Prediction of dry-cured ham weight loss and prospects of use in a pig breeding program

Large ham weight losses (WL) in dry-curing are undesired as they lead to a loss of marketable product and penalise the quality of the dry-cured ham. The availability of early predictions of WL may ease the adaptation of the dry-curing process to the characteristics of the thighs and increase the effectiveness of selective breeding in enhancing WL. Aims of this study were (i) to develop Bayesian and Random Forests (RFs) regression models for the prediction of ham WL during dry-curing using on-site infrared spectra of raw ham subcutaneous fat, carcass and raw ham traits as predictors and (ii) to estimate genetic parameters for WL and their predictions (P-WL). Visible-near infrared spectra were collected on the transversal section of the subcutaneous fat of raw hams. Carcass traits were carcass weight, carcass backfat depth, lean meat content and weight of raw hams. Raw ham traits included measures of ham subcutaneous fat depth and linear scores for round shape, subcutaneous fat thickness and marbling of the visible muscles of the thigh. Measures of WL were available for 1672 hams. The best prediction accuracies were those of a Bayesian regression model including the average spectrum, carcass and raw ham traits, with R2 values in validation of 0.46, 0.55 and 0.62, for WL at end of salting (23 days), resting (90 days) and curing (12 months), respectively. When WL at salting was used as an additional predictor of total WL, the R2 in validation was 0.67. Bayesian regressions were more accurate than RFs models in predicting all the investigated traits. Restricted maximum likelihood (REML) estimates of genetic parameters for WL and P-WL at the end of curing were estimated through a bivariate animal model including 1672 measures of WL and 8819 P-WL records. Results evidenced that the traits are heritable (h2 ± SE was 0.27 ± 0.04 for WL and 0.39 ± 0.04 for P-WL), and the additive genetic correlation is positive and high (ra = 0.88 ± 0.03). Prediction accuracy of ham WL is high enough to envisage a future use of prediction models in identifying batches of hams requiring an adaptation of the processing conditions to optimise results of the manufacturing process. The positive and high genetic correlation detected between WL and P-WL at the end of dry-curing, as well as the estimated heritability for P-WL, suggests that P-WL can be successfully used as an indicator trait of the measured WL in pig breeding programs

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

Health disorders and their association with production and functional traits in Holstein Friesian cows

Logistic regression models were used for studying the relationships between milk yield, body condition score (BCS), somatic cell score and some disorders of periparturient cows (mammary edema and retained placenta) with the occur- rence of ovarian cysts, clinical mastitis and lameness. Data from milk recording (milk yield and somatic cell content) col- lected at nearly monthly intervals (time period: 35 ± 3 d) were merged with BCS recorded on the same dates of milk recording on periparturient heifers, lactating and dry cows, and with health disorders data (retained placenta, severe mammary edema, ovarian cysts and clinical mastitis and lameness) collected during regular herd activities over nearly 3.5 years. Data were from one commercial herd consisting of over 200 lactating dairy cows and exhibiting an average 305-d milk yield of nearly 10,000 kg. A total of 5,315 records from 728 lactations and 429 cows were used in the analy- ses. The time period incidence rate was 11.9%, 6.6% and 4.6% for ovarian cysts, lameness and mastitis, respectively, and the lactational incidence rate was 44.1%, 33.4% and 28.1% for ovarian cysts, lameness and mastitis, respectively. Occurrence of both ovarian cysts and mastitis was more common in the early lactation than afterwards, whereas lame- ness tended to occurr erratically during lactation. The risk of occurrence of mastitis and lameness was lower in primi- parous when compared to multiparous cows. The increase of milk yield increased the risk of occurrence of ovarian cysts (odds ratio: 1.32, P < 0.01) and of mastitis (odds ratio: 1.12, P < 0.10), whereas no significant relationship was found between milk yield and lameness. An increase of somatic cell score was found to be a risk factor for mastitis (odds ratio: 1.36, P<0.01) and for the occurrence of lameness (odds ratio: 1.06, P<0.05). The occurrence of relative risk of disor- ders was not related to BCS at calving, and monthly variation of BCS was related to the onset of mastitis only. Retained placenta did not appear to present a risk factor for the occurrence of diseases of concern, whereas the presence of severe mammary edema at calving increased the risk of mastitis occurrence by nearly 50%. Regular recording of herd health data seems advisable for a better understanding of the relationships between production and functional traits and the occurrence of health disorders

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

Variability in candidate genes revealed associations with meat traits in the Piemontese cattle breed

In the last years an increasing number of associations between single nucleotide polymorphisms (SNPs) in candidate genes and production traits have been reported in beef cattle, but very often the results were not validated and few studies considered breeds homozygous for the allele responsible for the muscular hypertrophy. Therefore, we analysed the variability of 19 previously reported SNPs in 12 genes (GH, GHR, GDF8, GHRL, IGF2, LEP, LEPR, MYF5, NPY, POMC, UCP2, UCP3) in the hypertrophic Piemontese breed and investigated the effects of the observed polymorphisms on growth and conformation. Fourteen SNPs were polymorphic and a significant linkage disequilibrium was observed between SNPs in GHR, LEP and NPY genes, for which both single-SNP and haplotype effects were estimated. Negligible effects on the investigated traits were observed for GHRL, MYF5, NPY, POMC, UCP2 and UCP3 genes. The GHR gene significantly affected daily gain and its effect was further increased when haplotypes were considered. The C allele at LEP-1 and LEP- 2 had moderate negative effects on the considered traits, whereas the C allele at LEP-3 mostly had positive effects; haplotypes in the LEP gene showed weaker but favourable associations with all the traits. The C allele at IGF2 and LEPR had favourable effects on daily gain and negative effects on meat conformation traits. The associations observed for GHR and LEP were consistent with those of previous studies, providing additional evidence of their usefulness as markers. Practical aspects of the applications to the breeding programme of the Piemontese breed need to be examined

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