J. Altarriba

Effect of different Duroc line sires on carcass composition, meat quality and dry-cured ham acceptability.

Carcasses of 399 malignant hyperthermia gene free pigs from crosses sired by three types of Duroc (Virgen de la Fuente, DU1; Diputación de Teruel, DU2; DanBred, DU3) were analyzed for carcass and meat quality. Carcass leanness and fat parameters were measured at the last rib and at the space between the 3rd and 4th last ribs counting from the last one. Weights, pH, electrical conductivity, colour and intramuscular fat were also measured. A sample of 133 legs per cross were processed by dry-curing. The ham portion including Biceps femoris, Semimembranosus and Semitendinosus muscles was evaluated for instrumental texture and colour, biochemical and sensory analyses and acceptability (trained panel and consumers). DU3 carcasses were well conformed but lean. DU1 carcasses had a lower conformation but higher marbling. DU2 carcasses were intermediate. Dry-cured hams from DU1-sired pigs had a higher overall acceptability, although fat content influenced a consumers group negatively. Leaner DU3 hams had the lowest acceptability.

Multiple trait genetic analysis of underlying biological variables of production functions

Abstract A Bayesian procedure to analyze performance data from production functions is presented. The method implies the consideration of each parameter of the production function as a different trait. The systematic effects and genetic relationship between animals are taken into account in the adjustment of production for each animal. The method weights all possible sources of information. In this sense, it allows estimation of the parameters of production functions with only one data along the production cycle and to reduce the influence of outliers. Under analysis, marginal posterior distributions of the function parameters, breeding values, systematic effects and (co)variance components were obtained using the Gibbs sampling algorithm. The procedure requires the definition of the joint posterior distribution to be generalized to any production function. From this joint posterior distribution, the full set of posterior conditional distributions needed for the Gibbs sampling algorithm can be easily obtained.

Allelic incidence in several pig breeds of a missense variant of pig melanocortin-4 receptor (MC4R) gene associated with carcass and productive traits; its relation to IGF2 genotype

MC4R, melanocortin-4 receptor, is involved in feed intake regulation. A mutation in a single base of MC4R, a G/A substitution in position 1426, has been linked to enhanced backfat thickness, average daily gain and daily feed intake. We present in this work a method to diagnose this mutation using real time PCR (RT-PCR) which allows rapid, cheap and reliable analysis of hundreds of samples in just 2h after DNA extraction. We have used this RT-PCR based assay to study the incidence of the mutation in several pig breeds or crosses (Iberian, Duroc, Pietrain, Large White, Large White×Pietrain) and wild boars. IGF2, insuline like growth factor 2, a gene with well demonstrated effects on carcass composition, of all these animals has also been analyzed and we show, using linkage disequilibrium analysis that both genes are independent. The implications of our results for pig selection toward fatty or lean carcasses are discussed.

The effects of two alleles of IGF2 on fat content in pig carcasses and pork.

The different fat infiltration capabilities of two alleles of IGF2 (G3072A) have been investigated in pigs of a Landrace-Large White×Duroc cross. Paternally inherited G allele carrier pigs show an increased content of adipose rich meat cuts such as the lard or the belly and 4mm larger backfat thickness values. Paternally inherited A carrier pigs on the other hand contain larger muscle tissue rich cuts such as the loin, the ham and the tenderloin and have 0.19 units lower feed conversion index. No substantial differences have been found neither in intramuscular fat content in several muscles nor in meat quality in both pig groups. Hams of paternally inherited G carrier pigs are richer in both subcutaneous adipose tissue (23.1 vs 19.1mm backfat thickness) and intermuscular fat content. The suitability and the economics of using any of the two of both genotypes for cured ham production are discussed.

Consumer Beliefs and Attitudes Towards Dry-cured Ham and Protected Designation of Origin Teruel Ham in Two Spanish Regions Differing in Product Knowledge

This work compared the responses of a consumer survey on beliefs and attitudes towards dry-cured ham and protected designation of origin (PDO) Teruel ham carried out in two Spanish regions differing in Teruel ham knowledge: Aragon (high knowledge) and Catalonia (lower knowledge). Results revealed that only small differences were found regarding dry-cured ham consumption habits. With regard to beliefs related to factors affecting ham quality, differences were even lesser; raw material and maturing process, as well as marbling, colour and flavour and proper saltiness were rated as the most important quality factors. Nevertheless, large significant differences were evident between both regions in knowledge, consumption, beliefs and attitudes towards PDO Teruel ham. However, there were no differences regarding the willingness to pay a higher price for PDO ham. Multiple correspondence analysis of all data revealed large effects of age, education, income level and size of the place of residence, independent from the region of origin of the consumer.

A Bayesian Model for the Analysis of Transgenerational Epigenetic Variation

Epigenetics has become one of the major areas of biological research. However, the degree of phenotypic variability that is explained by epigenetic processes still remains unclear. From a quantitative genetics perspective, the estimation of variance components is achieved by means of the information provided by the resemblance between relatives. In a previous study, this resemblance was described as a function of the epigenetic variance component and a reset coefficient that indicates the rate of dissipation of epigenetic marks across generations. Given these assumptions, we propose a Bayesian mixed model methodology that allows the estimation of epigenetic variance from a genealogical and phenotypic database. The methodology is based on the development of a T matrix of epigenetic relationships that depends on the reset coefficient. In addition, we present a simple procedure for the calculation of the inverse of this matrix (T−1) and a Gibbs sampler algorithm that obtains posterior estimates of all the unknowns in the model. The new procedure was used with two simulated data sets and with a beef cattle database. In the simulated populations, the results of the analysis provided marginal posterior distributions that included the population parameters in the regions of highest posterior density. In the case of the beef cattle dataset, the posterior estimate of transgenerational epigenetic variability was very low and a model comparison test indicated that a model that did not included it was the most plausible.

Co) variance component estimation of yield traits between different lactations using an animal model

Abstract Additive and residual (co) variances between the first four lactations were estimated for milk, fat and protein yields. Results were obtained using restricted maximum likelihood and a multiple trait animal model with different design matrices in three sets of four traits per set. Model included different design matrices in the fixed effects and took into account missing records. An analysis was carried out from records of 18 658 cows (10 583 for protein yield), and the order of the coefficient matrix was 118 192 (93 732 for protein yield). A Monte Carlo procedure to approximate the traces involving the coefficient matrix of the mixed model equations was used in the EM algorithm. Heritabilities for milk yield ranged between 0.22 and 0.32, for fat yield between 0.20 and 0.30, and for protein yield between 0.19 and 0.26. Genetic correlations between adjacent lactations were greater than 0.85, with the exception of the third and fourth lactations for protein yield. A second analysis was carried out including the 12 traits and 156 (co) variance components simultaneously. In this case, the order of the coefficient matrix was 352 116. A result of this second analysis was that the genetic correlations between milk, fat and protein yields do not depend on the age of the cow.

Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip

The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD BeadChip genotyping array was used to describe the genetic variability and divergence among 7 important autochthonous Spanish beef cattle breeds. The within-breed genetic diversity, measured as the marker expected heterozygosity, was around 0.30, similar to other European cattle breeds. The analysis of molecular variance revealed that 94.22% of the total variance was explained by differences within individuals whereas only 4.46% was the result of differences among populations. The degree of genetic differentiation was small to moderate as the pairwise fixation index of genetic differentiation among breeds (F) estimates ranged from 0.026 to 0.068 and the Neis D genetic distances ranged from 0.009 to 0.016. A neighbor joining (N-J) phylogenetic tree showed 2 main groups of breeds: Pirenaica, Bruna dels Pirineus, and Rubia Gallega on the one hand and Avileña-Negra Ibérica, Morucha, and Retinta on the other. In turn, Asturiana de los Valles occupied an independent and intermediate position. A principal component analysis (PCA) applied to a distance matrix based on marker identity by state, in which the first 2 axes explained up to 17.3% of the variance, showed a grouping of animals that was similar to the one observed in the N-J tree. Finally, a cluster analysis for ancestries allowed assigning all the individuals to the breed they belong to, although it revealed some degree of admixture among breeds. Our results indicate large within-breed diversity and a low degree of divergence among the autochthonous Spanish beef cattle breeds studied. Both N-J and PCA groupings fit quite well to the ancestral trunks from which the Spanish beef cattle breeds were supposed to derive.

Identification of 14 new single nucleotide polymorphisms in the bovine SLC27A1 gene and evaluation of their association with milk fat content.

The solute carrier family 27 member 1 (SLC27A1) is an integral membrane protein involved in the transport of long-chain fatty acids across the plasma membrane. This protein has been implicated in diet-induced obesity and is thought to be important in the control of energy homeostasis. In previous reports, our group described the isolation and characterization of the bovine SLC27A1 gene. The bovine gene is organized in 13 exons spanning over more than 40 kb of genomic DNA and maps in BTA 7 where several quantitative trait loci for fat related traits have been described. Because of its key role in lipid metabolism and its genomic localization, in the present work the search for variability in the bovine SLC27A1 gene was carried out with the aim of evaluating its potential association with milk fat content in dairy cattle. By sequencing analysis of all exons and flanking regions 14 new single nucleotide polymorphisms (SNPs) were identified: 1 in the promoter, 7 in introns and 6 in exons. Allele frequencies of all the SNPs were calculated by minisequencing analysis in two groups of Holstein-Friesian animals with highest and lowest milk-fat content estimated breeding values as well as in animals of two Spanish cattle breeds, Asturiana de los Valles and Menorquina. In the conditions assayed, no significant differences between Holstein-Friesian groups were found for any of the SNPs, suggesting that the SLC27A1 gene may have a poor or null effect on milk fat content. In Asturiana and Menorquina breeds all the positions were polymorphic with the exception of SNPs 1 and 8 in which C allele was fixed in both of them.

A model with heterogeneous thresholds for subjective traits : Fat cover and conformation score in the Pirenaica beef cattle

Current selection schemes for livestock improvement use a wide variety of phenotypic traits. Some of them, such as sensory, type, or carcass traits, obtain their records from subjective grading performed by trained technicians. Data from this subjective evaluation usually involve classification under a categorical and arbitrary predefined scale, whose output may lead to strong departures from the Gaussian distribution. In addition, the scale of grading may be different according to different technicians. To study this phenomenon, we have analyzed subjective conformation (CON) and fat cover (FAT) scores in the Pirenaica beef cattle breed from data provided by 12 different slaughterhouses. Three statistical models were used: 1) a Gaussian linear model; 2) an ordered category threshold model; and 3) a specific slaughterhouse ordered category threshold model. These models were analyzed through a Bayesian analysis via a Gibbs sampler with a data augmentation step. Posterior mean estimates of heritability ranged from 0.23 to 0.26 for CON, and from 0.13 to 0.16 for FAT. Statistical models were compared by the deviance information criteria, and the slaughterhouse-specific ordered category threshold model was selected as the most plausible. This result was confirmed by the fact that the threshold estimates differed noticeably between slaughterhouses. Finally, the proposed model for genetic evaluation increased the expected selection response by up to 7.6% for CON and 11.2% for FAT.