studied to identify potential indicator traits of VNN resistance. RESULTS: The estimate of heritability for VNN mortality was moderate and ranged from 0.15 (HPD95%, 95% highest posterior density interval: 0.02, 0.31) to 0.23 (HPD95%: 0.06, 0.47). Heritability estimates for cortisol concentration, antibody titer, and body weight were 0.19 (HPD95%: 0.07, 0.34), 0.36 (HPD95%: 0.16, 0.59) and 0.57 (HPD95%: 0.33, 0.84), respectively. Phenotypic relationships between traits were trivial and not statistically significant, except for the estimated correlation between antibody titer and body weight (0.24). Genetic correlations of mortality with body weight or antibody titer (- 0.39) exhibited a 0.89 probability of being negative. A negligible genetic correlation between mortality and cortisol concentration was detected. Antibody titer was estimated to be positively correlated with body weight (0.49). CONCLUSIONS: Antibody titer against NNV offers the opportunity to use indirect selection to enhance resistance, while the use of cortisol concentration as an indicator trait in breeding programs for VNN resistance is questionable. The estimate of heritability for VNN mortality indicates the feasibility of selective breeding to enhance resistance to NNV and raises attention to the development of genomic prediction tools to simplify testing procedures for selection candidates.

Sex dimorphism in European sea bass (Dicentrarchus labrax L.): New insights into sex-related growth patterns during very early life stages.

The European sea bass (Dicentrarchus labrax) exhibits female-biased sexual size dimorphism (SSD) early in development. New tagging techniques provide the opportunity to monitor individual sex-related growth during the post-larval and juvenile stages. We produced an experimental population through artificial fertilization and followed a rearing-temperature protocol (~16°C from hatching to 112 days post-hatching, dph; ~20°C from 117 to 358 dph) targeting a roughly balanced sex ratio. The fish were tagged with microchips between 61 and 96 dph in five tagging trials of 50 fish each; individual standard length (SL) was recorded through repeated biometric measurements performed between 83 to 110 dph via image analyses. Body weight (BW) was modelled using the traits measured on the digital pictures (i.e. area, perimeter and volume). At 117 dph, the fish were tagged with microtags and regularly measured for SL and BW until 335 dph. The experiment ended at 358 dph with the sexing of the fish. The sex-ratio at the end of the experiment was significantly in favor of the females (65.6% vs. 34.4%). The females were significantly longer and heavier than the males from 103 dph (~30 mm SL, ~0.44 g BW) to 165 dph, but the modeling of the growth curves suggests that differences in size already existed at 83 dph. A significant difference in the daily growth coefficient (DGC) was observed only between 96 and 103 dph, suggesting a physiological or biological change occurring during this period. The female-biased SSD pattern in European sea bass is thus strongly influenced by very early growth differences between sexes, as already shown in previous studies, and in any case long before gonadal sex differentiation has been started, and thus probably before sex has been determined. This leads to the hypothesis that early growth might be a cause rather than a consequence of sex differentiation in sea bass.

Population-specific variations of the genetic architecture of sex determination in wild European sea bass Dicentrarchus labrax L.

Polygenic sex determination (PSD) may show variations in terms of genetic and environmental components between populations of fish species exposed/adapted to different environments. The European sea bass (Dicentrarchus labrax) is an interesting model, combining both a PSD system and a genetic subdivision into an Atlantic and a Mediterranean lineage, with genetic substructures within the Mediterranean Sea. Here, we produced experimental progeny crosses (N = 927) from broodstock sampled in four wild populations (North Atlantic, NAT; Western Mediterranean, WEM; North-Eastern Mediterranean, NEM; South-Eastern Mediterranean, SEM). We found less females than males in the progeny, both in the global dataset (32.5%) and within each paternal group (from 25.1% for NEM to 39.0% for WEM), with significant variation among populations, dams, and sires. Sex, body weight (BW), and body length (BL) showed moderate heritability (0.52 ± 0.17, 0.46 ± 0.17, 0.34 ± 0.15, respectively) and sex was genetically correlated with BW and BL, with rAsex/BW = 0.69 ± 0.12 and rA sex/BL = 0.66 ± 0.13. A weighted GWAS performed both on the global dataset and within each paternal group revealed a different genetic architecture of sex determination between Atlantic and Mediterranean populations (9 QTLs found in NAT, 7 in WEM, 5 in NEM, and 4 in SEM, with a cumulated variance explained of 27.04%, 21.87%, 15.89%, and 12.10%, respectively) and a more similar genetic architecture among geographically close populations compared to geographically distant populations, consistent with the hypothesis of a population-specific evolution of polygenic sex determination systems in different environments.