Jesús Piedrafita

Autonomous University of Barcelona | UAB · Department of Animal and Food Science

Background/Objectives: Understanding the genetic architecture of autochthonous European cattle breeds is important for developing effective conservation strategies and sustainable breeding programs. Spanish beef cattle, which trace their origins to ancient migrations from the Near East with later admixture from African populations, exhibit a rich g...

Caja, G., A. Nieto, A. Elhadi, A.A.K. Salama, J. Piedrafita, E. Albanell, C. Riba, C. De Linares, P. Cardellach, and J. Belmonte. 2021. Seguimiento de un colmenar periurbano en el Vallés occidental. p35 in Proc. XIX Jornadas de Producción Animal of AIDA, Zaragoza, Spain. https://www.aida-itea.org/aida-itea/files/jornadas/2021/comunicaciones/2021_SG...

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 rela...

29856 Dimensional reduction for breed assignment models with a high number of strongly linked markers Breed assignment is required as a forensic tool for detection of fraud on meat products for designated breed branding. Tests achieve only low levels of assignment power for sets of autochthonous cattle breeds that have been differentiating over a p...

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 int...

The EU is the second largest world producer of beef meat, but production is fragmented, consisting of highly variable local systems, compared with homogenous, highly intensive feedlot systems. The current EU agricultural policy requires a reorientation of beef market to take advantage of this diversity by creating meat quality labels relating to ge...

This study investigated the potential application of genomic selection under a multi-breed scheme in the Spanish autochthonous beef cattle populations using a simulation study that replicates the structure of linkage disequilibrium obtained from a sample of 25 triplets of sire/dam/offspring per population and using the BovineHD Beadchip . Purebred...

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...

Lamb meat is an important source of different fatty acids with numerous health benefits for the consumer. The aim of this study was to characterize carcass and meat traits in 14 Lacaune, 77 Ripollesa, and 33 Lacaune × Ripollesa pascual-type lambs (carcass weight, 13–16 kg) by using ultrasound and direct measurements on carcasses and laboratory anal...

This study analysed the haplotype diversity along the genome of seven Spanish Beef Cattle populations within regions of 500 kb using the information provided by the BovineHD Beadchip. The results of the analysis pointed out a strong variability of the haplotype diversity across the genome, which is greatly conserved across populations. This strong...

Abandoned lambs in sheep flocks use to involve few ewes at the same time; this phenomenon prevents the accurate collection of pedigree data and originates a moderate-to-low percentage of lambs with unknown or uncertain ancestors. Given the economic restrictions inherent to the sheep industry, the systematic implementation of laboratory paternity te...

The Spanish local beef cattle breeds have most likely common origin followed by a process of differentiation. This particular historical evolution has most probably left detectable signatures in the genome. The objective of this study was to identify genomic regions associated with differentiation processes in seven Spanish autochthonous population...

The objective of this study was to evaluate the pattern of linkage disequilibrium along the genome in seven autochthonous Spanish cattle beef populations (Asturiana de los Valles, Avileña Negra-Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta and Rubia Gallega). The BovineHD BeadChip was used to genotype 171 trios of individual/sire/dam. 5...

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 d...

Transmission ratio distortion (TRD) is the departure from the expected Mendelian ratio in offspring, a poorly investigated biological phenomenon in livestock species. Given the current availability of specific parametric methods for the analysis of segregation data, this study focused on the screening of TRD in 602 402 single nucleotide polymorphis...

Linkage disequilibrium (LD) and persistence of phase are fundamental approaches for exploring the genetic basis of economically important traits in cattle, including the identification of QTL for genomic selection and the estimation of effective population size (Ne) to determine the size of the training populations. In this study, we have used the...

Linkage disequilibrium (LD) and persistence of phase are fundamental approaches for exploring the genetic basis of economically important traits in cattle, including the identification of QTL for genomic selection and the estimation of effective population size () to determine the size of the training populations. In this study, we have used the Il...

The socio-economic context of the sheep industry in multiple regions worldwide has prevented the systematic implementation of efficient genetic selection programs, although they are essential to optimize the viability of multiple sheep flocks. Moreover, little is known abut the minimum requirements to launch a selection program in sheep flocks as w...

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 seven important autochthonous Spanish beef...

The advances in the area of molecular genetics have allowed the development of dense SNP genotyping devices that provide information throughout the genome of several livestock species. Along with these molecular advances, new statistical methods have been developed with the purpose of predicting the genomic breeding values of candidates to selectio...

This study analyzed the persistency of the linkage disequilibrium between 7 Spanish beef cattle populations. The persistency was calculated as the correlation between the LD values of the SNPs of regions of 1 Mb each, between two populations. The results yielded positive values in all cases of comparison and regions. The persistency values of 42 re...

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 seven important autochthonous Spanish beef...

We have used the BovineHD Genotyping BeadChip to obtain high density genotypes (>700,000 SNP after quality control) from 116 trios in five Spanish local beef cattle breeds. Linkage disequilibrium (LD) was measured through the r 2 statistic. Average r 2 for adjacent markers in the five breeds were very close, around 0.52, and decreased with increasi...

A total of 116 triplets from 5 Spanish beef cattle populations were genotyped using the BovineHD BeadChip. After the quality control, the phases of the parental chromosomes were established. From them, a base population for each breed was defined and 3 generations of 500, 1000 and 1000 individuals were simulated. Phenotypes and true genomic breedin...

High-density SNP genotyping was used to describe the genetic variability and relationships among five Spanish beef cattle breeds (Asturiana de los Valles, Avileña – Negra Ibérica, Bruna dels Pirineus, Pirenaica and Retinta). A total of 239 samples were genotyped with the BovineHD (778 K) Beadchip, which proved its suitability for the study of these...

Abstract Text: Several subpopulations were previously described in the Ripollesa sheep breed on a phenotypic basis, and this research focuses on the identification of the subsequent underlying genetic structure, if any. A total of 269 males and 2,366 females from 13 purebred Ripollesa flocks were genotyped for 49 SNP. Genetic differentiation acro...

Five Spanish autochthonous beef cattle breeds: Asturiana de los Valles, Avileña-Negra Ibérica, Bruna de los Pirineos, Pirenaica and Retinta, were sampled. The 246 animals obtained were genotyped with the Illumina HD 777K chip and the genotypic information was subjected to a factorial discriminant analysis (fda), yielding the following conclusions:...

Demographic and pedigree analyses are important tools that describe the structure and dynamics of livestock populations. We studied the information recorded in the herd-books of Asturiana de los Valles (AV), Avileña – Negra Ibérica (ANI), Bruna dels Pirineus (BP), Morucha (Mo), Pirenaica (Pi), Retinta (Re) and Rubia Gallega (RG) beef breeds, from t...

The aim of this study is to locate the genomic regions associated with selection and differentiation processes between ve Spanish autochthonous beef cattle populations. For this objective, we selected 25 trios (sire- dam-individual) from each one (Asturiana de los Valles, Avileña Negra-Ibérica, Bruna dels Pirineus, Retinta and Pirenaica). The crite...

Although heteroscedacity has been a topic of main interest in beef cattle during the last decades, current availability of canalisation models provided new insights for animal breeding programs. Within this context, birth BW (BWT) was analyzed in the Bruna des Pirineus beef cattle breed by implementing canalisation models that accounted for heterog...

The aim of this study was to assess the accuracy of the ultrasound measurements for predicting carcass traits in 124 Spanish 'pascual'-type lambs (13 to 16 kg of carcass weight). Ultrasound images were taken transversal and longitudinal to the vertebral column, and at thoracic (TV; between 12th and 13th ribs) and lumbar (LV; between 1st and 2nd lum...

This research investigated two sources of sire-specific genetic effects on the birth weight (BWT) and weaning weight (WWT) of Bruna dels Pirineus beef calves. More specifically, we focused on the influence of genes located in the non-autosomal region of the Y chromosome and the contribution of paternal imprinting. Our analyses were performed on 813...

The Ripollesa sheep breed is an important Spanish local breed mainly located in the Mediterranean mountains and cultivated plains of Catalonia, exploited under semi-extensive production systems and currently intended for meat production. The morphological characterization of the Ripollesa breed was carried out from the study of eight flocks represe...

E-Mails: p.a.koolmees@uu.nl (P.A.K.); l.t.g.theunissen@uu.nl (B.T.) Abstract: Classification of cattle breeds contributes to our understanding of the history of cattle and is essential for an effective conservation of genetic diversity. Here we review the various classifications over the last two centuries and compare the most recent classification...

En este trabajo se analiza la variabilidad genética de la raza autóctona en peligro de extinción Serrana de Teruel, así como su relación con las ra-zas bovinas explotadas en España: Albera, Pajuna, Avileña-Negra Ibérica, Serrana Negra, Pirenaica y Parda de Montaña. La caracterización genética se ha realizado mediante marcadores microsatélites, todo...

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. Five threshold m...

The dietary composition of the semiferal cattle population in the Alberes Natural Park in northeastern Spain was determined four times per year, from June 2002 to February 2004, by microhistological analysis of a total of 120 fecal samples. Woody species, mainly the Quercus and Erica genera, formed the bulk of the diet, reaching 89% of it in winter...

Fina, M., Casellas, J. and Piedrafita, J. 2011. Short Communication: Estimating abundance, survival and age structure of the Alberes cattle using recapture techniques. Can. J. Anim. Sci. 91: 343–347. The Alberes breed is an endangered bovine breed with an unknown population size. In this study, we estimated a total of 447.9 (435.5 to 456.6) individ...

In this work we analyze by microsatellite markers the genetic diversity, structure and relationships of the indigenous endangered Serrana de Teruel cattle breed with different breeds reared in Spain. All loci were polymorphic and a total of 198 alleles were observed across loci, with a mean of 6.79. Observed and expected heterozygosities values sho...

The aim of this study was to compare the goodness of fit of the threshold models with homoscedasticity or heteroscedasticity and the grouped data model for the analysis of calving ease in beef cattle by using a parametric bootstrap procedure. Field data included 8,205 records of the Bruna dels Pirineus beef cattle breed in the Pyrenean mountain are...

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. The CDs of comparisons among herds were calculated using a sampling-based method that esti...

Little is known about mutational variability in livestock, among which only a few mutations with relatively large effects have been reported. In this manuscript, mutational variability was analyzed in 1,765 litter size records from 404 Ripollesa ewes to characterize the magnitude of this genetic source of variation and check the suitability of incl...

Although inbreeding (F) is a topic of major concern in animal breeding, estimates of inbreeding depression are usually obtained by modeling the overall F coefficient of each individual, without considering that the recessive (deleterious) genetic load of a given population may be unevenly distributed among the founder genomes. The founder-specific...

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 (Alb...

Sensory characteristics of longissimus thoracis muscle from three local Spanish beef breed-production systems and their relationships with chemical and instrumental meat quality traits were studied. Young bulls of Bruna dels Pirineus (BP; n=69), Avileña-Negra Ibérica (A-NI; n=70) and Morucha (MO; n=70) breeds were reared in their own production sys...

The Alberes cattle breed is a Catalonian autochthonous bovine population located in the Alberes Massif (north east of Spain), in the eastern extreme of the Pyrenees Mountains, and is well adapted to this zone in which it mainly makes use of forest resources. Cows are small sized and rustic, living under a semi-feral management system with minimal h...

Haplotype probabilities have been implemented in association analyses performed between three candidate genes and the preweaning survival of F2 Iberian x Meishan piglets, under a categorical proportional hazard model. The additive effect of substitution of each haplotype was estimated using information of parental genotypes for non-genotyped piglet...

Birth weight plays a central role in lamb survival and growth, and the knowledge of its genetic determinism has become essential in worldwide selection programmes. Within this context, within-litter birth weight variation (BWV) has been suggested as an attractive trait to homogenise litters in prolific species, although it has not been analysed in...

A performance data set from 376 Ripollesa purebred ewes of the experimental flock of the Universitat Autònoma of Barcelona was analyzed using a bivariate Bayesian threshold-linear model. The data set contained 1,598 litter size records and 1,699 days-to-lambing records. The model included the additive genetic effect of each animal and 3 nongenetic...

The objective of this study was to analyze the association between the haplotypes of the prion protein (PrP) locus and several reproductive and lamb weight traits in Ripollesa sheep. Prion protein genotypes were available for a total of 310 sheep (7 rams, 114 ewes, and 189 lambs), all of them belonging to the purebred Ripollesa flock of the Univers...

The analysis focused on model fitting of 2 ewe reproductive traits, litter size, and days to lambing (interval between the introduction of the ram into the flock and the subsequent parturition of the ewes). The experimental data set of the Universitat Autònoma of Barcelona flock was used, including 1,598 records of litter size and 1,699 records of...

The survivability from birth to slaughter of 1,487 Ripollesa lambs with a preslaughter overall mortality of 9.6% was studied under the proportional hazards framework, assuming a Weibull distribution for the baseline hazards function. A sire frailty model was fitted, with the common environment received by the lamb as an additional random source of...

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...

Given that correct assumptions on the baseline survival function are determinant for the validity of further inferences, specific tools to test the fit of a model to real data become essential in proportional hazards models. In this sense, we have proposed a parametric bootstrap to test the fit of survival models. Monte Carlo simulations are used t...

The recent development of the Bayes factor methodology to test between nested competing models has allowed to evaluate the genetic component of continuous traits through a methodology based on the reparameterization of a variance component model in terms of intra-class correlation. In this study, we present a modification of that procedure to compa...

The aim of this study was to evaluate the progression of temperament in Alberes male calves during the fattening period. The Alberes breed is a semi-feral beef cattle breed of Catalonia (Spain) that lives endemically in the eastern extreme of the Pyrenees, a mountainous area. These animals were adapted to extensive management systems and their cont...

A competing risks approach was used to evaluate the influence of several pre-farrowing factors on risk of culling due to different causes in Duroc swine, these having low fertility, low productivity, lameness and mortality. Culling due to low fertility increased for average daily gains during the growth test lower than 585 g/day, whereas culling du...

The structure and typology of beef cattle farms from three autochthonous Spanish breeds (Avileña–Negra Ibérica, Morucha and Retinta) located in “dehesa” areas have been characterised from a survey including 130 farms. The questionnaire provided information on the structure of the farms, feeding practices, reproductive and sanitary management, produ...

The structure and typology of beef cattle farms from three autochthonous Spanish breeds (Avilena-Negra Iberica, Morucha and Retinta) located in "dehesa" areas have been characterised from a survey including 130 farms. The questionnaire provided information on the structure of the farms, feeding practices, reproductive and sanitary management, produ...

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....

Abstract 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...

Survival analysis techniques were used to analyze survival up to weaning of beef calves in the Pyrenean mountains areas of Catalonia, Spain. The Kaplan-Meier curve showed that the survival experience was not constant throughout the lactation period, as the mortality rate was more pronounced during the first month of life. The proportional hazards m...

The pre-weaning survival of 508 piglets was studied with a categorical survival analysis, evaluating the effect of medium-long-chain triglyceride (MCT-LCT) supplementation on small newborn pigs, and determining additional risk factors. Half of the 98 piglets born with birth weight (BW)<1250 g received 1.95 g of MCT-LCT each 24 h during the first 3...

The Bayes factor (BF) procedure was applied to examine the additive genetic component of several physiological and vitality variables for newborn pigs. Nine variables were studied: heart rate, arterial oxygen saturation, rectal temperature (all at birth and 60 min later), birth weight, interval between birth and first teats contact, and interval be...

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 tot...

Eight physiological and vitality variables related to the first minutes of the life of Iberian x Meishan F2 piglets were analyzed. Variables included rectal temperature, arterial oxygen saturation, heart rate (all were monitored at birth and 60 min later), time to reach the udder, and time to the first colostrum intake. Litter effect within boar, a...