Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data

[EN] Background: Porcine fatty acid composition is a key factor for quality and nutritive value of pork. Several QTLs for fatty acid composition have been reported in diverse fat tissues. The results obtained so far seem to point out different genetic control of fatty acid composition conditional on the fat deposits. Those studies have been conducted using simple approaches and most of them focused on one single tissue. The first objective of the present study was to identify tissue-specific and tissue-consistent QTLs for fatty acid composition in backfat and intramuscular fat, combining linkage mapping and GWAS approaches and conducted under single and multitrait models. A second aim was to identify powerful candidate genes for these tissue-consistent QTLs, using microarray gene expression data and following a targeted genetical genomics approach. Results: The single model analyses, linkage and GWAS, revealed over 30 and 20 chromosomal regions, 24 of them identified here for the first time, specifically associated to the content of diverse fatty acids in BF and IMF, respectively. The analyses with multitrait models allowed identifying for the first time with a formal statistical approach seven different regions with pleiotropic effects on particular fatty acids in both fat deposits. The most relevant were found on SSC8 for C16:0 and C16:1(n-7) fatty acids, detected by both linkage and GWAS approaches. Other detected pleiotropic regions included one on SSC1 for C16:0, two on SSC4 for C16:0 and C18:2, one on SSC11 for C20:3 and the last one on SSC17 for C16:0. Finally, a targeted eQTL scan focused on regions showing tissue consistent effects was conducted with Longissimus and fat gene expression data. Some powerful candidate genes and regions were identified such as the PBX1, RGS4, TRIB3 and a transcription regulatory element close to ELOVL6 gene to be further studied. Conclusions: Complementary genome scans have confirmed several chromosome regions previously associated to fatty acid composition in backfat and intramuscular fat, but even more, to identify new ones. Although most of the detected regions were tissue-specific, supporting the hypothesis that the major part of genes affecting fatty acid composition differs among tissues, seven chromosomal regions showed tissue-consistent effects. Additional gene expression analyses have revealed powerful target regions to carry the mutation responsible for the pleiotropic effects.This work was funded by the MICINN project AGL2011-29821-C02 (Ministerio de Economia y Competitividad). 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Luces y sombras del análisis de expresión génica utilizando microarrays. Un ejemplo en cerdo ibérico

Ponencia publicada en ITEA, vol.104La tecnología de los microarrays de expresión es la herramienta ideal para el estudio de patrones de expresión de miles de genes de forma simultánea. Sin embargo existe gran variabilidad de resultados atribuible a los aspectos técnicos y de análisis estadístico. En este trabajo presentamos algunos de los problemas surgidos en el estudio de las diferencias de expresión en hígado de cerdos ibéricos para los tratamientos sexo y alimentación empleando microarrays de Affymetrix. Los datos de expresión normalizados fueron analizados siguiendo dos aproximaciones de la metodología de los modelos mixtos. Para ambos tratamientos las diferencias de expresión detectadas fueron dependientes del modelo de análisis y solo un pequeño número de genes diferencialmente expresados fueron coincidentes en ambas estrategias estadísticas. Algunas de estas diferencias de expresión fueron validadas por PCR cuantitativa. Además identificamos errores de diseño y falta de anotación de las sondas del array. Los resultados de este estudio nos han permitido detectar diferencias de expresión de algunos genes de interés, pero también remarcan la necesidad de realizar estudios complementarios que confirmen las diferencias de expresión reveladas a través de la tecnología de los microarraysLights and darkness of gene expression analysis using microarrays: an example in Iberian pigs Expression microarray technology is the ideal tool for the study of thousands of gene expression patterns simultaneously. However there is a great variability of results attributed to technical and statistical analysis aspects. In this work we present several of the arisen problems of a differential expression study in liver of Iberian pigs under the treatments sex and feeding level using Affymetrix microarray. Normalized expression data were analyzed following two approaches of the mixed model methodology. In both treatments the detected differential expressions were dependent of the statistical model and just a small number of genes were coincident between both statistical strategies. Some of the expression differences were confirmed by quantitative PCR. Besides, we have identified design mistakes and missing annotation of the array probes. The results of this study have allowed us to detect differential expression of interesting genes, but it pointed out the necessity of carrying out complementary studies in order to confirm the differential expressions revealed using microarrays technology

Influencia de la restricción de vitamina A en la dieta de cerdos ibéricos sobre el metabolismo y la transcripción de genes relacionados con lipogénesis

Vitamin A is a liposoluble vitamin obtained from the diet with multiple physiological actions in all animal tissues, including an antiadipogenic action which seems to be limited to muscular tissues. Thus, vitamin A restriction has been proposed as a strategy for improving meat and carcass quality in farm animals. In this work we have studied the effects of vitamin A dietary restriction on productive traits, tissue fatty acid composition and expression of a panel of adipogenic and lipogenic candidate genes in Iberian pigs. Forty Torbiscal pigs were fed with a standard or a Vitamin A restricted diet from two months of age till their sacrifice conducted in two batches, at 100 and 160 Kg live weight. Diet had no significant effect on growth, fatness, yields or intramuscular fat, but animals receiving no vitamin A supplementation showed higher monounsaturated fatty acids and lower saturated fatty acids in back fat and loin samples than the control ones. Adipose tissue SCD gene expression was higher in vitamin A restricted animals, as occurs with CRABP II expression. On the other hand, RXRG expression was higher in control group, in agreement with the influence on transcription of retinoic acid and its potential relationship with adipogenesis and lipogenesis.La vitamina A es una vitamina liposoluble obtenida de la dieta con numerosas funciones fisiológicas en los tejidos animales, incluyendo un efecto antiadipogénico aparentemente limitado al tejido muscular. La restricción de vitamina A se ha propuesto como una herramienta para mejorar la calidad de la canal y de la carne en animales de abasto. En el presente trabajo hemos estudiado el efecto de la restricción de vitamina A en el pienso sobre caracteres productivos, composición tisular de ácidos grasos y expresión de un panel de genes candidato con funciones adipogénicas y lipogénicas en cerdos ibéricos. Cuarenta cerdos de la estirpe Torbiscal fueron alimentados con pienso estándar o con pienso sin vitamina A en el corrector desde los dos meses de edad hasta su sacrificio, realizado en dos lotes (a 100 y 160 kg de peso vivo). La dieta no afectó al crecimiento, engrasamiento, rendimientos ni a la cantidad de grasa intramuscular, pero los animales restringidos mostraron una cantidad mayor de ácidos grasos monoinsaturados y menor de saturados en el tocino dorsal y en el lomo. El análisis de expresión génica en el tocino dorsal mostró una mayor expresión de SCD y CRABP II en el grupo restringido. Por otro lado, la expresión de RXRG fue mayor en el grupo control, en concordancia con el efecto modulador de la transcripción génica del ácido retinoico y su potencial relación con la adipogénesis y lipogénesis

Recombination of the porcine X chromosome : a high density linkage map

Linkage maps are essential tools for the study of several topics in genome biology. High density linkage maps for the porcine autosomes have been constructed exploiting the high density data provided by the PorcineSNP60 BeadChip. However, a high density SSCX linkage map has not been reported up to date. The aim of the current study was to build an accurate linkage map of SSCX to provide precise estimates of recombination rates along this chromosome and creating a new tool for QTL fine mapping. A female-specific high density linkage map was built for SSCX using Sscrofa10.2 annotation. The total length of this chromosome was 84.61 cM; although the average recombination rate was 0.60 cM/Mb, both cold and hot recombination regions were identified. A Bayesian probabilistic to genetic groups and revealed that the animals used in the current study for linkage map construction were likely to be carriers of X chromosomes of European origin. Finally, the newly generated linkage map was used to fine-map a QTL at 16 cM for intramuscular fat content (IMF) measured on longissimus dorsi. The sulfatase isozyme S gene constitutes a functional and positional candidate gene underlying the QTL effect. The current study presents for the first time a high density linkage map for SSCX and supports the presence of cold and hot recombination intervals along this chromosome. The large cold recombination region in the central segment of the chromosome is not likely to be due to structural differences between X chromosomes of European and Asian origin. In addition, the newly generated linkage map has allowed us to fine-map a QTL on SSCX for fat deposition. The online version of this article (doi:10.1186/s12863-014-0148-x) contains supplementary material, which is available to authorized users

Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics

Background The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in piglets of both genetic types, in order to identify genes, pathways and regulatory factors responsible for their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DU×IB) were generated. Piglets (14 from each genetic type) were slaughtered at weaning (28 days) and longissimus dorsi was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays.Results Loin muscle chemical composition showed significant differences between genetic types in intramuscular fat content (6.1% vs. 4.3% in IB and DUxIB animals, respectively, P = 0.009) and in saturated (P = 0.019) and monounsaturated fatty acid proportions (P = 0.044). The statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR < 0.10), 102 upregulated in IB and 154 upregulated in DU×IB. Transcript differences were validated for a subset of DE genes by qPCR. We observed alteration in biological functions related to extracellular matrix function and organization, cellular adhesion, muscle growth, lipid metabolism and proteolysis. Candidate genes with known effects on muscle growth were found among the DE genes upregulated in DU×IB. Genes related to lipid metabolism and proteolysis were found among those upregulated in IB. Regulatory factors (RF) potentially involved in the expression differences were identified by calculating the regulatory impact factors. Twenty-nine RF were found, some of them with known relationship with tissue development (MSTN, SIX4, IRX3), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these RF and DE genes show relevant differences between genetic types.Conclusion These results provide valuable information about genetic mechanisms determining the phenotypic differences on growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. Transcription factors and regulatory mechanisms are proposed for these altered biological functions. © 2014 Óvilo et al.; licensee BioMed Central Ltd

CoastColour Round Robin data sets: A database to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters

The use of in situ measurements is essential in the validation and evaluation of the algorithms that provide coastal water quality data products from ocean colour satellite remote sensing. Over the past decade, various types of ocean colour algorithms have been developed to deal with the optical complexity of coastal waters. Yet there is a lack of a comprehensive intercomparison due to the availability of quality checked in situ databases. The CoastColour Round Robin (CCRR) project, funded by the European Space Agency (ESA), was designed to bring together three reference data sets using these to test algorithms and to assess their accuracy for retrieving water quality parameters. This paper provides a detailed description of these reference data sets, which include the Medium Resolution Imaging Spectrometer (MERIS) level 2 match-ups, in situ reflectance measurements, and synthetic data generated by a radiative transfer model (HydroLight). These data sets, representing mainly coastal waters, are available from doi:10.1594/PANGAEA.841950. The data sets mainly consist of 6484 marine reflectance (either multispectral or hyperspectral) associated with various geometrical (sensor viewing and solar angles) and sky conditions and water constituents: total suspended matter (TSM) and chlorophyll a (CHL) concentrations, and the absorption of coloured dissolved organic matter (CDOM). Inherent optical properties are also provided in the simulated data sets (5000 simulations) and from 3054 match-up locations. The distributions of reflectance at selected MERIS bands and band ratios, CHL and TSM as a function of reflectance, from the three data sets are compared. Match-up and in situ sites where deviations occur are identified. The distributions of the three reflectance data sets are also compared to the simulated and in situ reflectances used previously by the International Ocean Colour Coordinating Group (IOCCG, 2006) for algorithm testing, showing a clear extension of the CCRR data which covers more turbid waters

Molecular mechanism of dynein recruitment to kinetochores by the Rod-Zw10-Zwilch complex and Spindly

The molecular motor dynein concentrates at the kinetochore region of mitotic chromosomes in animals to accelerate spindle microtubule capture and to control spindle checkpoint signaling. In this study, we describe the molecular mechanism used by the Rod-Zw10-Zwilch complex and the adaptor Spindly to recruit dynein to kinetochores in Caenorhabditis elegans embryos and human cells. We show that Rod's N-terminal beta-propeller and the associated Zwilch subunit bind Spindly's C-terminal domain, and we identify a specific Zwilch mutant that abrogates Spindly and dynein recruitment in vivo and Spindly binding to a Rod beta-propeller-Zwilch complex in vitro. Spindly's N-terminal coiled-coil uses distinct motifs to bind dynein light intermediate chain and the pointed-end complex of dynactin. Mutations in these motifs inhibit assembly of a dynein-dynactin-Spindly complex, and a null mutant of the dynactin pointed-end subunit p27 prevents kinetochore recruitment of dynein-dynactin without affecting other mitotic functions of the motor. Conservation of Spindly-like motifs in adaptors involved in intracellular transport suggests a common mechanism for linking dynein to cargo.This work was supported by a European Research Council Starting Grant (Dyneinome 338410) and a European Molecular Biology Organization Installation Grant to R. Gassmann. This work was also supported by funding from the Fundacao para a Ciencia e a Tecnologia to R. Gassmann (IF/01015/2013/CP1157/CT0006), C. Pereira (SFRH_BPD_95648_2013), and D.J. Barbosa (SFRH_BPD_101898_2014). Some C. elegans strains were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40 OD010440)