Andrea Albera

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.

Investigation on variability of candidate genes for meat quality traits in Piemontese cattle.

Abstract This study aimed to investigate the variability of 15 genes chosen according to their function as markers of meat quality traits in Piemontese cattle. Meat samples of Longissimus thoracis muscle and data on carcass weight (CW), shear force (SF), cooking loss (CL), and pH collected on 1,208 Piemontese young bulls progeny of 109 AI sires were available for this investigation. For each trait considered (CW, SF, CL, pH), 48 samples were chosen from each tail of normal distribution, and one or more single nucleotide polymorphisms (SNPs) were determined for the following loci: growth hormone (GH), growth hormone receptor (GHR), pro-opiomelanocortin (POMC), pituitary-specific positive transcription factor 1 (POU1F1), melanocortin-4 receptor (MC4R), corticotrophin-realising hormone (CRH), insulin-like growth factor binding protein- 3 (IGFBP3), diacylglycerol acyltransferase 1 (DGAT1), thyroglobulin (TG), carboxypeptidase E (CPE), calpain 1 (CAPN1), calpastatin (CAST), cathepsin B and D (CATB, CATD), and protein kinase adenosine monophosphate-activated 3-subunit (PRKAG3). Eight SNPs were characterized by a high, 4 by an intermediate and 2 by a low variability; 6 may be almost fixed. Based on these results, variable loci will be investigated on the entire available data set in order to ????????????study their effects on meat quality traits.

Effect of polymorphisms in candidate genes on carcass and meat quality traits in double muscled Piemontese cattle

The aim of this study was to investigate the association between 10 candidate genes and carcass weight and conformation, carcass daily gain, and meat quality (pH, color, cooking loss, drip loss and shear force) in 990 double-muscled Piemontese young bulls. Animals were genotyped at each of the following genes: growth hormone, growth hormone receptor, pro-opiomelanocortin, pro-opiomelanocortin class 1 homeobox 1, melanocortin-4 receptor, corticotrophin-releasing hormone, diacylglycerol O-acyltransferase-1, thyroglobulin, carboxypeptidase E and gamma-3 regulatory subunit of the AMP-activated protein kinase. All the investigated SNPs had additive effects which were relevant for at least one of the traits. Relevant associations between the investigated SNPs and carcass weight, carcass daily gain and carcass conformation were detected, whereas associations of SNPs with meat quality were moderate. Results confirmed some of previously reported associations, but diverged for others. Validation in other cattle breeds is required to use these SNPs in gene-assisted selection programs for enhancement of carcass traits and meat quality.

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.

Comparison of four Italian beef cattle breeds by means of functional genes

Piemontese, Chianina, Marchigiana and Romagnola are the main Italian beef breeds, and the quality of their products is largely recognised all over the world. Here, 18 single nucleotide polymorphisms (SNPs) in 12 candidate genes involved on meat traits were investigated on 1055 candidates for selection in order to analyse the within- and between-breed variability with a functional marker approach. Three SNPs (GDF8-3, GH and NPY-3) were monomorphic and most of the polymorphic SNPs showed an allele distribution quite similar in the four breeds. High variability at LEP-2, LEP-3 and LEPR markers was detected across breeds and the analysis of the relationship between genetic differentiation and heterozygosity indicated significant deviation from a neutral-equilibrium model for LEP-2. The highest pairwise fixation index values (0.1189 to 0.1877) were obtained for the comparisons of Piemontese with the other breeds, while the lowest value (0.0296) was observed in Chianina and Marchigiana. The Piemontese differentiation from the other breeds could be due to its geographical isolation and selection targets. The results for breed assignment follows the genetic differentiation, in fact, Piemontese had the highest percentage of correct assignment (87.6), while Marchigiana had the lowest (47.5). These findings suggest that functional markers can be more suitable than neutral markers in discriminating breeds similar in morphology if selection plays some role in their differentiation.