J. A. Baro

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.

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.ResultsAnalysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic–pituitary–thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors.ConclusionsWe show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits.

Monitoring changes in the demographic and genealogical structure of the main Spanish local beef breeds1

Demographic and pedigree analyses describe the structure and dynamics of livestock populations. We studied information recorded in the herdbooks of Asturiana de los Valles (AV; N = 458,806), Avileña-Negra Ibérica (ANI; N = 204,623), Bruna dels Pirineus (BP; N = 62,138), Morucha (Mo; N = 65,350), Pirenaica (Pi; N = 217,428), Retinta (Re; N = 135,300), and Rubia Gallega (RG; N = 235,511) beef breeds from their creation until 2009. All breeds have increased in the number of registered cows in recent years. In all breeds, herds do not behave as isolated entities and a high rate of exchange of breeding males between herds exists. A percentage of herds (12-52%) make some type of selection and sell bulls to other herds. There were large differences in average number of progeny per bull, ranging from 15.6 (AV) to 373.7 animals (RG, with a high incidence of AI). Generation interval estimates ranged from 4.7 (AV) to 7.6 (RG) yr in the sire pathway and from 5.95 (AV) to 7.8 (Mo) yr in the dam pathway. Density of pedigrees varied among breeds, with Pi, ANI, and Re having the more dense pedigrees, with average completeness indexes of more than 96% in the first generation and 80% when 6 generations were considered. A general increase in average inbreeding was observed in all breeds in the years analyzed. For animals born in 2009, average inbreeding coefficients ranged from 0.6 (BP) to 7.2% (Re) when all animals were considered and from 3.6 (Pi) to 17.6% (BP) when only inbred animals were considered. Due to the lack of completeness of pedigrees in most populations, inbreeding coefficients may be considered as a lower bound of the true parameters. The proportion of inbred animals tended to increase in the periods analyzed in all breeds. Differences between inbreeding and coancestry rates (except in RG) suggest the presence of population structure. Effective population size (Ne) based on the inbreeding rate estimated by regression ranged from 43 to 378 for Re and BP, whereas Ne estimates based on coancestry were greater, with a range of 100 for RG to 9,985 for BP. These facts suggest that an adequate mating policy can help to monitor inbreeding so as not to lose genetic variability. Effective number of ancestors in 2009 for 6 of the breeds ranged from 42 (RG) to 220 (AV), with BP having much a greater value, and was lower than was the effective number of founders in all breeds, suggesting the existence of bottlenecks.

PocketELISA: A low-cost portable ELISA reader based on image analysis over PDA platform for clinical diagnose in medical veterinary

ELISA (enzyme linked inmuno-specific assay) diagnostic plates are widely used for the screening of viral infections. Currently, plates are measured either photometrically, which is costly, or manually, unacceptably subjective and dependent on training and illumination. In this paper, we propose an instrument for ubiquitously reading out plates by digital analysis of images. The main challenge is designing a versatile platform using standard, low-cost elements, such as PDAs or embedded PCs, open libraries, and consumer-grade digital cameras. All these alternative solutions can provide similar results with small differences in the final solution and costs. The purpose of this paper is the use of a PDA (personal digital assistant) witch includes a digital camera to constitute a portable and low-cost analyzer of ELISA plates, able to be used in field applications. Tests were performed using several plates from routine monitoring in cattle of Brucelosis, red nose (Infectious Bovine Rhinotraqueitis, IBR) and Bovine Virus Diarrhoea (BVD). This work shows promise as technique to improve the efficiency of clinical interpretation ELISA diagnostic plates.

Linkage disequilibrium, persistence of phase, and effective population size in Spanish local beef cattle breeds assessed through a high-density single nucleotide polymorphism chip1

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 Illumina BovineHD chip in 168 trios of 7 Spanish beef cattle breeds to obtain an overview of the magnitude of LD and the persistence of LD phase through the physical distance between markers. Also, we estimated the time of divergence based on the persistence of the LD phase and calculated past from LD estimates using different alternatives to define the recombination rate. Estimates of average (as a measure of LD) for adjacent markers were close to 0.52 in the 7 breeds and decreased with the distance between markers, although in long distances, some LD still remained (0.07 and 0.05 for markers 200 kb and 1 Mb apart, respectively). A panel with a lower boundary of 38,000 SNP would be necessary to launch a successful within-breed genomic selection program. Persistence of phase, measured as the pairwise correlations between estimates of in 2 breeds at short distances (10 kb), was in the 0.89 to 0.94 range and decreased from 0.33 to 0.52 to a range of 0.01 to 0.08 when marker distance increased from 200 kb to 1 Mb, respectively. The magnitude of the persistence of phase between the Spanish beef breeds was similar to those found in dairy breeds. For across-breed genomic selection, the size of the SNP panels must be in the range of 50,000 to 83,000 SNP. Estimates of past showed values ranging from 26 to 31 for 1 generation ago in all breeds. The divergence among breeds occurred between 129 and 207 generations ago. The results of this study are relevant for the future implementation of within- and across-breed genomic selection programs in the Spanish beef cattle populations. Our results suggest that a reduced subset of the SNP panel would be enough to achieve an adequate precision of the genomic predictions.

Ratiometric Oxygen Imaging to Predict Oxygen Diffusivity in Oak Wood During Red Wine Barrel Aging

In this work, we present a high-resolution oxygen imaging approach to study the two-dimensional oxygen distribution inside an oak stave in contact with wine and that applies the series resistance model to explain the dynamic evolution of oak wood oxygen transfer rate (OTR). Oxygen flux throughout the oak stave has been studied by considering the wood as a permeable membrane with moisture content (MC) in a decreasing gradient from the wine-contacting side of the oak stave to the side in contact with atmospheric air in cellar conditions. The presence of different levels of liquid across the thickness of the wet stave modifies the oxygen diffusion flux, as the diffusion coefficient of oxygen in water is four orders of magnitude lower than in air. The stave resembles a multilayered membrane, where wood with an MC over the fiber saturation point represents a distinct layer. To that end, three simultaneous measurements were made, namely the MC profile of the wood within the thickness of the stave at different liquid-wood contact times, the OTR of the stave at those times, and finally the oxygen concentration profile within the thickness of the stave using planar optical sensors, a color camera, and ratiometric image analysis. The results show heat flux and oxygen flux that is analogous to that in a multilayer.

Optical fiber turbidimeter for full range measurement in wine industrial processes

This paper presents a new type of nephelometric turbidimeter capable of really functioning on-line. In addition, it takes advantage of the possibility of light conduction via optical fibres to avoid the electrical parts coming into contact with or close proximity to the liquid; the use of optical fibres also avoids interference, improving the Signal-to-Noise ratio and offering remote measuring. This type of turbidimeter is for general application in the literal sense but, the application is presented for measuring turbidity in the wine industry during wine-making processes, which presents added problems such as colour interference and the high interval of recordable values, which can reach levels of almost nil to over 4000 NTUs.

Method Comparison for Diagnose of Subclinical Mastitis and Milk Quality Determination in Raw Milk

Mastitis is a serious problem for milk cattle farming and one of the worst worries for farmers. Somatic cell count (SCC) is both a diagnostic tool and a cause of concern by itself as milk quality and yield are affected by somatic cell activity. This work examines the tools available for the estimation of somatic cell counts in raw milk, including methods based on rheology, ionic properties, presence of energetic molecules, cell counting, and dielectric permittivity. We conclude that the last of these methods offers an optimal combination of ease of implementation and low cost that permits its use for on-line, parlor-side measurement devices

Genomic differentiation between Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta and Rubia Gallega cattle breeds

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 populations (Asturiana de los Valles (AV), Avileña-Negra Ibérica (ANI), Bruna dels Pirineus (BP), Morucha (Mo), Pirenaica (Pi), Retinta (Re) and Rubia Gallega (RG)). The BovineHD 777K BeadChip was used on 342 individuals (AV, n=50; ANI, n=48; BP, n=50; Mo, n=50; Pi, n=48; Re, n=48; RG, n=48) chosen to be as unrelated as possible. We calculated the fixation index (F ST ) and performed a Bayesian analysis named SelEstim. The output of both procedures was very similar, although the Bayesian analysis provided a richer inference and allowed us to calculate significance thresholds by generating a pseudo-observed data set from the estimated posterior distributions. We identified a very large number of genomic regions, but when a very restrictive significance threshold was applied these regions were reduced to only 10. Among them, four regions can be highlighted because they comprised a large number of single nucleotide polymorphisms and showed extremely high signals (Kullback-Leiber divergence (KLD)>6). They are located in BTA 2 (5 575 950 to 10 152 228 base pairs (bp)), BTA 5 (17 596 734 to 18 850 702 bp), BTA 6 (37 853 912 to 39 441 548 bp) and BTA 18 (13 345 515 to 15 243 838 bp) and harbor, among others, the MSTN (Myostatin), KIT-LG (KIT Ligand), LAP3 (leucine aminopeptidase 3), NAPCG (non-SMC condensing I complex, subunit G), LCORL (ligand dependent nuclear receptor corepressor-like) and MC1R (Melanocortin 1 receptor) genes. Knowledge on these genomic regions allows to identify potential targets of recent selection and helps to define potential candidate genes associated with traits of interest, such as coat color, muscle development, fertility, growth, carcass and immunological response.

Biofilm monitoring of dissolved oxygen in wine aging barrel wood with optical chemical sensors

Micro-oxygenation processes that happen while aging wine in barrels give the necessary final traits to reach quality and determine the wine aging rates. The measurement of oxygen transfer rates across wood and the oxygen distribution within the wood can provide data on the kinetics of the oxygen dosage by wine barrels. Previous attempts at measurement with electrochemical probes achieved the required detection limits of ppb (μg/L), but oxygen consumption by the probes prevented usage for dynamic measurements. Microfluidic chips with integrated optical luminiscent sensor layers provide a robust and sensitive platform for ratiometric imaging using the color channels of a CCD camera. In this study, preliminary results were obtained for the dosage of oxygen in wine barrels.