Three inquiries into the origin of Manchado de Jabugo pigs

Ponencia publicada en ITEA, vol.104El origen de la población Manchado de Jabugo se atribuye a cruces realizados en el siglo XIX entre cerdos Ibéricos negros y colorados. Se supone que animales de razas Large White y Berkshire contribuyeron además a fundar esta población, que ha permanecido aislada durante décadas en algunos pueblos de la Sierra de Aracena. El objetivo de este trabajo fue rastrear posibles huellas genéticas de las variedades y razas fundadoras en la población actual, conservada por la Diputación de Huelva. El ADN mitocondrial de animales Manchado de Jabugo y Large White presenta secuencias coincidentes tanto para la región de control D-loop, como para los genes Cyt b, ATPasa8, ATPasa6 y NADH5. La mutación IGF2 g.3072G>A, ocurrida en un cromosoma asiático, se detecta en la población Manchado, y está presente asimismo en Large White y Berkshire. Ello concuerda con la posible contribución fundacional de ambas razas británicas, en las que se introdujeron genes de origen asiático a partir del siglo XVIII. Finalmente, esta población presenta cuatro alelos del gen MC1R. El alelo MC1R*3 es característico de la variedad negra de cerdo Ibérico y del Large White. Los alelos MC1R*6 y MC1R*7 de la variedad colorada, y el primero también del Berkshire. La presencia del alelo MC1R*4, característico de la raza Duroc indica una contribución más reciente de esta otra raza foránea al germoplasma del Manchado de Jabugo.Animals born at the end of the XIX century from crosses between Red and Black Iberian pigs were the main founders of the black spotted population named Manchado de Jabugo. Pigs of the Large White and Berkshire breeds had also contributed to the foundation of this population, which was isolated for several decades in some villages of Huelva. Our objective was to verify the possible genetic traces of founder varieties and breeds in this population, preserved by the Diputación de Huelva. The mitochondrial DNA from Manchado and Large White animals shows identical sequences for the control region D-loop, and also for the Cyt b ATPase8, ATPase6 and NADH5 genes. The IGF2 g.3072G>A mutation, apparently occurred in an Asian chromosome, is also present in the Manchado population. Both results agree with the quoted founder contribution of two British breeds, because Asian germplasm was introgressed into these breeds from the XVIII century. Finally, four alleles of the MC1R gene are segregating in this small population. The MC1R*3 allele is characteristic of Black Iberian variety and Large White breed. The MC1R*6 and MC1R*7 alleles are characteristic of Red Iberian pigs, and the first one of the Berkshire pigs. The unexpected presence of the MC1R*4 allele, characteristic of Duroc, indicates the contribution of this breed to the current Manchado germplasm

Evaluación genética del tamaño y peso de camada para sucesivos partos en cerdas Ibéricas

Genetic progress for reproductive performance in pigs is limited by mothering ability. It is a critical aspect for dam lines, in which litter weight at weaning could be included with litter size in the selection goal. Our objective was to investigate in Iberian pigs the genetic basis of the number of alive born piglets (NBA) and the litter weight at 21days (LW21) over the successive parities (t). Records for NBA were available from 6,775 litters born from 1,893 sows of the Torbiscal line, and LW21 records proceeded from 1,431 sows and 2,963 litters without crossfostering. Genetic parameters were estimated using an animal model with repeatability, a multi-trait animal model, and a random regression model. Estimated values of heritabilities for NBA and genetic correlations between parities confirm a partially different genetic control of prolificacy at parity 1 and at later parities. Results for LW21 indicate that this trait may be partially controlled by different genes at the first two parities and at the later ones. Estimated genetic parameters for NBA (t = 1), NBA (t >/= 2), LW21 (t /= 3) were: heritability, hE2 = 0.15, 0.12, 0.22 and 0.15, respectively, and coefficient of permanent environmental effects, pE2 = 0.05, 0.02 and 0.24, respectively for the three last traits. The values of genetic correlations ranged from 0.44 to 0.84. A multitrait approach would be useful to estimate accurate genetic parameters, and to improve the low persistency of reproductive performance in the later parities of Iberian sows.La mejora genética de la eficiencia reproductiva en cerdos está limitada por su aptitud maternal. Es éste un aspecto crítico en las líneas maternas, en las que el peso de la camada al destete podría ser incluido junto al tamaño de camada en el objetivo de selección. El objetivo del trabajo fue investigar en cerdos Ibéricos la base genética del número de lechones nacidos vivos (NBA) y el peso de camada a 21 días (LW21) a lo largo de los sucesivos partos (t). Se dispuso de registros de NBA de 6.775 camadas nacidas de 1.893 cerdas, y registros de LW21 procedentes de 1.431 cerdas y 2.963 camadas sin adopciones. Se estimaron parámetros genéticos mediante tres modelos: con repetibilidad, multicarácter y de regresión aleatoria. Los valores de las heredabilidades y las correlaciones genéticas entre NBA en diferentes partos confirman su control genético, parcialmente distinto en el parto primero y posteriores. Los resultados para LW21 indican que este carácter puede estar parcialmente controlado por diferentes genes en los dos primeros partos y en los sucesivos. Los parámetros genéticos estimados para NBA (t = 1), NBA (t >/= 2), LW21 (t /= 3) fueron: heredabilidad, hE2 = 0,15, 0,12, 0,22 y 0,15, respectivamente, y coeficiente de efectos de ambiente permanente, pE2 = 0,05, 0,02 y 0,24, respectivamente para los tres últimos caracteres. El rango de las correlaciones genéticas fue de 0,44 a 0,84. Un enfoque genético multicarácter sería útil para estimar parámetros genéticos precisos y mejorar la escasa persistencia del rendimiento reproductivo en los últimos partos

Limited genetic antagonism between premium cuts yield and intramuscular fat content in Iberian pigs

Ponencia publicada en ITEA, vol.104La producción de cerdo ibérico está orientada a la obtención de materia prima para la elaboración de productos curados de alta calidad, determinada entre otros factores por el contenido en grasa intramuscular. Este trabajo tiene como objetivo estimar las correlaciones genéticas entre el contenido de grasa intramuscular, medido mediante tecnología NIRS en M. longissimus, y los principales caracteres productivos: porcentaje de jamones, paletas y lomos del peso de la canal, y la ganancia media diaria durante el periodo de ‘Montanera’. Los registros analizados proceden de 6.103 cerdos castrados de 56 ganaderías y controlados desde 1993 al 2007 por AECERIBER. Los animales con un manejo extensivo común fueron sacrificados, en 79 lotes, a un peso medio de aproximadamente 160 kg. Las heredabilidades estimadas presentaron valores altos para todos los caracteres (0,37 a 0,48) indicando que la selección para todos los caracteres puede ser efectiva. Las correlaciones genéticas entre el porcentaje de las principales piezas nobles fueron altas y positivas (de 0,36 a 0,69) lo cual indica que dichos caracteres están en parte controlados por un mismo grupo de genes. Las correlaciones genéticas entre el contenido en grasa intramuscular y ganancia media diaria y el porcentaje de paletas no fueron significativamente diferentes de cero. Sin embargo, se estimaron efectos negativos significativos entre el contenido en grasa intramuscular y el porcentaje de jamones (-0.19 ± 0.04) y lomos (-0.23 ± 0.03). Estos valores indican que una intensa selección orientada a mejorar el porcentaje de piezas nobles de la canal, puede a medio plazo deteriorar la calidad de los productos curados en cerdos Ibéricos.The production of Iberian pigs is mainly focused to obtain raw meat to elaborate dry-cured products of high sensorial quality, mainly influenced by the intramuscular fat content. The objective of this work was to estimate the genetic correlations between intramuscular fat content in M. longissimus, measured using NIRS technology, and the main productive traits: percentages on carcass weight of hams, forelegs and loins, and the daily growth along the final fattening period. Records for this analysis came from 6,103 castrate males, born in 56 herds and controlled by AECERIBER from 1993 to 2007. All the animals were fattened with a common extensive management system and slaughtered, distributed in 79 batches, at approximately 160 kg. Heritability estimates presented high values for all the traits (ranging between 0.37 and 0.48) indicating that the selection for these traits could be effective. Genetic correlations between percentages of premium cuts were high and positive (from 0.36 to 0.69). This fact indicates that these traits are partially controlled by the same group of genes. Genetic correlations between intramuscular fat content and the daily growth and percentage of forelegs showed estimated values statistically non different from cero. However, significant negative values of genetic correlations were estimated between intramuscular fat content and the percentages of hams (-0.19 ± 0.04) and loins (-0.23 ± 0.03). These last values indicate that a strong selection in Iberian pigs focused to the improvement of the carcass percentage of premium cuts, could cause a deterioration of the meat suitability for dry-curing in a medium-time horizon

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

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). We thank to Fabian Garcia, Anna Mercade and Carmen Barragan for their assistance in DNA preparation and SNP genotyping.Muñoz, M.; Rodríguez, MC.; Alves, E.; Folch, J.; Ibañez Escriche, N.; Silió, L.; Fernández, A. (2013). Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data. BMC Genomics. 14. https://doi.org/10.1186/1471-2164-14-845S14Lichtenstein, A. H. (2003). Dietary Fat and Cardiovascular Disease Risk: Quantity or Quality? Journal of Women’s Health, 12(2), 109-114. doi:10.1089/154099903321576493Jiménez-Colmenero, F., Ventanas, J., & Toldrá, F. (2010). Nutritional composition of dry-cured ham and its role in a healthy diet. Meat Science, 84(4), 585-593. doi:10.1016/j.meatsci.2009.10.029Webb, E. C., & O’Neill, H. A. (2008). The animal fat paradox and meat quality. Meat Science, 80(1), 28-36. doi:10.1016/j.meatsci.2008.05.029Wood, J. D., Enser, M., Fisher, A. V., Nute, G. R., Sheard, P. R., Richardson, R. I., … Whittington, F. M. (2008). Fat deposition, fatty acid composition and meat quality: A review. Meat Science, 78(4), 343-358. doi:10.1016/j.meatsci.2007.07.019Martı́n, L., Timón, M. L., Petrón, M. J., Ventanas, J., & Antequera, T. (2000). Evolution of volatile aldehydes in Iberian ham matured under different processing conditions. Meat Science, 54(4), 333-337. doi:10.1016/s0309-1740(99)00107-2Fernández, A., de Pedro, E., Núñez, N., Silió, L., Garcı́a-Casco, J., & Rodrı́guez, C. (2003). Genetic parameters for meat and fat quality and carcass composition traits in Iberian pigs. Meat Science, 64(4), 405-410. doi:10.1016/s0309-1740(02)00207-3Sellier, P., Maignel, L., & Bidanel, J. P. (2009). Genetic parameters for tissue and fatty acid composition of backfat, perirenal fat and longissimus muscle in Large White and Landrace pigs. animal, 4(4), 497-504. doi:10.1017/s1751731109991261Suzuki, K., Ishida, M., Kadowaki, H., Shibata, T., Uchida, H., & Nishida, A. (2006). Genetic correlations among fatty acid compositions in different sites of fat tissues, meat production, and meat quality traits in Duroc pigs. Journal of Animal Science, 84(8), 2026-2034. doi:10.2527/jas.2005-660Clop, A., Ovilo, C., Perez-Enciso, M., Cercos, A., Tomas, A., Fernandez, A., … Noguera, J. L. (2003). Detection of QTL affecting fatty acid composition in the pig. Mammalian Genome, 14(9), 650-656. doi:10.1007/s00335-002-2210-7Nii, M., Hayashi, T., Tani, F., Niki, A., Mori, N., Fujishima-Kanaya, N., … Mikawa, S. (2006). Quantitative trait loci mapping for fatty acid composition traits in perirenal and back fat using a Japanese wild boar × Large White intercross. Animal Genetics, 37(4), 342-347. doi:10.1111/j.1365-2052.2006.01485.xRamayo-Caldas, Y., Mercadé, A., Castelló, A., Yang, B., Rodríguez, C., Alves, E., … Folch, J. M. (2012). Genome-wide association study for intramuscular fatty acid composition in an Iberian × Landrace cross1. Journal of Animal Science, 90(9), 2883-2893. doi:10.2527/jas.2011-4900Uemoto, Y., Soma, Y., Sato, S., Ishida, M., Shibata, T., Kadowaki, H., … Suzuki, K. (2011). Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population. Animal Genetics, 43(1), 27-34. doi:10.1111/j.1365-2052.2011.02218.xGuo, T., Ren, J., Yang, K., Ma, J., Zhang, Z., & Huang, L. (2009). Quantitative trait loci for fatty acid composition in longissimus dorsi and abdominal fat: results from a White Duroc × Erhualian intercross F2population. Animal Genetics, 40(2), 185-191. doi:10.1111/j.1365-2052.2008.01819.xRamos, A. M., Crooijmans, R. P. M. A., Affara, N. A., Amaral, A. J., Archibald, A. L., Beever, J. E., … Groenen, M. A. M. (2009). Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS ONE, 4(8), e6524. doi:10.1371/journal.pone.0006524Corominas, J., Ramayo-Caldas, Y., Puig-Oliveras, A., Pérez-Montarelo, D., Noguera, J. L., Folch, J. M., & Ballester, M. (2013). Polymorphism in the ELOVL6 Gene Is Associated with a Major QTL Effect on Fatty Acid Composition in Pigs. PLoS ONE, 8(1), e53687. doi:10.1371/journal.pone.0053687Ponsuksili, S., Jonas, E., Murani, E., Phatsara, C., Srikanchai, T., Walz, C., … Wimmers, K. (2008). Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle. BMC Genomics, 9(1), 367. doi:10.1186/1471-2164-9-367Steibel, J. P., Bates, R. O., Rosa, G. J. M., Tempelman, R. J., Rilington, V. D., Ragavendran, A., … Ernst, C. W. (2011). Genome-Wide Linkage Analysis of Global Gene Expression in Loin Muscle Tissue Identifies Candidate Genes in Pigs. PLoS ONE, 6(2), e16766. doi:10.1371/journal.pone.0016766C�novas, A., Quintanilla, R., Amills, M., & Pena, R. N. (2010). Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits. BMC Genomics, 11(1), 372. doi:10.1186/1471-2164-11-372Uemoto, Y., Sato, S., Ohnishi, C., Terai, S., Komatsuda, A., & Kobayashi, E. (2009). The effects of single and epistatic quantitative trait loci for fatty acid composition in a Meishan × Duroc crossbred population. Journal of Animal Science, 87(11), 3470-3476. doi:10.2527/jas.2009-1917Muñoz, M., Alves, E., Ramayo-Caldas, Y., Casellas, J., Rodríguez, C., Folch, J. M., … Fernández, A. I. (2011). Recombination rates across porcine autosomes inferred from high-density linkage maps. Animal Genetics, 43(5), 620-623. doi:10.1111/j.1365-2052.2011.02301.xQuintanilla, R., Pena, R. N., Gallardo, D., Cánovas, A., Ramírez, O., Díaz, I., … Amills, M. (2011). Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects1. Journal of Animal Science, 89(10), 2963-2971. doi:10.2527/jas.2011-3974Liaubet, L., Lobjois, V., Faraut, T., Tircazes, A., Benne, F., Iannuccelli, N., … Cherel, P. (2011). Genetic variability of transcript abundance in pig peri-mortem skeletal muscle: eQTL localized genes involved in stress response, cell death, muscle disorders and metabolism. BMC Genomics, 12(1). doi:10.1186/1471-2164-12-548Mitchell-Olds, T. (2010). Complex-trait analysis in plants. Genome Biology, 11(4), 113. doi:10.1186/gb-2010-11-4-113Scoggan, K. A., Jakobsson, P.-J., & Ford-Hutchinson, A. W. (1997). Production of Leukotriene C4in Different Human Tissues Is Attributable to Distinct Membrane Bound Biosynthetic Enzymes. Journal of Biological Chemistry, 272(15), 10182-10187. doi:10.1074/jbc.272.15.10182JAKOBSSON, A., WESTERBERG, R., & JACOBSSON, A. (2006). Fatty acid elongases in mammals: Their regulation and roles in metabolism. Progress in Lipid Research, 45(3), 237-249. doi:10.1016/j.plipres.2006.01.004Iankova, I., Chavey, C., Clapé, C., Colomer, C., Guérineau, N. C., Grillet, N., … Fajas, L. (2008). Regulator of G Protein Signaling-4 Controls Fatty Acid and Glucose Homeostasis. Endocrinology, 149(11), 5706-5712. doi:10.1210/en.2008-0717Angyal, A., & Kiss-Toth, E. (2012). The tribbles gene family and lipoprotein metabolism. Current Opinion in Lipidology, 23(2), 122-126. doi:10.1097/mol.0b013e3283508c3bÓvilo, C., Pérez-Enciso, M., Barragán, C., Clop, A., Rodríguez, C., Oliver, M. A., … Noguera, J. L. (2000). A QTL for intramuscular fat and backfat thickness is located on porcine Chromosome 6. Mammalian Genome, 11(4), 344-346. doi:10.1007/s003350010065Veroneze, R., Lopes, P. S., Guimarães, S. E. F., Silva, F. F., Lopes, M. S., Harlizius, B., & Knol, E. F. (2013). Linkage disequilibrium and haplotype block structure in six commercial pig lines. Journal of Animal Science, 91(8), 3493-3501. doi:10.2527/jas.2012-6052Storey, J. D., & Tibshirani, R. (2003). Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences, 100(16), 9440-9445. doi:10.1073/pnas.1530509100Tsai, S., Cassady, J. P., Freking, B. A., Nonneman, D. J., Rohrer, G. A., & Piedrahita, J. A. (2006). Annotation of the Affymetrix1 porcine genome microarray. Animal Genetics, 37(4), 423-424. doi:10.1111/j.1365-2052.2006.01460.xNyholt, D. R. (2004). A Simple Correction for Multiple Testing for Single-Nucleotide Polymorphisms in Linkage Disequilibrium with Each Other. The American Journal of Human Genetics, 74(4), 765-769. doi:10.1086/383251Moskvina, V., & Schmidt, K. M. (2008). On multiple-testing correction in genome-wide association studies. Genetic Epidemiology, 32(6), 567-573. doi:10.1002/gepi.20331Benjamini, Y., & Yekutieli, D. (2005). Quantitative Trait Loci Analysis Using the False Discovery Rate. Genetics, 171(2), 783-790. doi:10.1534/genetics.104.03669

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

Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip

[EN] Background: The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP) and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses. Results: Three generations (F3, Backcross 1 and Backcross 2) of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes. Conclusions: The use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine genome annotation.This work was funded by MICINN projects AGL2008-04818-C03/GAN and CSD2007-00036. DPM was funded by a FPI Ph.D grant from the Spanish Ministerio de Educacion (BES-2009-025417). YR was funded by a FPU Ph.D grant from the Spanish Ministerio de Educacion (AP2008-01450). We want to thanks to Dr. Martien Groenen (Wageningen, NL) for the SNP annotation on porcine genome assembly, to Anna Mercade for her technical assistance with the SNPs genotyping and to Rita Benitez and Fabian Garcia for technical support.Fernández, A.; Pérez-Montarelo, D.; Barragan, C.; Ramayo-Caldas, Y.; Ibáñez-Escriche, N.; Castelló, A.; Noguera, J.... (2012). Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip. BMC Genetics. 13:1-11. https://doi.org/10.1186/1471-2156-13-41S11113Van Laere, A.-S., Nguyen, M., Braunschweig, M., Nezer, C., Collette, C., Moreau, L., … Andersson, L. (2003). A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature, 425(6960), 832-836. doi:10.1038/nature02064John, S., Shephard, N., Liu, G., Zeggini, E., Cao, M., Chen, W., … Kennedy, G. C. (2004). Whole-Genome Scan, in a Complex Disease, Using 11,245 Single-Nucleotide Polymorphisms: Comparison with Microsatellites. The American Journal of Human Genetics, 75(1), 54-64. doi:10.1086/422195Mercadé, A., Estellé, J., Noguera, J. L., Folch, J. M., Varona, L., Silió, L., … Pérez-Enciso, M. (2005). On growth, fatness, and form: A further look at porcine Chromosome 4 in an Iberian × Landrace cross. Mammalian Genome, 16(5), 374-382. doi:10.1007/s00335-004-2447-4Óvilo, C., Pérez-Enciso, M., Barragán, C., Clop, A., Rodríguez, C., Oliver, M. A., … Noguera, J. L. (2000). A QTL for intramuscular fat and backfat thickness is located on porcine Chromosome 6. Mammalian Genome, 11(4), 344-346. doi:10.1007/s003350010065Cristina, Ó., Oliver, A., Noguera, J. L., Clop, A., Barragán, C., Varona, L., … Silió, L. (2002). Test for positional candidate genes for body composition on pig chromosome 6. Genetics Selection Evolution, 34(4). doi:10.1186/1297-9686-34-4-465ÓVILO, C., FERNÁNDEZ, A., NOGUERA, J. L., BARRAGÁN, C., LETÓN, R., RODRÍGUEZ, C., … TORO, M. (2005). Fine mapping of porcine chromosome 6 QTL and LEPR effects on body composition in multiple generations of an Iberian by Landrace intercross. Genetical Research, 85(1), 57-67. doi:10.1017/s0016672305007330Óvilo, C., Fernández, A., Fernández, A. I., Folch, J. M., Varona, L., Benítez, R., … Silió, L. (2010). Hypothalamic expression of porcine leptin receptor (LEPR), neuropeptide Y (NPY), and cocaine- and amphetamine-regulated transcript (CART) genes is influenced by LEPR genotype. Mammalian Genome, 21(11-12), 583-591. doi:10.1007/s00335-010-9307-1Estellé, J., Fernández, A. I., Pérez-Enciso, M., Fernández, A., Rodríguez, C., Sánchez, A., … Folch, J. M. (2009). A non-synonymous mutation in a conserved site of theMTTPgene is strongly associated with protein activity and fatty acid profile in pigs. Animal Genetics, 40(6), 813-820. doi:10.1111/j.1365-2052.2009.01922.xEstellé, J., Pérez-Enciso, M., Mercadé, A., Varona, L., Alves, E., Sánchez, A., & Folch, J. M. (2006). Characterization of the porcine FABP5 gene and its association with the FAT1 QTL in an Iberian by Landrace cross. Animal Genetics, 37(6), 589-591. doi:10.1111/j.1365-2052.2006.01535.xMercadé, A., Pérez-Enciso, M., Varona, L., Alves, E., Noguera, J. L., Sánchez, A., & Folch, J. M. (2006). Adipocyte fatty-acid binding protein is closely associated to the porcine FAT1 locus on chromosome 41. Journal of Animal Science, 84(11), 2907-2913. doi:10.2527/jas.2005-663Evans, D. M., & Cardon, L. R. (2004). Guidelines for Genotyping in Genomewide Linkage Studies: Single-Nucleotide–Polymorphism Maps Versus Microsatellite Maps. The American Journal of Human Genetics, 75(4), 687-692. doi:10.1086/424696Gonzalez-Neira, A., Rosa-Rosa, J., Osorio, A., Gonzalez, E., Southey, M., Sinilnikova, O., … Benitez, J. (2007). Genomewide high-density SNP linkage analysis of non-BRCA1/2 breast cancer families identifies various candidate regions and has greater power than microsatellite studies. BMC Genomics, 8(1), 299. doi:10.1186/1471-2164-8-299Chioza, B. A., Aicardi, J., Aschauer, H., Brouwer, O., Callenbach, P., Covanis, A., … Everett, K. V. (2009). Genome wide high density SNP-based linkage analysis of childhood absence epilepsy identifies a susceptibility locus on chromosome 3p23-p14. Epilepsy Research, 87(2-3), 247-255. doi:10.1016/j.eplepsyres.2009.09.010Ramos, A. M., Crooijmans, R. P. M. A., Affara, N. A., Amaral, A. J., Archibald, A. L., Beever, J. E., … Groenen, M. A. M. (2009). Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS ONE, 4(8), e6524. doi:10.1371/journal.pone.0006524Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., … Sham, P. C. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. The American Journal of Human Genetics, 81(3), 559-575. doi:10.1086/519795Barrett, J. C., Fry, B., Maller, J., & Daly, M. J. (2004). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265. doi:10.1093/bioinformatics/bth457Andersson, L., Haley, C., Ellegren, H., Knott, S., Johansson, M., Andersson, K., … et, al. (1994). Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science, 263(5154), 1771-1774. doi:10.1126/science.8134840Marklund, L., Nyström, P.-E., Stern, S., Andersson-Eklund, L., & Andersson, L. (1999). Confirmed quantitative trait loci for fatness and growth on pig chromosome 4. Heredity, 82(2), 134-141. doi:10.1038/sj.hdy.6884630Fan, B., Onteru, S. K., Du, Z.-Q., Garrick, D. J., Stalder, K. J., & Rothschild, M. F. (2011). Genome-Wide Association Study Identifies Loci for Body Composition and Structural Soundness Traits in Pigs. PLoS ONE, 6(2), e14726. doi:10.1371/journal.pone.0014726Bidanel, J.-P., Milan, D., Iannuccelli, N., Amigues, Y., Boscher, M.-Y., Bourgeois, F., … Chevalet, C. (2001). Detection of quantitative trait loci for growth and fatness in pigs. Genetics Selection Evolution, 33(3). doi:10.1186/1297-9686-33-3-289Geldermann, H., Čepica, S., Stratil, A., Bartenschlager, H., & Preuss, S. (2010). Genome-wide mapping of Quantitative Trait Loci for fatness, fat cell characteristics and fat metabolism in three porcine F2 crosses. Genetics Selection Evolution, 42(1). doi:10.1186/1297-9686-42-31Quintanilla, R., Milan, D., & Bidanel, J.-P. (2002). A further look at quantitative trait loci affecting growth and fatness in a cross between Meishan and Large White pig populations. Genetics Selection Evolution, 34(2), 193. doi:10.1186/1297-9686-34-2-193Sławińska, A., Siwek, M., Knol, E. F., Roelofs-Prins, D. T., van Wijk, H. J., Dibbits, B., & Bednarczyk, M. (2009). Validation of the QTL on SSC4 for meat and carcass quality traits in a commercial crossbred pig population. Journal of Animal Breeding and Genetics, 126(1), 43-51. doi:10.1111/j.1439-0388.2008.00753.xMilan, D., Bidanel, J.-P., Iannuccelli, N., Riquet, J., Amigues, Y., Gruand, J., … Chevalet, C. (2002). Detection of quantitative trait loci for carcass composition traits in pigs. Genetics Selection Evolution, 34(6), 705. doi:10.1186/1297-9686-34-6-705Guo, T., Ren, J., Yang, K., Ma, J., Zhang, Z., & Huang, L. (2009). Quantitative trait loci for fatty acid composition in longissimus dorsi and abdominal fat: results from a White Duroc × Erhualian intercross F2population. Animal Genetics, 40(2), 185-191. doi:10.1111/j.1365-2052.2008.01819.xLiu, G., Kim, J. J., Jonas, E., Wimmers, K., Ponsuksili, S., Murani, E., … Schellander, K. (2008). Combined line-cross and half-sib QTL analysis in Duroc–Pietrain population. Mammalian Genome, 19(6), 429-438. doi:10.1007/s00335-008-9132-yKIM, C. W., HONG, Y. H., YUN, S.-I., LEE, S.-R., KIM, Y. H., KIM, M.-S., … CHANG, K.-T. (2006). Use of Microsatellite Markers to Detect Quantitative Trait Loci in Yorkshire Pigs. Journal of Reproduction and Development, 52(2), 229-237. doi:10.1262/jrd.17046Liu, G., Jennen, D. G. J., Tholen, E., Juengst, H., Kleinwächter, T., Hölker, M., … Wimmers, K. (2007). A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Animal Genetics, 38(3), 241-252. doi:10.1111/j.1365-2052.2007.01592.xXu, X. L., Xu, X. W., Pan, P. W., Li, K., Jiang, Z. H., Yu, M., … Liu, B. (2009). Porcine skeletal muscle differentially expressed geneCMYA1: isolation, characterization, mapping, expression and association analysis with carcass traits. Animal Genetics, 40(3), 255-261. doi:10.1111/j.1365-2052.2008.01825.xRamos, A. M., Bastiaansen, J. W. M., Plastow, G. S., & Rothschild, M. F. (2009). Genes located on a SSC17 meat quality QTL region are associated with growth in outbred pig populations. Animal Genetics, 40(5), 774-778. doi:10.1111/j.1365-2052.2009.01907.xRusso, V., Fontanesi, L., Scotti, E., Beretti, F., Davoli, R., Nanni Costa, L., … Buttazzoni, L. (2008). Single nucleotide polymorphisms in several porcine cathepsin genes are associated with growth, carcass, and production traits in Italian Large White pigs1. Journal of Animal Science, 86(12), 3300-3314. doi:10.2527/jas.2008-0920Tsai, F.-J., Yang, C.-F., Chen, C.-C., Chuang, L.-M., Lu, C.-H., Chang, C.-T., … Wu, J.-Y. (2010). A Genome-Wide Association Study Identifies Susceptibility Variants for Type 2 Diabetes in Han Chinese. PLoS Genetics, 6(2), e1000847. doi:10.1371/journal.pgen.1000847Silva, K. M., Bastiaansen, J. W. M., Knol, E. F., Merks, J. W. M., Lopes, P. S., Guimarães, S. E. F., & van Arendonk, J. A. M. (2010). Meta-analysis of results from quantitative trait loci mapping studies on pig chromosome 4. Animal Genetics, 42(3), 280-292. doi:10.1111/j.1365-2052.2010.02145.xFontanesi, L., Scotti, E., Buttazzoni, L., Dall’Olio, S., Davoli, R., & Russo, V. (2009). A single nucleotide polymorphism in the porcine cathepsin K (CTSK) gene is associated with back fat thickness and production traits in Italian Duroc pigs. Molecular Biology Reports, 37(1), 491-495. doi:10.1007/s11033-009-9678-0Ojeda, A., Estellé, J., Folch, J. M., & Pérez-Enciso, M. (2008). Nucleotide variability and linkage disequilibrium patterns at the porcineFABP5gene. Animal Genetics, 39(5), 468-473. doi:10.1111/j.1365-2052.2008.01752.xHan, S.-H., Shin, K.-Y., Lee, S.-S., Ko, M.-S., Jeong, D. K., Oh, H.-S., … Cho, I.-C. (2009). SINE indel polymorphism of AGL gene and association with growth and carcass traits in Landrace × Jeju black pig F2 population. Molecular Biology Reports, 37(1), 467-471. doi:10.1007/s11033-009-9644-xYamauchi, T., Kamon, J., Ito, Y., Tsuchida, A., Yokomizo, T., Kita, S., … Kadowaki, T. (2003). Cloning of adiponectin receptors that mediate antidiabetic metabolic effects. Nature, 423(6941), 762-769. doi:10.1038/nature01705Grundberg, E., Brandstrom, H., Ribom, E., Ljunggren, O., Mallmin, H., & Kindmark, A. (2004). Genetic variation in the human vitamin D receptor is associated with muscle strength, fat mass and body weight in Swedish women. European Journal of Endocrinology, 323-328. doi:10.1530/eje.0.1500323Muñoz, G., Alcázar, E., Fernández, A., Barragán, C., Carrasco, A., de Pedro, E., … Rodríguez, M. C. (2011). Effects of porcine MC4R and LEPR polymorphisms, gender and Duroc sire line on economic traits in Duroc×Iberian crossbred pigs. Meat Science, 88(1), 169-173. doi:10.1016/j.meatsci.2010.12.018Krzęcio, E., Koćwin-Podsiadła, M., Kurył, J., Zybert, A., Sieczkowska, H., & Antosik, K. (2008). The effect of interaction between genotype CAST/RsaI (calpastatin) and MYOG/MspI (myogenin) on carcass and meat quality in pigs free of RYR1T allele. Meat Science, 80(4), 1106-1115. doi:10.1016/j.meatsci.2008.05.002Wyszyńska-Koko, J., Pierzchała, M., Flisikowski, K., Kamyczek, M., Różycki, M., & Kurył, J. (2006). Polymorphisms in coding and regulatory regions of the porcineMYF6 andMYOG genes and expression of theMYF6 gene inm. longissimus dorsi versus productive traits in pigs. Journal of Applied Genetics, 47(2), 131-138. doi:10.1007/bf03194612IKEDA, T., KANAZAWA, T., OTSUKA, S., ICHII, O., HASHIMOTO, Y., & KON, Y. (2009). Expression of Caspase Family and Muscle- and Apoptosis-Specific Genes during Skeletal Myogenesis in Mouse Embryo. Journal of Veterinary Medical Science, 71(9), 1161-1168. doi:10.1292/jvms.71.1161Lin, Z., Lou, Y., & Squires, E. J. (2006). Functional polymorphism in porcine CYP2E1 gene: Its association with skatole levels. The Journal of Steroid Biochemistry and Molecular Biology, 99(4-5), 231-237. doi:10.1016/j.jsbmb.2005.07.001Aubert, J., Begriche, K., Knockaert, L., Robin, M. A., & Fromenty, B. (2011). Increased expression of cytochrome P450 2E1 in nonalcoholic fatty liver disease: Mechanisms and pathophysiological role. Clinics and Research in Hepatology and Gastroenterology, 35(10), 630-637. doi:10.1016/j.clinre.2011.04.015Latreille, M., Laberge, M.-K., Bourret, G., Yamani, L., & Larose, L. (2011). Deletion of Nck1 attenuates hepatic ER stress signaling and improves glucose tolerance and insulin signaling in liver of obese mice. American Journal of Physiology-Endocrinology and Metabolism, 300(3), E423-E434. doi:10.1152/ajpendo.00088.2010Akerfeldt, M. C., & Laybutt, D. R. (2011). Inhibition of Id1 Augments Insulin Secretion and Protects Against High-Fat Diet-Induced Glucose Intolerance. Diabetes, 60(10), 2506-2514. doi:10.2337/db11-008

Inference of hidden population substructure of the Iberian pig breed using multilocus microsatellite data

Abstract The census and structure of Iberian pig breed have experienced important changes along the last decades. Bayesian methods based on multilocus genotypes have been applied for ascertaining the actual breed structure and for identifying genetically distinctive populations. DNA samples from 170 Iberian pigs previously assigned to the strains or varieties Torbiscal, Guadyerbas, Retinto, Entrepelado and Lampiño and 64 Duroc pigs were genotyped for 36 microsatellites. A best partition of only five clusters was estimated in the clustering analysis at group level, when the previous assignation to populations was taken into account. But the individual-based assessment of population structure, ignoring the previous assignation of animals to populations, showed a more complex partition of ten clusters. Results of admixture analyses for partitioning individuals into the inferred clusters showed an important proportion of admixed individuals pre-assigned to the Retinto, Entrepelado and Lampiño varieties. The frequencies of private alleles of the MC1R gene also evidenced an important genetic flow between these varieties. The future definition of conservation units in the Iberian breed should consider these results. Additional key words: clustering, MC1R gene, mixture and admixture analysis, within-breed variation. Resumen Inferencia de la subestructura de la raza porcina Ibérica a partir de genotipos multigénicos de microsatélites El censo y la estructura de la raza porcina Ibérica han experimentado cambios importantes durante las últimas décadas. Se han utilizado métodos bayesianos basados en genotipos multigénicos para discernir la actual estructura de la raza e identificar en ella poblaciones genéticamente singulares. Con este objetivo, se genotiparon 36 microsatélites en muestras de ADN procedentes de 170 cerdos Ibéricos asignados previamente a las estirpes o variedades Torbiscal, Guadyerbas, Retinto, Entrepelado y Lampiño además de 64 cerdos Duroc. Cuando se tuvo en cuenta esta asignación previa en el análisis, se obtuvo una partición óptima de sólo cinco clases, una de las cuales agrupaba las variedades Retinto y Entrepelado. El análisis individual, ignorando la asignación previa de los animales a las razas o variedades, permitió inferir una partición más compleja de diez clases. Los resultados de los análisis con modelos de mestizaje mostraron una importante proporción de animales mestizos preasignados a las variedades Retinto, Entrepelado y Lampiño. Las frecuencias de los alelos específicos del gen MC1R confirmaron el importante flujo genético producido entre estas variedades. Una futura definición de unidades de conservación en la raza Ibérica debería considerar estos resultados. Palabras clave adicionales: análisis de mezcla y mestizaje de poblaciones, clusters, gen MC1R, variación intrarracial

Influencia de la composición de la dieta sobre el perfil de ácidos grasos y la expresión génica en tejidos adiposo, muscular y hepático de cerdos ibéricos

La composición de los tejidos animales es determinante en la calidad de los productos y está influida por varios factores como la dieta, el tipo genético, la edad y el sexo. En este trabajo se ha evaluado el efecto de la composición de ácidos grasos (AG) de la dieta de cerdos ibéricos en fase de cebo, sobre la composición de AG de los tejidos y la transcripción de genes codificantes para enzimas clave del metabolismo lipídico (SCD, ME1, FASN, ACACA, LEP, CPT, HADH). Se utilizaron 40 machos Torbiscal que recibieron diferentes dietas: saturada (S), monoinsaturada (M) y poliinsaturada (P). La composición de AG de los tejidos adiposo, hepático y muscular mostró grandes diferencias del grupo P respecto a M y S, que mostraron un perfil similar. La dieta afectó también a la expresión génica en hígado y tejido adiposo, sugiriendo una mayor expresión de enzimas lipogénicas en el grupo M y menor en el P. Estos resultados no explican la mayor capacidad del grupo S para la síntesis endógena de AG, que podría deducirse de los análisis de composición tisular.La composición de los tejidos animales es determinante en la calidad de los productos y está influida por varios factores como la dieta, el tipo genético, la edad y el sexo. En este trabajo se ha evaluado el efecto de la composición de ácidos grasos (AG) de la dieta de cerdos ibéricos en fase de cebo, sobre la composición de AG de los tejidos y la transcripción de genes codificantes para enzimas clave del metabolismo lipídico (SCD, ME1, FASN, ACACA, LEP, CPT, HADH). Se utilizaron 40 machos Torbiscal que recibieron diferentes dietas: saturada (S), monoinsaturada (M) y poliinsaturada (P). La composición de AG de los tejidos adiposo, hepático y muscular mostró grandes diferencias del grupo P respecto a M y S, que mostraron un perfil similar. La dieta afectó también a la expresión génica en hígado y tejido adiposo, sugiriendo una mayor expresión de enzimas lipogénicas en el grupo M y menor en el P. Estos resultados no explican la mayor capacidad del grupo S para la síntesis endógena de AG, que podría deducirse de los análisis de composición tisular

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