Genetic relationships between weight gain and feeding behaviour of ad libitum-fed pigs and weight gain of heavy pigs under restricted feeding

Pig breeding in Italy aims to obtain heavy pigs for production of typical cured end products. Detailed guidelines related to animals, weight, age, feeding regime, carcass and fresh ham traits impose constraints on this type of production

Survival analysis of piglet pre-weaning mortality

Survival analysis methodology was applied in order to analyse sources of variation of preweaning survival time and to estimate variance components using data from a crossbred piglets population. A frailty sire model was used with the litter effect treated as an additional random source of variation. All the variables considered had a significant effect on survivability: sex, cross-fostering, parity of the nurse-sow and litter size. The variance estimates of sire and litter were closed to 0.08 and 2 respectively and the heritability of pre-weaning survival was 0.03

On-site visible-near IR prediction of iodine number and fatty acid composition of subcutaneous fat of raw hams as phenotypes for a heavy pig breeding program.

Abstract The quality of subcutaneous fat of raw hams is a trait of interest in selective breeding programs for pig lines used in dry-cured ham production, and rapid, non-invasive methods for its assessment are available. However, the efficacy of such methods to provide indicator traits for breeding programs needs to be proven. The study investigated the accuracy of on-site visible–near IR spectroscopy predictions of iodine number and fatty acid (FA) composition of raw ham subcutaneous fat, and it evaluated their effectiveness as indicator traits of ham fat quality in a pig breeding program. Prediction equations were developed using visible–near IR spectra acquired at the slaughterhouse from five sites in subcutaneous fat of raw hams of 1025 crossbred pigs. Pigs were raised, under standardized rearing and feeding conditions, in the sib-testing program of the Goland C21 boar line and slaughtered at nine months of age and average body weight of 166 ± 15 kg. Accuracy was generally relatively poor, but R2 in external validation was > 0.7 for iodine number and concentration of C18:2n-6, polyunsaturated FAs and omega-6 FAs. To assess the effectiveness of the on-site predictions as indicator traits in a breeding program, (co)variance components of the measured traits (OBS) and of their predictions using in-lab (in-lab-PR) or on-site (on-site-PR) spectrometers were estimated. Available records for OBS were 6814 and 2048, for iodine number and FA composition, respectively. Predictions using in-lab were available for pigs slaughtered between 2006 and 2014, for a total of 10 153 records. Predictions using on-site were obtained from spectra collected since 2011, for a total of 10 296 records. The estimated heritabilities for the investigated traits ranged from 0.34 to 0.50 and were greater for on-site-PR than for OBS. Genetic correlations between OBS and in-lab-PR were very close to 1.00 for all the investigated traits, whereas those between OBS and on-site-PRED ranged from 0.86 to 0.94. On-site visible-IR predictions are accurate enough to support the use of this technique for large-scale phenotyping of raw ham fat quality, even when dealing with animals of a single genetic line raised in standardized conditions, and may be implemented as indicator traits in breeding programs

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax)

Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified. The two GWAS candidate markers were located on ChrX and Chr17, both in close proximity with the peaks of the two most significant QTLs. Notably, the SNP marker on Chr17 was positioned within the Sobp gene coding region, which plays a pivotal role in craniofacial development. The analysis of differentially expressed genes in jaw-deformed animals highlighted the "nervous system development" as a crucial pathway in MP. In particular, Zic2, a key gene for craniofacial morphogenesis in model species, was significantly down-regulated in MP-affected animals. Gene expression data revealed also a significant down-regulation of Sobp in deformed larvae. Our analyses, integrating transcriptomic and GWA methods, provide evidence for putative mechanisms underlying seabass jaw deformity

Effects of κ-CN Glycosylation on Rennet Coagulation Properties of Milk in Simmental Cattle

Contents of casein fractions are known to affect coagulation properties and cheese yield of milk, but studies on the effects of κ-CN composition on variation of coagulation properties of milk are still very scarce. Effects exerted by κ-CN composition on variation of milk coagulation properties (MCP) were investigated using 2,084 individual milk samples of Simmental cows. Rennet coagulation time (RCT), and curd firmness (A30) were measured using a computerized renneting meter. Milk protein composition and genotypes at CSN2, CSN3 and BLG were obtained by reversed-phase HPLC. The percentage ratios of κ-CN (κCN%), of Glycosylated-κ-CN (G-κCN%), and Unglycosylated-κ-CN (U-κCN%) to total casein were measured. The degree of glycosylation (GD) was measured as the percentage ratio of glycosylated-κ-CN to total κ-CN. A difference of 1.7 min (corresponding to 0.37 SD of the trait) was observed for the average RCT of the two extreme classes of κCN% content. RCT decreased when κCN% and G-κCN% increased, whereas U-κCN% exhibited a slightly unfavourable effect on the onset of the coagulation process. A slight decrease of RCT was also observed for high GD, although this effect was less clear than that of G-κCN%. A favourable effect of κCN%, G-κCN% and GD on A30 was also detected

Comparison between Direct and Competitive Models to Investigate Variation of Carcass and Ham Quality Traits in Heavy Pigs

Social interactions among animals raised in pens can affect their performance. In this study direct and competitive models were compared to investigate the influence of social genetic effects on variation of carcass weight (CW), carcass lean meat content (LM) and ham round shape (RS) in heavy pigs. Four sequential models including, in addition to sex and slaughter group fixed effects, the random effects of the social group, litter (full-sibs family), direct and social genetic effects of pigs were evaluated. Social group and litter effects accounted for about 4 and 3% of the phenotypic variance, respectively. When social genetic effects were added to model, a small social heritability was estimated for all traits (from 0.3 to 0.7% of the phenotypic variance). A negative correlation between direct and social effects was estimated for LM and RS, reducing the total heritable variance available for selection. Model comparison showed that the best fit was provided by the model including only direct additive genetic effects of pigs. So, this model seems still preferable for the genetic evaluation of the investigated traits

Genetic correlations between measures of beef quality traits and their predictions by near-infrared spectroscopy in the Piemontese cattle breed.

The aims of this study were to predict beef quality traits (BQ: colour, shear force, drip and cooking losses) of Piemontese cattle using near-infrared spectroscopy (NIRS) and to estimate genetic parameters for measured BQ and their predictions by NIRS. Heritabilities and genetic correlations for measured BQ and their predictions based on NIRS were estimated through bivariate Bayesian analyses. Heritability estimates for measured BQ were of intermediate magnitude (from 0.10 to 0.63) and similar to those for NIRS predictions. The genetic correlations between BQ measures and their predictions by NIRS were very high for colour traits, high for drip loss, and nil for shear force and cooking loss. NIRS predictions can be proposed as indicator traits in breeding programs for enhancement of colour traits and drip loss

Cumulative t-link threshold models for the genetic analysis of calving ease scores

In this study, a hierarchical threshold mixed model based on a cumulative t-link specification for the analysis of ordinal data or more, specifically, calving ease scores, was developed. The validation of this model and the Markov chain Monte Carlo (MCMC) algorithm was carried out on simulated data from normally and t4 (i.e. a t-distribution with four degrees of freedom) distributed populations using the deviance information criterion (DIC) and a pseudo Bayes factor (PBF) measure to validate recently proposed model choice criteria. The simulation study indicated that although inference on the degrees of freedom parameter is possible, MCMC mixing was problematic. Nevertheless, the DIC and PBF were validated to be satisfactory measures of model fit to data. A sire and maternal grandsire cumulative t-link model was applied to a calving ease dataset from 8847 Italian Piemontese first parity dams. The cumulative t-link model was shown to lead to posterior means of direct and maternal heritabilities (0.40 ± 0.06, 0.11 ± 0.04) and a direct maternal genetic correlation (-0.58 ± 0.15) that were not different from the corresponding posterior means of the heritabilities (0.42 ± 0.07, 0.14 ± 0.04) and the genetic correlation (-0.55 ± 0.14) inferred under the conventional cumulative probit link threshold model. Furthermore, the correlation (> 0.99) between posterior means of sire progeny merit from the two models suggested no meaningful rerankings. Nevertheless, the cumulative t-link model was decisively chosen as the better fitting model for this calving ease data using DIC and PBF