Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain.

In organisms with sexual reproduction, genetic diversity, and genome evolution are governed by meiotic recombination caused by crossing-over, which is known to vary within the genome. In this study, we propose a simple method to estimate the recombination rate that makes use of the persistency of linkage disequilibrium (LD) phase among closely related populations. The biological material comprised 171 triplets (sire/dam/offspring) from seven populations of autochthonous beef cattle in Spain (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta, and Rubia Gallega), which were genotyped for 777,962 SNPs with the BovineHD BeadChip.

Effects of breed-production system on collagen, textural, and sensory traits of 10 European beef cattle breeds.

Unlabelled: In the current study the collagen, texture, and sensory characteristics of meat from 712 yearling males of 10 local Spanish and French beef breeds raised in their typical production systems were described. The breed-production system affected collagen and texture variables but affected sensory variables only slightly. There was a large amount of intra breed-production system variation for all the variables.

Fine mapping by composite genome-wide association analysis.

Genome-wide association (GWA) studies play a key role in current genetics research, unravelling genomic regions linked to phenotypic traits of interest in multiple species. Nevertheless, the extent of linkage disequilibrium (LD) may provide confounding results when significant genetic markers span along several contiguous cM. In this study, we have adapted the composite interval mapping approach to the GWA framework (composite GWA), in order to evaluate the impact of including competing (possibly linked) genetic markers when testing for the additive allelic effect inherent to a given genetic marker.

On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations.

Background: Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations.

Proteomic analysis reveals oxidative stress response as the main adaptative physiological mechanism in cows under different production systems.

Three groups of cows representing three ranges of welfare in the production system were included in the study: two groups of Bruna dels Pirineus beef cattle maintained under different management systems (good and semiferal conditions) and a group of Alberes cows, a breed that lives in the mountains (hardest conditions). In order to identify new stress/welfare biomarkers, serum from Bruna cows living in both environments was subjected to DIGE labelling, two-dimensional electrophoresis and MALDI-MS or ion trap MS. Identification was achieved for 15 proteins, which mainly belonged to three biological functions, the oxidative stress pathway (glutathione peroxidase (GPx) and paraoxonase (PON-1)), the acute phase protein family (Heremans Schmid glycoprotein alpha2 (α2-HSG)) and the complement system.

Carcass conformation and fat cover scores in beef cattle: a comparison of threshold linear models vs grouped data models.

Background: Beef carcass conformation and fat cover scores are measured by subjective grading performed by trained technicians. The discrete nature of these scores is taken into account in genetic evaluations using a threshold model, which assumes an underlying continuous distribution called liability that can be modelled by different methods.

Methods: Five threshold models were compared in this study: three threshold linear models, one including slaughterhouse and sex effects, along with other systematic effects, with homogeneous thresholds and two extensions with heterogeneous thresholds that vary across slaughterhouses and across slaughterhouse and sex and a generalised linear model with reverse extreme value errors.

Connectedness among herds of beef cattle bred under natural service.

Background: A procedure to measure connectedness among herds was applied to a beef cattle population bred by natural service. It consists of two steps: (a) computing coefficients of determination (CDs) of comparisons among herds; and (b) building sets of connected herds.

Methods: The CDs of comparisons among herds were calculated using a sampling-based method that estimates empirical variances of true and predicted breeding values from a simulated n-sample.

Evaluation of serum cortisol, metabolic parameters, acute phase proteins and faecal corticosterone as indicators of stress in cows.

To assess the validity of laboratory parameters in blood and faeces as indicators of stress in cows, concentrations of cortisol, non-esterified fatty acids (NEFAs), 3-hydroxybutyrate, glucose, triglycerides, cholesterol, serum amyloid A (SAA) and haptoglobin in serum, as well as corticosterone in faeces, were determined in two breeds of cattle (Alberes and Bruna dels Pirineus) under different systems of housing and feeding. Serum cortisol concentrations were markedly elevated in the Alberes group, probably because they were less habituated to human handling. Corticosterone concentrations in faeces were significantly increased in the Bruna dels Pirineus cattle on Alberes pastures.

Bayes factor for testing between different structures of random genetic groups: a case study using weaning weight in Bruna dels Pirineus beef cattle.

The implementation of genetic groups in BLUP evaluations accounts for different expectations of breeding values in base animals. Notwithstanding, many feasible structures of genetic groups exist and there are no analytical tools described to compare them easily. In this sense, the recent development of a simple and stable procedure to calculate the Bayes factor between nested competing models allowed us to develop a new approach of that method focused on compared models with different structures of random genetic groups.

Validation of an approximate approach to compute genetic correlations between longevity and linear traits.

The estimation of genetic correlations between a nonlinear trait such as longevity and linear traits is computationally difficult on large datasets. A two-step approach was proposed and was checked via simulation. First, univariate analyses were performed to get genetic variance estimates and to compute pseudo-records and their associated weights.

Effect of muscular hypertrophy on physico-chemical, biochemical and texture traits of meat from yearling bulls.

The effect of the presence of the double-muscling gene either homozygous (mh/mh) or heterozygous (mh/+) on the physico-chemical, biochemical and texture traits of Longissimus thoracis muscle of yearling bulls of the Asturiana de los Valles (AV) breed was studied. Meat of mh/mh bulls had lower amount of intramuscular fat (p<0.001) and also lower total (p<0.

Pedigree analysis of eight Spanish beef cattle breeds.

The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records. The populations studied were: Alistana and Sayaguesa (minority breeds), Avileña - Negra Ibérica and Morucha ("dehesa" breeds, with a scarce incidence of artificial insemination), and mountain breeds, including Asturiana de los Valles, Asturiana de la Montaña and Pirenaica, with extensive use of AI. The Bruna dels Pirineus breed possesses characteristics which make its classification into one of the former groups difficult.