Diversidad genética de las razas porcinas ibérica y alentejana mediante el genotipado de variantes genéticas en genes mayores y genes candidatos

Las razas porcinas ibérica y alentejana se encuentran biogeográficamente localizadas en el suroeste de la península Ibérica. Estas razas comparten un conjunto de características comunes. Ambas son fenotípicamente muy similares; muestran un bajo índice de crecimiento y una elevada deposición grasa y tienen un sistema común de producción al aire libre en el que se explotan los recursos de la Dehesa. El objetivo del presente trabajo, dentro del marco del proyecto TREASURE, consistió en caracterizar la diversidad genética de ambas razas usando los datos de genotipado de 39 polimorfismos localizados en 34 genes previamente asociados a distintos caracteres de interés económico. Estos polimorfismos fueron genotipados en 950 cerdos pertenecientes a las razas ibérica y alentejana y a 18 razas europeas autóctonas adicionales. Los bajos valores para heterozigosidad observada y esperada indican una baja diversidad genética en ibéricos y alentejanos. Las distancias genéticas estimadas usando DS y FST fueron cercanas a 0 (0.007 y 0.039, respectivamente), sugieren que estas razas son genéticamente muy similares. Asimismo, las técnicas de análisis multivariante utilizadas como análisis de componentes principales y asignación a grupos mostraron que los individuos de estas razas están muy próximos formando clusters diferenciados del resto de razas. Estos resultados concuerdan con los de otros autores que ya mostraron distancias genéticas cortas entre ambas razas usando secuencias de ADN mitocondrial

Potential Use of Near-Infrared Spectroscopy to Predict Fatty Acid Profile of Meat from Different European Autochthonous Pig Breeds

Autochthonous pig breeds provide products of differentiated quality, among which quality control is difficult to perform and insufficient for current market requirements. The present research evaluates the predictive ability of near‐infrared (NIR) spectroscopy, combined with chemometric methods as a rapid and affordable tool to assure traceability and quality control. Thus, NIR technology was assessed for intact and minced muscle Longissimus thoracis et lumborum samples collected from 12 European autochthonous pig breeds for the quantification of lipid content and fatty acid composition. Different tests were performed using different numbers of samples for calibration and validation. The best predictive ability was found using minced presentation and set with 80% of the samples for the calibration and the remaining 20% for the external validation test for the following traits: lipid content and saturated and polyunsaturated fatty acids, which attained both the highest determination coefficients (0.89, 0.61, and 0.65, respectively) and the lowest root mean square errors in external validation (0.62, 1.82, and 1.36, respectively). Lower predictive ability was observed for intact muscles. These results could contribute to improve the management of autochthonous breeds and to ensure quality of their products by traditional meat industry chains

Determination of fatty acid groups in intramuscular fat of various local pig breeds by FT-NIRS

The objective of the present study is to evaluate the potential use of FT-NIRS for predicting intramuscular fat (IMF) and fatty acid groups (MUFA; PUFA; PUFA n-3, PUFA n-6; SFA) on pig grounded muscles. The research considered 160 fresh samples of Longissimus collected from 12 European local pig breeds (TREASURE* project). For every sample, lipids were extracted from IMF and fatty acid profile was determinate by gas chromatography. Two aliquots of each sample were scanned using FT-NIRS Antaris II model. Mathematical pre-treatments (multiplicative scatter correction, 1st and 2nd derivate) were applied and outliers’ spectra were identified and removed when necessary. Partial least square regression was used on the average spectrum and the models validated using an external data set. Results are evaluated in terms of coefficient of regression and root mean square errors in calibration (R2-RMSE) and validation (Rp2-RMSEP). As expected, the best results were obtained for IMF with R2 higher than 0.99 and RMSE lower than 0.2. Unsaturated fatty acids, probably due to the absorption of the cis double bond in a specific region of near infrared spectra, obtain acceptable R2 (0.89 for MUFA and 0.75 for PUFA n-3 and PUFA n-6). SFA achieved a R2 of 0.81 that is lower than values reported in other studies probably because of the large variability of genotypes used. The validation models achieved both lower coefficients of determination and higher RMSEP than the calibration models; however, R2 differences between calibration and validation were smaller than 5%, except for SFA. Hence, the FT-NIRS seems promising to estimate the principal parameters of fatty acid groups on muscle samples from different European autochthonous pig breeds. Inclusion of other samples can improve the accuracy and the robustness of the models, especially considering the high variability of the samples. *Funded by European Union’s H2020 program (grant agreement No 634476)

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

Characterization and diversity analysis of European local pig breeds and production systems under Treasure project framework

International audienceTreasure is a multidisciplinary European Union H2020 funded project focused on the research and development of activities for the benefit of sustainable pork chains based on European local pig breeds and their production systems. One of the main objectives of the project is to demonstrate singularity of about 20 untapped local pig populations from nine European countries (Portugal, Spain, France, Italy, Slovenia, Croatia, Serbia, Germany and Lithuania) through phenotypic, genomic and transcriptomic activities. Genomic approaches include the use of high density SNP data, candidate gene analyses and whole genome sequencing (WGS). Untapped breeds are first characterized at the production system level through a specific survey addressed to collect census data, breed distribution and phenotypic traits and information on breed organizations and production chains. Genomic data analyses bring the possibility for the estimation of different population genetics and population genomics indicators, such as relative homozygosity and observed and expected genetic diversity of the studied local pig breeds, as well as the definition of the structure of meta-populations through the proportion of shared alleles/haplotypes among animals and population admixture parameters. Comparative analyses including commercial pig populations in Europe identify genome regions with evidence of selective sweeps or signatures of demographic events across breeds. WGS analyses are focused on population adaptation and resilience signatures. To complete the local pig breed characterization, identification of population-specific biological processes responsible for specific production traits and product quality will be achieved through transcriptomic and metagenomic assays under specific production systems and management conditions. Together all these analyses are expected to provide useful methods and DNA markers for authentication and traceability of mono-breed products, conservation of local pig genetic resources and development of specific breeding programs for sustainable pork production chains in Europe. The Treasure project is funded under European Union’s Horizon 2020 research and innovation program, Grant No. 634476

Proyecto TREASURE: Diversidad de las razas porcinas locales y sus sistemas del produccion para la obtencion de productos tradicionales de calidad y el mantenimento de cadenas de produccion sostenibles

El objetivo general que se persigue en este proyecto es profundizar en el conocimiento, las técnica y las competencias necesarias para desarrollar los sistemas de produccion porcina existentes y crear nuevas cadenas de produccion, basados todos privilegiada en comparacion a la de otras razas europeas que cuentan con un numero escaso de individuos, e incluso con riesgo de desaparicion, si no se crean y se contribuya a su mantenimiento y expansion. De esta forma, los problemas que se intentan resolver con es ensayar nuevas estrategias nutricionales y de manejo y estudiar sus efectos sober la calidad del producto final. En cierto sentido menos desarrollados, y a las que pueden se de utilidad las conclusiones que se deriven de los estudios realizados en ibérico. Las actividades que se plantean responden a las demandas del consumidor en cuanto a calidad de productos con identidad regional, su desarrollo economico. Se hara una descripcion y evaluacion exhaustiva de las razas porcinas que forman parte del estudio, con especial énfasis en las muy poco explotadas, para lo cual se dispondra de herramientas de analisis genetico de ultima generacion. Se evaluara también la productividad de estas razas, encuadradas en ambitos climaticos diversos, bajo distintos sistemas de produccion (ecologico, extensivo, intensivo), y se pondra especial enfasis en la evaluacion de recursos y subproductos agroindustriales locales para su alimentacion, asi como de practicas de manejo innovadoras. Se evaluara la calidad intrinseca tanto comprar este tipo de productos. Para el desarollo de todas estas actividades se fortaleceran las redes de colaboracion existentes y se crearan otras nuevas entre los distintos participantes, partenecientes a sectores diversos y complementarios existentes y academico y professional, y se reforzan las relaciones entre la distintas ragiones europeas implicadas, poniendo special atencion en la razas poco explotadas, sus sistemas de produccion y los productos derivados

Precious metals in magmatic Fe-Ni-Cu sulfides from the Potosí chromitite deposit, eastern Cuba

The Moa-Baracoa ophiolite in eastern Cuba is one of the few known ophiolites that display sulfide mineralization attributable to a magmatic origin in association with podiform-chromite ores hosted in the mantle-crust transition. These sulfide ores chiefly consist of Fe-Ni-Cu sulfides, namely pyrrhotite, pentlandite, chalcopyrite and cubanite partly altered to valleriite. The sulfide mineralization is located along the contact between the podiform-like chromite ores and intruding pegmatitic gabroic dykes. The detailed mineralogical study of the sulfide mineralization coupled with the first ever laser ablation ICP-MS analysis reveals that this sulfide mineralization show contents of the precious metals (Os, Ir, Ru, Pt, Re, Au, Ag) and other (semi)-metals (Co, Ni, Cu, Se, Te, Bi, Pb, As Sb) comparable to those sulfides from the magmatic sulfide deposits associated with mafic complexes hosted in the continental crust. The results obtained from this study confirm that Fe-Ni-Cu sulfides at Potosí are magmatic in origin, and very likely derived from the solidification of droplets of sulfide melt segregated by immiscibility from the intruding mafic melts once they interacted with the pre-existing chromitite at the mantle-crust transition zone of the ophiolite. The immiscibility of sulfide melt was achieved as a result of a progressive increase of fS, very likely triggered by a set of circumstances, including the progressive fractionation of the intruding mafic melt leading to increase of aSiO and accumulation of volatiles as well as the crystallization of oxides. Two main generations of pentlandite were observed. One generation is primary in origin and it was locally exsolved along with pyrrhotite from monosulfide solid solution (MSS) during low-temperature cooling. The second type of pentlandite resulted from the reaction of MSS with coexisting droplets of Cu-and Ni-rich sulfide melt. LA-ICP-MS analysis reveals that most precious metals (Ru, Os, Ir, Re, Au, Ag) were concentrated along with the base-metal sulfides (BMS), although their distribution among the different BMS (pyrrhotite, pentlandite, chalcopyrite and cubanite) does not strictly follow the expected distribution according to the known melt-solid and solid-solid partition coefficients. Unlike the other analyzed PGEs, Pt was not preferentially concentrated in BMS but as discrete micrometer-sized sperrylite grains. The crystallization of sperrylite took place before and contemporaneous to sulfide segregation, and Pt-As nanoparticles probably played an important role in the Pt uptake as nucleation seeds for the formation of micron-sized sperrylite grains. These observations highlight the open-system nature of the ore forming system as well as the important role of arsenic in concentrating PGE in high-temperature silicate and sulfide melts.This research was supported by Spanish projects: RTI2018-099157-A-I00 and CGL2015-65824-P granted by the “ Ministerio de Ciencia, Innovación y Universidades ” and Ministerio de Economía y Competitividad ” (MINECO), respectively. Additional funding for LA–ICP–MS analysis was provided by the Ramón y Cajal Fellowship RYC-2015-17596 to JMGJ. Rosanna Murphy (GAU of Macquarie University) is acknowledged for her assistance with LA-ICP-MS analysis. We are also indebted to Xavier Llovet from the Centres Científics i Tecnològics of the Universitat of Barcelona (CCiTUB) for his careful help with EMPA

Tracing autochthonous pig breeds with meat near-infrared spectra data pig

Near Infrared spectroscopy (NIRS) offers an easy to use and cost-effective tool for quantitative and qualitative application in animal science. Of special interest could be considered the use of NIRS for tracing meat origin on the basis of breed specification. The aim of this study was to investigate the potential use of meat NIRS as a “fingerprint” of autochthonous pig breeds. The research considered intact and grounded sample of Longissimus Dorsi (n=371) collected from 11 European local pig breeds from the TREASURE project, namely: Alentejana (ALE), Bisara (BIS), Crna Slawonska (CRN), Gascon (GAS), Iberian (IBE), Krskopolje (KRS), Lithuanian Wattle (LIA), Lithuanian White (LIH), Negre Mallorqui (NEG), Schwabish Hallisches (SCH) and Turopolje (TUR). For each muscle sample, two aliquots were scanned using FT-NIRS Antaris II model (Thermo Fisher Scientific) in absorbance mode considering the infrared region (3999 to 9999 cm-1) and averaged. Discriminant analysis of principal components (DAPC) on meat NIRS was used to assess: i) breed traceability and ii) similarity among breeds. DAPC was applied on standardised (centred and scaled) spectra using the R package. For breed traceability, cross-validation was applied: five samples per breed were sampled at random, without replacement, and used in validation. The procedure was repeated ten times and each breed was analysed separately. In this case, all breeds were present in the training set. Similarity among breeds was assessed by excluding each breed from the training set and assigning the samples in the validation set to the breeds in the training one. Overall correct classification was 68.0 and 77.6% for intact and grounded meat, respectively. Alentejana had 100% correct classification for both intact and grounded meat. For CRN, KRS, LIA, LIH and NEG use of grounded meat spectra resulted in higher classification rates from 44 to 64% for intact and from 66 to 90% for grounded meat), while for GAS the opposite was found (80% for intact vs. 70% for grounded). For the rest of the breeds slight or no differences were observed between intact and grounded samples and classification rates ranged between 66 (CRN and SCH) to 72% (BIS). The lowest classification rates were observed in both cases for CRN. Similarity among breeds was greatly varied upon dataset used (e.g. ALE samples were classified as IBE (40%), TUR (40%) and SCH (10%) using intact meat while 100% were classified as CRN using grounded meat). Our results mark NIRS as a promising tool for traceability of pig breed meat origin and support the use of grounded over intact samples

SNP discovery and association study for growth, fatness and meat quality traits in Iberian crossbred pigs

Iberian pigs and its crosses are produced to obtain high-quality meat products. The objective of this work was to evaluate a wide panel of DNA markers, selected by biological and functional criteria, for association with traits related to muscle growth, fatness, meat quality and metabolism. We used 18 crossbred Iberian pigs with divergent postnatal growth patterns for whole genome sequencing and SNP discovery, with over 13 million variants being detected. We selected 1023 missense SNPs located on annotated genes and showing different allele frequencies between pigs with makerdly different growth patterns. We complemented this panel with 192 candidate SNPs obtained from literature mining and from muscle RNAseq data. The selected markers were genotyped in 480 Iberian × Duroc pigs from a commercial population, in which phenotypes were obtained, and an association study was performed for the 1005 successfully genotyped SNPs showing segregation. The results confirmed the effects of several known SNPs in candidate genes (such as LEPR, ACACA, FTO, LIPE or SCD on fatness, growth and fatty acid composition) and also disclosed interesting effects of new SNPs in less known genes such as LRIG3, DENND1B, SOWAHB, EPHX1 or NFE2L2 affecting body weight, average daily gain and adiposity at different ages, or KRT10, NLE1, KCNH2 or AHNAK affecting fatness and FA composition. The results provide a valuable basis for future implementation of marker-assisted selection strategies in swine and contribute to a better understanding of the genetic architecture of relevant traits

Potential use of near-infrared spectroscopy to predict fatty acid profile of meat from different european autochthonous pig breeds

Autochthonous pig breeds provide products of differentiated quality, among which quality control is difficult to perform and insufficient for current market requirements. The present research evaluates the predictive ability of near-infrared (NIR) spectroscopy, combined with chemometric methods as a rapid and affordable tool to assure traceability and quality control. Thus, NIR technology was assessed for intact and minced muscle Longissimus thoracis et lumborum samples collected from 12 European autochthonous pig breeds for the quantification of lipid content and fatty acid composition. Different tests were performed using different numbers of samples for calibration and validation. The best predictive ability was found using minced presentation and set with 80% of the samples for the calibration and the remaining 20% for the external validation test for the following traits: lipid content and saturated and polyunsaturated fatty acids, which attained both the highest determination coefficients (0.89, 0.61, and 0.65, respectively) and the lowest root mean square errors in external validation (0.62, 1.82, and 1.36, respectively). Lower predictive ability was observed for intact muscles. These results could contribute to improve the management of autochthonous breeds and to ensure quality of their products by traditional meat industry chains.This research was funded by the European Union’s Horizon 2020 research and innovation program, grant number 634476, for the project with acronym TREASURE. The content of this article reflects only the authors’ view and the European Union Agency is not responsible for any use that may be made of the information it contains. Junta of Extremadura and the European Social Fund for the pre-doctoral grant (PD16057) and the GR18098