Discriminant analysis using fatty acids profile, stable carbon isotopes and tocopherols content as tool for feeding system prediction in Iberian pigs

Aim of study: The application of three analytical methods (fatty acids: FA, tocopherols: TOC, and isotope ratio: ISO) to distinguish the feeding type received by Iberian pigs during the fattening stage.Area of study: This distinction is very important for the labelling of Iberian high-quality products in the Quercus forest located on the southwest of Iberian Peninsula, where several production systems coexist.Material and methods: Discriminant analysis on fat samples with unknown background obtained from commercial pigs was applied. The feasibility of the combination method to determine the authentication of feeding background was studied on samples from different fattening system: free-range feeding with acorn and pastures (BE); free-range feeding acorn and pastures plus commercial feeds (RE); open-air feeding with commercial feeds (CA); standard feeding with commercial feeds (CE).Main results: In a first application of the methods, the overall success rate was 60.1% for FA, 49.7% for ISO and 49.3% for TOC. When some of the batches were reclassified attending to those previous results and additional information available about farm characteristics, ISO and TOC analyses had a 70% of success rate in the four categories, whereas FA showed 40.5%, attributable to the use of high-oleic commercial diets. The predictions improved with the method combination. The ISO+TOC combination achieved a 84.1% of success in prediction. When it was reduced to just two categories (acorn vs non-acorn), the success reached a 95% for FA+TOC and ISO+TOC.Research highlights: The use of these methods as a complementary tool for quality controls is highly recommended to avoid undesirable misclassifications

Alternative Feeding in Iberian Pigs during Growth Period: Incorporation of Olive Cake in a Dry or Wet (silage) Form

During the last years, the high growth of the livestock production sector has caused a high demand of raw material in order to feed the animals. This higher demand has environmental consequences and a more sustainable strategy is required for livestock production. Some agro-industrial by-products such as olive cake may be beneficially used without a decrease in production traits. Here, we studied the effect of three different dietary regimens given to Iberian pigs in growing period (42 kg to 95 kg) on several growth and slaughter traits. A control standard diet group (CD) was compared with two diets based on olive by-products, one incorporating dry olive pulp in the feed (DD), and the other one incorporating olive cake in wet form (WD). This last one consisted of olive cake in a silage presentation offered ad libitum and supplemented with a specific feed given once a day in a restricted regimen as the CD and DD diets. A significantly higher average daily gain during the growing period was observed for WD diet compared with DD diet. However, this was compensated with a higher average daily gain of DD pigs during the fattening period (acorn and grass). Carcass yield was lower in DD than CD and WD pigs, but no significant differences were observed for premium cut yields, which are more important for the Iberian industry. Therefore, the diets based on olive cake does not seem to alter the growth and slaughter traits studied, however, before its implementation in feeds used for the growing period, further studies analyzing their effects on meat quality and production costs should be carried out

Diseño de servicios cuánticos a través de la especificación AsyncAPI

La computación cuántica ha evolucionado de ser una idea teórica a convertirse en una realidad tangible. Aunque no es posible acceder directamente a un ordenador cuántico de la misma manera que a los ordenadores convencionales, existen proveedores de servicios que ofrecen la posibilidad de utilizar esta tecnología. Sin embargo, estos servicios presentan ciertas limitaciones, especialmente la falta de herramientas que simplifiquen su uso y manejo. Este trabajo se enfoca en Amazon Braket, un servicio de computación cuántica ofrecido por Amazon, el cual procesa las solicitudes en colas de espera, lo que puede resultar en tiempos prolongados para obtener los resultados. Además, los resultados se almacenan en un servicio de almacenamiento proporcionado por el proveedor, lo que permite a los desarrolladores verificar el estado de las tareas cuánticas y recuperar los resultados obtenidos. No obstante, dado que el tiempo de finalización de la operación es incierto, este enfoque puede resultar ineficiente. Por lo tanto, se propone una solución alternativa que utiliza una arquitectura asíncrona e se integra con otro servicio, mediante una modificación de la especificación AsyncAPI. El objetivo es generar sistemas basados en eventos para integrar de manera programática los servicios cuánticos como parte de otros sistemas de software. Esto implica enviar el código cuántico a ejecutar al proveedor y obtener los datos resultantes de manera asíncrona.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Trace-elemental and multi-isotopic (Sr-Nd-Pb) discrimination of jade in the circum-Caribbean: Implications for pre-colonial inter-island exchange networks

Dense and strong, hydrothermal-metasomatic jadeitite and jadeite-omphacite rocks were used as tools and adornments throughout the wider Caribbean since initial inhabitation. Regionally, rich sources of jadeitite and jadeite-omphacite jade are known only in Guatemala (north and south of the Motagua Fault Zone), eastern Cuba and the northern Dominican Republic, establishing that humans transported jadeitic material over vast distances. This study validates that geochemical fingerprinting is a viable provenance method for Caribbean pre-colonial jadeitic lithologies. An assemblage of 101 source rocks has been characterised for trace element and combined Sr-Nd-Pb isotope compositions. Four statistical approaches (Principal Component Analysis, t-Distributed Stochastic Neighbour Embedding, Decision Tree, and Multiclass Regression) were assessed, employing source-distinct trace element ratios. A multiclass regression technique based on trace element ratios of immobile high field strength, light to medium rare earth and fluid-mobile, large-ion-lithophile elements is shown to be most effective in discriminating the four source regions. Ninety-one % of the Guatemalan samples can be discriminated from the Dominican and Cuban sources using La/Th, Zr/Hf and Y/Th ratios. Jadeitic rocks cropping out in the Dominican Republic can be distinguished from Cuban jades employing Er/Yb, Nb/Ta and Ba/Rb ratios with 71% certainty. Furthermore, the two Guatemala sources, north and south of the Motagua Fault Zone, can be discriminated by using (among others) Zr/Hf, Ta/Th, La/Sm and Dy/Y ratios with an 89% success rate. This raises the possibility of determining, in detail, former trading and mobility networks between different islands and the Meso- and Central American mainland within the Greater Caribbean. The provenance technique was applied to 19 pre-colonial jade celts excavated from the Late Ceramic Age Playa Grande archaeological site in the northern Dominican Republic. Three artefacts are discriminated as derived from the Guatemalan source, indicating that, despite a source of jade within 25 km, material was traded from Guatemala. The presence of Guatemalan jade in the Playa Grande lithic assemblage provides further evidence of large scale (>3000 km), regional trading and indigenous knowledge transfer networks.This research received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007–2013)/ERC grant agreement No 319209 (ERC-Synergy NEXUS 1492) and the European Union’s Horizon 2020 research and innovation programme under grant agreement No 654208 (Europlanet 2020 RI). We are grateful to the Museo del Hombre Dominicano for providing the Playa Grande samples. Thanks to Richard Smeets, Bas van der Wagt, Kirsten van Zuilen, Bouke Lacet, Eva Kelderman and Quinty Boosten for analytical assistance

Association between the pig genome and its gut microbiota composition

The gut microbiota has been evolving with its host along the time creating a symbiotic relationship. In this study, we assess the role of the host genome in the modulation of the microbiota composition in pigs. Gut microbiota compositions were estimated through sequencing the V3-V4 region of the 16S rRNA gene from rectal contents of 285 pigs. A total of 1,261 operational taxonomic units were obtained and grouped in 18 phyla and 101 genera. Firmicutes (45.36%) and Bacteroidetes (37.47%) were the two major phyla obtained, whereas at genus level Prevotella (7.03%) and Treponema (6.29%) were the most abundant. Pigs were also genotyped with a high-throughput method for 45,508 single nucleotide polymorphisms that covered the entire pig genome. Subsequently, genome-wide association studies were made among the genotypes of these pigs and their gut microbiota composition. A total of 52 single-nucleotide polymorphisms distributed in 17 regions along the pig genome were associated with the relative abundance of six genera; Akkermansia, CF231, Phascolarctobacterium, Prevotella, SMB53, and Streptococcus. Our results suggest 39 candidate genes that may be modulating the microbiota composition and manifest the association between host genome and gut microbiota in pigs.info:eu-repo/semantics/publishedVersio

Diversity across major and candidate genes in European local pig breeds

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships

Genotype by environment interaction for carcass traits and intramuscular fat content in heavy Iberian pigs fattened in two different free-range systems

Genotype by environment interaction (G×E) is a potential source of reduced efficiency in genetic improvement programs in livestock. The objective of the current work consisted of checking the existence of G×E interaction in carcass traits and in intramuscular fat content (IMF) in Iberian pigs fattened in two free-range systems. Genetic component and estimated breeding values (EBV) of the percentage of hams, shoulders and loins and IMF in loin were obtained from records of 4,348 and 1,818 pigs fattened in campo (C) and montanera (M) systems, respectively. A multitrait model where the performances of each system are considered as different traits was implemented. Three selection indexes were built with different treatments about the quality trait, two of them based in the optimal trait theory. The Pearson correlation between EBV and indexes and the Spearman correlation between the rankings of progenies of 21 boars fattened in both systems were calculated. Heritability results were different in both systems (h2 range from 0.43 to 0.66 and from 0.24 to 0.33 in C and M system, respectively) and genetic correlation of same traits expressed in the two systems also pointed out to a weak G×E interaction (0.64, 0.67 and 0.66 in hams, shoulders and IMF, respectively). Pearson and Spearman correlations were always significantly different to 1. The obtained results advised to consider this G×E interaction in the analysis model of a breeding program focused on free range production system and to include IMF in the index selection assuming an optimum range for this quality trait, in order to avoid negative effects of selection for carcass performances

Heterosis for litter size and growth in crosses of four strains of Iberian pig

Data collected from a complete diallel cross scheme with four ancient lines of Iberian pigs have been analyzed in order to estimate genetic line and heterotic effects on litter size and growth traits. Records of the number of piglets born alive (NBA) and total number of piglets born (TB) from 2768 litters of 817 dams were analyzed using different animal models fitting crossbreeding parameters. Estimated values of genetic correlations between NBA or TB records at early and later parities were close to 0.60. Significant differences in litter size at first and second parities were observed between some dam lines, but not at the third and later parities. Negligible progeny specific heterotic effects on litter size traits were estimated in early parities, but they were significant at the third and later parities (ranging from +0.5 to +1.0 alive piglets and from +0.6 to +0.9 born piglets). All these results reinforce the evidence supporting the hypothesis of a partially different genetic basis of litter size at early and later parities. Growth performance in the final fattening period (100-160. kg) of purebred and crossbred pigs was analyzed with a Bayesian procedure modeled by a linear growth function. Data consisted of 2103 weight records from 579 pigs of 352-493 days of age. Relevant heterotic effects on weight at 420 days of age (intercept of the growth function) were inferred for the different crosses with mean values ranging from +12.7 to +17.7. kg. Heterotic values for daily growth rate (slope of the linear function) were not significantly different from zero for five out of the six combinations of lines but an important heterosis (+66. g/d) was estimated between the remaining combinations. The implications of this remarkable heterosis between Iberian pig lines on breeding schemes are discussed in the context of the current breeding structures of this breed. © 2012 Elsevier B.V.

A further look of the genetic origin and singularity of the Torbiscal Iberian pig line

Although the Torbiscal line of Iberian pigs has been largely studied, some aspects of its history are not well known. In this paper, we used pedigree-based methods on a complete genealogy of 4,077 entries in order to get a comprehensive analysis of its four founder strains and to evaluate the expected genetic contribution of each ancestral strain to the successive generations of the composite Torbiscal line. Between-strain differences and specific heterotic effects on piglet weight at 50 days of age were estimated from records of 9,052 piglets born in 1,571 litters of a complete diallel cross among the four strains. Moreover, we assessed the genetic singularity of the current Torbiscal pigs by other three studies, based on whole genome SNP genotypes, focused on the measure of its genetic diversity and differentiation with respect to other domestic and wild pig populations. The STRUCTURE algorithm detected two uppermost levels of the whole population structure, corresponding to European and Asian ancestries. These results confirmed the exclusive European origin of the Torbiscal and other Iberian pigs and the admixed origin of the Duroc breed. Finally, the comparison of Torbiscal with a representative pool of Iberian pigs showed a maximum genetic differentiation in regions of chromosomes three and seven, including some genes related to the regulation of muscle development

Assessing effective population size, coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed

The complete pedigree of two closed Iberian pig lines (Gamito and Torbiscal), with 798 and 4077 reproducers, has been used to measure the evolution of coancestry (f) and inbreeding (F) for autosomal and X-linked genes along 16 and 28 respective equivalent discrete generations. At the last generation, the mean values of each line were f = 0.41 and 0.22, F = 0.35 and 0.18, fX = 0.46 and 0.22 and FX = 0.47 and 0.19, respectively. Other calculated parameters were the effective number of founders (final values, 6.8 and 35.2) and non-founders (1.5 and 2.4), founder genome equivalents (1.2 and 2.3) and effective population size (16.0 and 57.7). Measures of Torbiscal effective size based on rates of coancestry (66.1), inbreeding (65.0) and linkage disequilibrium (71.0) were estimated from whole-genome SNP genotyping data. Values of new and old inbreeding and their respective rates by generation were computed to detect purging effects of natural selection. The analysis of 6854 Torbiscal litters showed significant negative impacts of new and fast inbreeding on litter size, as expected from the purging hypothesis -0.20 born piglets per litter by a 10% of new inbreeding, and -0.03 and -0.02 piglets by 1% of total and new inbreeding rates, respectively. The analysis performed on 1274 litters of the Gamito line failed to show purging effects. The only significant results were reductions in -0.91 and -0.17 piglets by a 10% of old and X-linked genes inbreeding, respectively. These results may be useful for some practical issues in conservation programs of farm or captive wild animals. © 2016 Blackwell Verlag GmbH