Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism.

Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences, transcriptional regulation and genetic polymorphisms that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth. Morphometric measures and blood samples were obtained and samples from Biceps femoris muscle were employed for compositional and transcriptome analysis by RNA-Seq technology. Phenotypic differences were evident at this early age, including greater body size and weight in IBxDU and greater Biceps femoris intramuscular fat and plasma cholesterol content in IB newborns. We detected 149 differentially expressed genes between IB and IBxDU neonates (p < 0.01 and Fold-Change > 1. 5). Several were related to adipose and muscle tissues development (DLK1, FGF21 or UBC). The functional interpretation of the transcriptomic differences revealed enrichment of functions and pathways related to lipid metabolism in IB and to cellular and muscle growth in IBxDU pigs. Protein catabolism, cholesterol biosynthesis and immune system were functions enriched in both genotypes. We identified transcription factors potentially affecting the observed gene expression differences. Some of them have known functions on adipogenesis (CEBPA, EGRs), lipid metabolism (PPARGC1B) and myogenesis (FOXOs, MEF2D, MYOD1), which suggest a key role in the meat quality differences existing between IB and IBxDU hams. We also identified several polymorphisms showing differential segregation between IB and IBxDU pigs. Among them, non-synonymous variants were detected in several transcription factors as PPARGC1B and TRIM63 genes, which could be associated to altered gene function. Taken together, these results provide information about candidate genes, metabolic pathways and genetic polymorphisms potentially involved in phenotypic differences between IB and IBxDU pigs associated to meat quality and production traits

Estimation of Genetic Parameters of Heat Tolerance for Production Traits in Canadian Holsteins Cattle.

Understanding how cows respond to heat stress has helped to provide effective herd management practices to tackle this environmental challenge. The possibility of selecting animals that are genetically more heat tolerant may provide additional means to maintain or even improve the productivity of the Canadian dairy industry, which is facing a shifting environment due to climate changes. The objective of this study was to estimate the genetic parameters for heat tolerance of milk, fat, and protein yields in Canadian Holstein cows. A total of 1.3 million test-day records from 195,448 first-parity cows were available. A repeatability test-day model fitting a reaction norm on the temperature-humidity index (THI) was used to estimate the genetic parameters. The estimated genetic correlations between additive genetic effect for production and for heat tolerance ranged from -0.13 to -0.21, indicating an antagonistic relationship between the level of production and heat tolerance. Heritability increased marginally as THI increased above its threshold for milk yield (0.20 to 0.23) and protein yield (0.14 to 0.16) and remained constant for fat yield (0.17). A Spearman rank correlation between the estimated breeding values under thermal comfort and under heat stress showed a potential genotype by environmental interaction. The existence of a genetic variability for heat tolerance allows for the selection of more heat tolerant cows

Genomic screening of allelic and genotypic transmission ratio distortion in horse

The phenomenon in which the expected Mendelian inheritance is altered is known as transmission ratio distortion (TRD). The TRD analysis relies on the study of the transmission of one of the two alleles from a heterozygous parent to the offspring. These distortions are due to biological mechanisms affecting gametogenesis, embryo development and/or postnatal viability, among others. In this study, TRD phenomenon was characterized in horses using SNP-by-SNP model by TRDscan v.2.0 software. A total of 1,041 Pura Raza Español breed horses were genotyped with 554,634 SNPs. Among them, 277 horses genotyped in trios (stallion-mare-offspring) were used to perform the TRD analysis. Our results revealed 140 and 42 SNPs with allelic and genotypic patterns, respectively. Among them, 63 displayed stallion-TRD and 41 exhibited mare-TRD, while 36 SNPs showed overall TRD. In addition, 42 SNPs exhibited heterosis pattern. Functional analyses revealed that the annotated genes located within the TRD regions identified were associated with biological processes and molecular functions related to spermatogenesis, oocyte division, embryonic development, and hormonal activity. A total of 10 functional candidate genes related to fertility were found. To our knowledge, this is the most extensive study performed to evaluate the presence of alleles and functional candidate genes with transmission ratio distortion affecting reproductive performance in the domestic horse.Fil: Laseca, Nora. Universidad de Córdoba; EspañaFil: Cánovas, Ángela. University of Guelph; CanadáFil: Valera, Mercedes. Universidad de Sevilla; EspañaFil: Id Lahoucine, Samir. Scotland’s Rural College; Reino UnidoFil: Perdomo González, Davinia Isabel. Universidad de Sevilla; EspañaFil: Fonseca, Pablo A. S.. Universidad de León; EspañaFil: Demyda-peyrás, Sebastian. Universidad de Córdoba; España. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Molina, Antonio. Universidad de Córdoba; Españ

Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

Background: The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content). Results: Our analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 log2fold-change). Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing (q-value < 0.05 and ±0.6 log2fold-change), being upregulated in HIGH pigs. Conclusions: The increased levels of specific ITGA5, LITAF, TIMP1 and ANXA2 mRNA isoforms in HIGH pigs is consistent with reports indicating that the overexpression of these four genes is associated with obesity and metabolic disorders in humans. A broader knowledge about the functional attributes of these mRNA variants would be fundamental to elucidate the consequences of transcript diversity on the determinism of porcine phenotypes of economic interest. Keywords: Alternative splicing, mRNA isoform, Swine, Differential expressioninfo:eu-repo/semantics/publishedVersio

Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

Background: the identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content). -Results: our analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 log2fold-change). Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing (q-value < 0.05 and ±0.6 log2fold-change), being upregulated in HIGH pigs. - conclusions: the increased levels of specific ITGA5, LITAF, TIMP1 and ANXA2 mRNA isoforms in HIGH pigs is consistent with reports indicating that the overexpression of these four genes is associated with obesity and metabolic disorders in humans. A broader knowledge about the functional attributes of these mRNA variants would be fundamental to elucidate the consequences of transcript diversity on the determinism of porcine phenotypes of economic interest

RNA-seq based detection of differentially expressed genes in the skeletal muscle of Duroc pigs with distinct lipid profiles

We have used a RNA-seq approach to investigate differential expression in the skeletal muscle of swine (N=52) with divergent lipid profiles i.e. HIGH (increased intramuscular fat and muscle saturated and monounsaturated fatty acid contents, higher serum lipid concentrations and fatness) and LOW pigs (leaner and with an increased muscle polyunsaturated fatty acid content). The number of mRNAs and non-coding RNAs (ncRNAs) expressed in the porcine gluteus medius muscle were 18,104 and 1,558, respectively. At the nominal level of significance (P-value≤0.05), we detected 1,430 mRNA and 12 non-coding RNA (ncRNA) transcripts as differentially expressed (DE) in the gluteus medius muscle of HIGH vs LOW pigs. This smaller contribution of ncRNAs to differential expression may have biological and technical reasons. We performed a second analysis, that was more stringent (P-value≤0.01 and fold-change≥ 1.5), and only 96 and 0 mRNA-and ncRNA-encoding genes happened to be DE, respectively. The subset of DE mRNA genes was enriched in pathways related with lipid (lipogenesis and triacylglycerol degradation) and glucose metabolism. Moreover, HIGH pigs showed a more lipogenic profile than their LOW counterparts

About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

Background The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we have compared the transcriptomic and eQTL profiles of two porcine tissues (skeletal muscle and liver) which typically show highly divergent expression profiles, in 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray-based measurements of hepatic and muscle mRNA levels. Since structural variation could have effects on gene expression, we have also investigated the co-localization of cis-eQTLs with copy number variant regions (CNVR) segregating in this Duroc population. Results The analysis of differential expresssion revealed the existence of 1204 and 1490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value < 0.05). By performing genome scans in 103 Duroc pigs with available expression and genotypic data, we identified 76 and 28 genome-wide significant cis-eQTLs regulating gene expression in the gluteus medius muscle and liver, respectively. Twelve of these cis-eQTLs were shared by both tissues (i.e. 42.8% of the cis-eQTLs identified in the liver were replicated in the gluteus medius muscle). These results are consistent with previous studies performed in humans, where 50% of eQTLs were shared across tissues. Moreover, we have identified 41 CNVRs in a set of 350 pigs from the same Duroc population, which had been genotyped with the Porcine SNP60 BeadChip by using the PennCNV and GADA softwares, but only a small proportion of these CNVRs co-localized with the cis-eQTL signals. Conclusion Despite the fact that there are considerable differences in the gene expression patterns of the porcine liver and skeletal muscle, we have identified a substantial proportion of common cis-eQTLs regulating gene expression in both tissues. Several of these cis-eQTLs influence the mRNA levels of genes with important roles in meat (CTSF) and carcass quality (TAPT1), lipid metabolism (TMEM97) and obesity (MARC2), thus evidencing the practical importance of dissecting the genetic mechanisms involved in their expression.Part of the research presented in this publication was funded by grants AGL2013–48742-C2–1-R and AGL2013–48742-C2–2-R awarded by the Spanish Ministry of Economy and Competitivity. We also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016–2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics. Ángela Cánovas was funded under the Juan de la Cierva program awarded by the Spanish Ministry of Science. Taina F Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education (MEC) of the Federal Government of Brazil. Rayner González-Prendes was funded by a FPU Ph.D. grant from the Spanish Ministry of Education (FPU12/00860). Emilio Mármol-Sánchez was funded by a FPU Ph.D. grant from the Spanish Ministry of Education (FPU15/01733)

Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i. e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (-104 Mb), SSC5 (-15 Mb) and SSC13 (-137 Mb), while several additional regions were signifcantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associatlons found for LD and GM traits, a feature that refiects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism

Impacto de la COVID-19 en los servicios de cirugía cardiovascular en España: Análisis de los grupos relacionados con el diagnóstico (Estudio SECCE-COVID-19 fase 2)

Introducción y objetivos La pandemia por COVID-19 causada por infección del virus SARS-CoV-2 ha saturado al sistema sanitario español, afectándose la atención de las enfermedades cardiovasculares. Queremos cuantificar el impacto de la pandemia en el número de las intervenciones quirúrgicas cardíacas analizando los grupos relacionados con el diagnóstico (GRD) más prevalentes de nuestra especialidad. Métodos A instancias de la Sociedad Española de Cirugía Cardiovascular y Endovascular, se solicitó a todos los centros nacionales que quisieron participar, los datos de los códigos de GRD números 162 (cirugía sobre válvulas cardíacas con infarto o diagnóstico complejo), 163 (cirugía sobre válvulas cardíacas sin infarto o diagnóstico complejo), 165 (bypass coronario con infarto o diagnóstico complejo), 166 (bypass coronario sin infarto o diagnóstico complejo) y 167 (otros procedimientos cardiotorácicos o vasculares torácicos) entre el 1 de marzo de 2020 y el 30 de septiembre de 2020 (siete meses), y como período control las mismas fechas de 2019. Resultados Se recibieron los datos de 24 hospitales, 22 públicos y dos privados. Existió un descenso global en el número de intervenciones del 30% (rango -19 a -42%, p < 0,001) de 4.648 en 2019 a 3.262 en 2020 (-1.386 de diferencia), siendo +7% para el GRD 162 (p = 0,500), -37% para el 163 (p = 0,001), -9% para el 165 (p = 0,304), -32% para el 166 (p = 0,001), y -16% para el 167 (p = 0,062). Conclusiones Existió un descenso global de cirugías estadísticamente significativo en 2020 del 30% respecto del 2019 entre el 1 de marzo y el 30 de septiembre

I.amAble: la ciencia (química) al alcance de toda la sociedad

En este proyecto de innovación, que nace con vocación de continuar en años sucesivos, se persigue mejorar la calidad de la formación de los estudiantes de la Facultad de Ciencias Químicas (F. CC.QQ.) en el ámbito de la docencia teórico-práctica y de la divulgación científica. El trabajo ha consistido en la preparación de unos experimentos prácticos para llevarlos a cabo en centros educativos no universitarios en los que se ha tenido en cuenta la participación conjunta de personas con y sin diversidad funcional, desde una perspectiva inclusiva colaborativa. Estas actividades las han realizado los estudiantes bajo la supervisión de profesores (PDI) y personal de administración y servicios (PAS). Los experimentos se han recogido en fichas didácticas para facilitar su desarrollo y aplicación por parte de otros usuarios. En estas fichas se explica detalladamente cómo realizar las experiencias en formato de taller. Las fichas de los talleres realizados están disponibles en una página web vinculada a la Universidad Complutense bajo el título I.amAble (iamable.ucm.es). Está página ha sido construida por un estudiante de la Facultad de Informática , bajo la supervisión de profesionales, tanto de esa facultad como del Instituto de Tecnología del Conocimiento, y está abierta a contribuciones similares de otras facultades y otras instituciones. La página web está diseñada de manera que resulte lo más intuitiva y accesible posible para todo tipo de público. Entre todos los experimentos se han elegido cuatro para llevarlos a la práctica en centros educativos como actividades inclusivas en las que han participado conjuntamente personas con y sin discapacidad. Con este proyecto se pretende mejorar la calidad docente al ofrecer a los estudiantes la posibilidad de aprender enseñando mediante una actividad semipresencial. El desarrollo por parte de los estudiantes de competencias transversales en educación y en divulgación de la ciencia facilitarán algunas salidas profesionales en el ámbito educativo formal (centros de enseñanza) o informal (museos, animación sociocultural). Otro aspecto importante a resaltar es la potenciación de la colaboración entre todos los miembros de la institución universitaria. Este proyecto pretende contribuir a la mejora de la cultura científica, así como al establecimiento de puentes entre la UCM y la sociedad a la que debe servir. Finalmente, es importante subrayar que incidirá en la inclusión de las personas con discapacidad como parte de la sociedad, a través del acercamiento compartido a la ciencia (Dimensiones de inclusión social y derechos de Schalock; NAVAS MACHO, P. y otros, 2012. Derechos de las personas con discapacidad intelectual: implicaciones de la Convención de Naciones Unidas. Siglo Cero. 43 (243): 7-28.)