Camillo Pieramati

Heritability estimation of osteochondrosis dissecans in Maremmano horses

Abstract The heritability of radiographic findings of osteochondrosis dissecans (OCD) and its effect on the frequency of this disease under different selection strategies were estimated in a population of Maremmano horses. Three hundred and fifty offspring of 75 sires were examined: all 3-year-old animals clinically evaluated for admission to the Performance Test from 1993 to 1998 and a sample of 2-year-old horses. The clinical procedure included radiographic examination of the tibio-tarsal, the femoro-patellar, and the metacarpo-phalangeal joints. The heritability was analyzed by two statistical methods: a threshold animal model based on the underlying liability concept and an animal model on the 0–1 observable scale. The h 2 estimate ranged between 0.09 and 0.14 for the first and second method, respectively. Also, the efficiency of different selection strategies on the prevalence of OCD was tested on this basis. The simulated results indicate that the incidence of osteochondrosis in the Maremmano population could be reduced; active selection, simulating five generations, for both stallions and mares reduced the frequency of OCD from 16 to 2%.

Using eigenvalues as variance priors in the prediction of genomic breeding values by principal component analysis

Genome-wide selection aims to predict genetic merit of individuals by estimating the effect of chromosome segments on phenotypes using dense single nucleotide polymorphism (SNP) marker maps. In the present paper, principal component analysis was used to reduce the number of predictors in the estimation of genomic breeding values for a simulated population. Principal component extraction was carried out either using all markers available or separately for each chromosome. Priors of predictor variance were based on their contribution to the total SNP correlation structure. The principal component approach yielded the same accuracy of predicted genomic breeding values obtained with the regression using SNP genotypes directly, with a reduction in the number of predictors of about 96% and computation time of 99%. Although these accuracies are lower than those currently achieved with Bayesian methods, at least for simulated data, the improved calculation speed together with the possibility of extracting principal components directly on individual chromosomes may represent an interesting option for predicting genomic breeding values in real data with a large number of SNP. The use of phenotypes as dependent variable instead of conventional breeding values resulted in more reliable estimates, thus supporting the current strategies adopted in research programs of genomic selection in livestock.

Pre-selection of most significant SNPS for the estimation of genomic breeding values

The availability of a large amount of SNP markers throughout the genome of different livestock species offers the opportunity to estimate genomic breeding values (GEBVs). However, the estimation of many effects in a data set of limited size represent a severe statistical problem. A pre-selection of SNPS based on single regression may provide a reasonable compromise between accuracy of results, number of independent variables to be considered and computing requirements.A total of 595 and 618 SNPS were pre-selected using a simple linear regression for each SNP, based on phenotypes or polygenic EBVs, respectively, with an average distance of 9–10 cM between them. Chromosome four had the largest frequency of selected SNPS. Average correlations between GEBVs and TBVs were about 0.82 and 0.73 for the TRAINING generations when phenotypes or polygenic EBVs were considered as dependent variable, whereas they tend to decrease to 0.66 and 0.54 for the PREDICTION generations. The pre-selection of SNPs using the phenotypes as dependent variable together with a BLUP estimation of marker genotype effects using a variance contribution of each marker equal to σ2a/nsnps resulted in a remarkable accuracy of GEBV estimation (0.77) in the PREDICTION generations.

Exercise-induced up-regulation of MMP-1 and IL-8 genes in endurance horses

BackgroundThe stress response is a critical factor in the training of equine athletes; it is important for performance and for protection of the animal against physio-pathological disorders.In this study, the molecular mechanisms involved in the response to acute and strenuous exercise were investigated using peripheral blood mononuclear cells (PBMCs).ResultsQuantitative real-time PCR (qRT-PCR) was used to detect modifications in transcription levels of the genes for matrix metalloproteinase-1 (MMP-1) and interleukin 8 (IL-8), which were derived from previous genome-wide expression analysis. Significant up-regulation of these two genes was found in 10 horses that had completed a race of 90–120 km in a time-course experimental design.ConclusionThese results suggest that MMP-1 and IL-8 are both involved in the exercise-induced stress response, and this represents a starting point from which to understand the adaptive responses to this phenomenon.

Effect of including inbreeding coefficients for animal and dam on estimates of genetic parameters and prediction of breeding values for reproductive and growth traits of Piedmontese cattle

Abstract Effects of inbreeding of animal and dam on estimates of genetic parameters and predictions of breeding values for five productive and reproductive traits of Piedmontese cattle were studied. Traits were (a) age at first insemination, (b) age at first calving, (c) 120-day weight, (d) yearling weight of males, and (e) yearling weight of females. Data for animals born from 1970 to 1995 were used. Inbreeding coefficients were computed using pedigree records back to 1900. A sire model was used for estimating genetic parameters and predicting breeding values. Two models were used for each trait. Model 1 included fixed effects of herd–year (for traits a, b, d, and e) or herd–year and sex–age of dam (trait c) and covariates for inbreeding coefficient of animal for traits a and b and inbreeding of animal and dam for traits c, d and e. Random effects were associated with sires and dams for traits c, d, and e. Model 2 did not include covariates for inbreeding. Inbreeding increased age at first insemination and calving and decreased 120-day and yearling weights of males and females. Inbreeding was not needed in the model for estimation of variance components or for prediction of breeding values for this population.

Suitability of linear scoring in meat sheep: the practical case of Merinizzata Italiana breed

Linear scoring is widely applied in domestic animal species, mainly in cattle and horses. There are only few cases of linear scoring in sheep, probably because the small body size and the narrow range of the classes make difficult to correctly evaluate the measures. In this paper the results of a linear scoring test carried out on Merinizzata Italiana sheep breed in order to verify the feasibility of this method in sheep, are reported. Twenty untrained people, with three different levels of scoring experience in meat sheep morphology, evaluated 52 pluriparous ewes for body length, chest circumference, chest width, rump height, rump width, and withers height; to check for misclassification, their scores were compared with a reference score, previously obtained measuring the same animals by the suitable tools (measuring tape and a Lydtin stick). The percentage of correct scoring ranged from 44.4% for body length to 61.8% for withers height, and was not affected by the experience of the judge. In all characters, the distance of the class from the trait mean had a significant effect in increasing the intensity of misclassifications; the judge’s experience showed a positive effect in reducing the intensity of the misclassification for body length, that was the hardest trait to score. These results encourage to further verifying in practice the linear scoring in the Merinizzata Italiana sheep and in other meat breeds.

Genetic parameters for the weights and yields of carcass cuts in Chianina cattle.

Chianina is the tallest and heaviest beef cattle breed in the world and 1 of the most appreciated breeds on the Italian meat market. A selection program focused on improving Chianina carcass quality could provide a further economic advantage to Chianina breeders. However, the current European carcass scoring system [i.e., the SEUROP (S=superior, E=excellent, U= very good, R=good, O=fair, and P=poor) grid] is not suitable for use in selective breeding programs; methods based on carcass cuts would be much more efficient. Here, the genetic parameters of weights and yields (percentage of carcass weight) of the main commercial cuts were estimated on 842 Chianina carcasses (heifers and bullocks) using a mixed model that takes into account the fixed effects of herd, year of slaughter, and sex and the random additive effect of the animal; the carcass weight was also considered in cuts yield. The average carcass weights were 492.6 ± 86.52 kg (males) and 312.1 ± 68.74 kg (females), and the largest cut was the round, with a weight of 58.6 ± 19.35 kg and yield of 24.4 ± 1.28% in males and 40.2 ± 17.59 kg and 25.3 ± 1.41% in females. The variability in cut weight was greater than that in yield percentage. The cut weight heritabilities ranged from 0.74 (chuck) to 0.21 (short plate) whereas the yield heritabilities ranged from 0.88 (loin) to 0.40 (brisket). The genetic correlations were generally high and positive between weights; correlation values with yields were lower and could be positive or negative. These findings suggest that a selection program to improve the carcass quality of Chianina beef using cuts data could potentially achieve good results.

On the use of Elo rating on harness racing results in the genetic evaluation of trotter

Abstract The official results of trotters in Italian harness racings have been used to get AM-BLUP estimates of genetic parameters, EBVs and rTI of three groups of traits: speed (racing time, annual best time, best time in career between 2- and 5-year old), earnings (earnings/start, annual earnings, total earnings between 2- and 5-year old) and Elo system traits (underlying performance and final rating). The Elo system has been used for half a century in chess players rating, and it has been modified and fitted to several games and sports: it has already been used for genetic evaluation of sport horses in France. The highest heritability estimates in each group of traits have been found for best time (.430±.014), total earnings (.271±.013) and Elo final rating (.270±.008). The choice of “k”, the Elo ratings updating factor, did not show a key role in affecting the results. The underlying performance heritability and repeatability have been estimated .159±.004 and .420±.007 respectively. The Elo-based systems proved to be very promising in objectively evaluating trotters.

Frequencies of Fleece Color Genes in Upper Visso Sheep

Abstract Frequencies of fleece color genes were evaluated in Italian Merino-crossbred Upper Visso sheep. Assuming panmixy, the frequencies of alleles at the A (Agouti), B (Brown) and S (Spotting) loci have been calculated in 1328 viable lambs, born by 90 rams and 1384 ewes in 4 flocks. The frequencies are: Awt = 0.866±0.014; Aa = 0.134±0.014; Bb = 0.204±0.100; B+ = 0.796±0.100; Ss = 0.998±0.000; S+ = 0.002±0.000. At the locus E (Extension) the dominant epistatic allele Ed was not found. The frequency of Aa, the only mutant existing at locus A besides Awt, is higher than in other Merino crossbreds.

Oregano dietary supplementation modifies the liver transcriptome profile in broilers: RNASeq analysis

Intensive farming of broilers involves stressful conditions that reduce animal welfare and performance. New dietary strategies to improve performance and meat quality include the administration of plant extracts. Oregano (Origanum vulgare L.) is known for its antimicrobial, anti-fungal, insecticidal and antioxidant properties. However, studies on diet supplementation with oregano are mainly focused on the evaluation of animal performance, while partial information is available on transcriptomics and nutrigenomics and, in particular, Next Generation Sequencing (NGS) is not widely applied. In this study we tested the effect of an oregano aqueous extract supplemented diet on gene expression in broiler chickens. Whole liver transcriptome of 10 birds fed with a supplemented diet versus 10 controls was analyzed using the RNA-Seq technique. One hundred and twenty-nine genes were differentially expressed with an absolute log fold change >1. The analysis reveals a massive down-regulation of genes involved in fatty acid metabolism and insulin signaling pathways in broilers fed with the oregano aqueous extract supplementation. Down-regulated genes could be associated to chicken lean line, suggesting the potential beneficial effect of oregano supplementation in reducing both abdominal and visceral fat deposition. Down-regulation of insulin signaling pathway related genes suggest that dietary oregano supplementation might be an option in obesity and diabetes conditions.