Design of a low-density SNP panel for intramuscular fat content and fatty acid composition of backfat in free-range Iberian pigs.

Intramuscular fat (IMF) content and fatty acids (FA) profile determine important sensory and technological characteristics of the meat, being interesting traits to be included in breeding programs for Iberian pig. In a previous study, we analyzed the longissimus dorsi transcriptome of Iberian pigs with divergent breeding values for IMF identifying 63 and 12 functional candidate genes and long non-coding RNA being differentially expressed. The first objective of this work was to use the RNA-seq data generated in that study in order to design a low-density panel with 50 single-nucleotide polymorphisms (SNP). The second aim was to evaluate the effects of this SNP panel on IMF content and backfat FA profile in a closed commercial population of Iberian pigs. The IMF content and backfat FA composition were determined in 940 Iberian pigs. A total of 837 SNPs were identified in the selection of genes and lncRNA. Out of the 50 selected SNP, 11 were monomorphic in the population and 2 failed in their genotyping. Association analyses were carried out for the 37 SNP segregating in the population (minor allele frequency, MAF > 0.05). Regarding IMF content, a significant additive effect (q-value < 0.05) was observed for ADIPOQ:g.124646194T > G SNP, in which the G allele was linked to an increase of 7.59% (additive effect expressed as a percentage of the mean of the trait). For the backfat FA composition, we observed 24 SNP with significant associations. The strongest effects were detected for the ELOVL6:g.112186423A > G and FASN_rs331694510G > A SNP. The A allele of both SNPs were associated to a lower percentage of palmitic (C16:0) and palmitoleic (C16:1) acids and an increase in oleic acid (C18:1). In addition, the AMPD3:g.49043886C > G SNP had significant effects on C16:0, stearic (C18:0), C18:1 and on the sum of saturated and monounsaturated fatty acids. Finally, significant effects of the EGR2:66286345G > T SNP on C18:0 and C18:1 and other minor FA were observed. Our findings reveal ADIPOQ:g.124646194T > G, ELOVL6:g.112186423A > G, and FASN_rs331694510G > A may be useful in breeding programs for Iberian pigs including FA profile and IMF content as selection goals, provided that their potential effects on other traits of interest are controlled.

Fat infiltration of muscle and fatty acid profile of cover fat are essential traits in Iberian pig industry. However, their inclusion in genetic selection schemes can be tangled, since their determination is laborious and expensive. Molecular markers can be a useful alternative to improve these traits. In a previous study, we analyzed the longissimus dorsi transcriptome of Iberian pigs with divergent breeding values for intramuscular fat (IMF) identifying 63 and 12 functional candidate genes and long non-coding RNA being differentially expressed. From this information, we designed a low-density panel with 50 single-nucleotide polymorphisms, which we subsequently evaluated for IMF content and fatty acids (FA) backfat profile of 940 pigs. The present research identified five polymorphisms mapped to ADIPOQ, ELOVL6, FASN, AMPD3, and EGR2 genes that are associated to IMF content and backfat FA profile.

Differences in the Loin Tenderness of Iberian Pigs Explained through Dissimilarities in Their Transcriptome Expression Profile.

Tenderness is one of the most important meat quality traits and it can be measured through shear force with the Warner-Bratzler test. In the current study, we use the RNA-seq technique to analyze the transcriptome of Longissimus dorsi (LD) muscle in two groups of Iberian pigs (Tough and Tender) divergent for shear force breeding values. We identified 200 annotated differentially expressed genes (DEGs) and 245 newly predicted isoforms. The RNAseq expression results of 10 genes were validated with quantitative PCR (qPCR). Functional analyses showed an enrichment of DE genes in biological processes related to proteolysis (CTSC, RHOD, MYH8, ACTC1, GADD45B, CASQ2, CHRNA9 and ANKRD1), skeletal muscle tissue development (ANKRD1, DMD, FOS and MSTN), lipid metabolism (FABP3 and PPARGC1A) and collagen metabolism (COL14A1). The upstream analysis revealed a total of 11 transcription regulatory factors that could regulate the expression of some DEGs. Among them, IGF1, VGLL3 and PPARG can be highlighted since they regulate the expression of genes involved in biological pathways that could affect tenderness. The experiment revealed a set of candidate genes and regulatory factors suggestive to search polymorphisms that could be incorporated in a breeding program for improving meat tenderness.

Genetic parameter estimation and gene association analyses for meat quality traits in open-air free-range Iberian pigs.

Meat quality of Iberian pigs is defined by the combination of their genetic characteristics and the particular production system. To carry out a genetic analysis of the main meat quality traits, we estimated their heritabilities, genetic correlations and the association effects of 32 selected SNPs of 12 candidate genes. A total of ten traits were measured in longissimus dorsi samples from 1,199 Iberian pigs fattened in the traditional free-range system: water holding capacity (thawing, cooking and centrifuge force water losses), instrumental colour (lightness L*, redness a* and yellowness b*), myoglobin content, shear force on cooked meat, and shear force and maximum compression force on dry-cured loin. Estimated heritability values were low to moderate (0.01 to 0.43) being the lowest for L* and the highest for cooking loss. Strong genetic correlations between water holding capacity traits (0.93 to 0.96) and between myoglobin content and a* (0.94) were observed. The association analyses revealed 19 SNPs significantly associated with different traits. Consistent and strong effects were observed between PRKAG3 SNPs (rs319678464G > C and rs330427832C > T), MYH3_rs81437544T > C, CASP3_rs319658214G > T and CTSL_rs332171512A > G and water losses. Also for CAPN1_rs81358667G > A and CASP3_rs319658214G > T and shear force. The SNPs mapping on PRKAG3 showed the highest effects on Minolta colour traits. Genotyping of these SNPs could be useful for the selection of Iberian young boars with similar estimated breeding values for productive traits.

Validez y fiabilidad del instrumento para evaluación de calidad de vida relacionada con la salud en epilepsia QOLIE-10 en pacientes adultos con epilepsia refractaria en un centro neurológico colombiano / Validity and reliability of the QOLIE-10 instrument for assessing health related quality of life in epilepsy of refractory epilepsy adult patients at a Colombian neurological center

Objetivo: Determinar la factibilidad, la fiabilidad y la validez de la versión en castellano del cuestionario breve de calidad de vida relacionada con la salud en epilepsia QOLIE-10 en una población de pacientes adultos con epilepsia refractaria de un centro de referencia de enfermedades neurológicas del Caribe colombiano. Pacientes y métodos: Se recogieron datos de 63 pacientes con epilepsia refractaria. Los 10 ítems del cuestionario QOLIE-10 se derivaron de la versión en castellano del cuestionario QOLIE-89. Se evaluó la factibilidad, la validez, el análisis factorial con comunalidades, la fiabilidad a través de la consistencia interna y la sensibilidad al cambio. Resultados: Se determinaron las características demográficas y clínicas, y se determinó la calidad de vida por medio de las frecuencias. Validez de constructo: análisis factorial y comunalidades, no se encontraron ítems no relevantes y se agruparon en una sola dimensión. Kaiser-Meyer-Olkin: 0,891. Esfericidad de Barlett: p < 0,001. Coeficiente de correlación intraclase media: 0,843. Fiabilidad: consistencia interna alfa de Cronbach, 0,98. Se validó el cuestionario QOLIE-10 de calidad de vida relacionada con la salud en adultos con epilepsia refractaria en castellano, con excelentes parámetros de fiabilidad y validez, y una administración rápida y fácil. Conclusiones: El cuestionario QOLIE-10 se considera una herramienta válida y fiable para su uso en la población de pacientes con epilepsia refractaria en Colombia. Se alienta a los profesionales de la salud a usar este cuestionario para examinar de manera rutinaria la influencia del proceso de enfermedad en la calidad de vida de los pacientes con epilepsia

Aim: To determine feasibility, reliability and validity of the shortened version of the Quality of Life in Epilepsy Inventory-10 (QOLIE-10) in a population of refractory epilepsy adult patients in the Colombian Caribbean. Patients and methods: Data were collected from 63 adult refractory epilepsy patients. The ten items of QOLIE-10 were derived from the Spanish version of QOLIE-89. We assess feasibility, validity, factorial analysis with communalities, reliability through internal consistency and sensitivity to change. Results: Clinical and demographic features were determined; quality of life was established through frequencies. Construct validity: through factor analysis communalities there were no items considered irrelevant and were grouped into one single dimension. Kaiser-Meyer-Olkin: 0.891. Bartlett’s test of sphericity: p < 0.001. Average intraclass correlation coefficient 0.843. The internal consistency reliability coefficient (Cronbach’s alpha) was 0.98. The QOLIE-10 questionnaire for the assessment of health-related quality of life was validated in Spanish for adult patients with refractory epilepsy with excellent validity, reliability parameters and easy, quick filling. Conclusions: The QOLIE-10 questionnaire is a valid and reliable tool for use in adult patients with refractory epilepsy in Colombia. Health professionals are encouraged to use this questionnaire to routinely examine the influences of the disease process in epilepsy patients

Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs.

One of the most important determinants of meat quality is the intramuscular fat (IMF) content. The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the present study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for their IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq allowed identifying ∼10,000 of the 25,878 annotated genes in the analyzed samples. In addition to this, 42.46% of the identified transcripts corresponded to newly predicted isoforms. Differential expression analyses revealed a total of 221 DE annotated genes and 116 DE new isoforms. Functional analyses identified an enrichment of overexpressed genes involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC, and ADIPOQ) in animals with a higher content of IMF and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB, and SEMA4D) in the animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. Co-expression networks analyses revealed six long non-coding RNAs (lncRNAs) (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, and ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1, and CIDEC. Analyses of the regulatory impact factors (RIFs) revealed 301 transcriptionally regulatory factors involved in expression differences, with five of them involved in adipogenesis (ARID5B, CREB1, VDR, ATF6, and SP1) and other three taking part of myogenesis and development of skeletal muscle (ATF3, KLF11, and MYF6). The results obtained provide relevant insights about the genetic mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors for further identification of polymorphisms susceptible of being incorporated in a selection program.

The temporal structure of pollution levels in developed cities.

Currently, the need for mobility can cause significant pollution levels in cities, with important effects on health and quality of life. Any approach to the study of urban pollution and its effects requires an analysis of spatial distribution and temporal variability. It is a crucial dilemma to obtain proven methodologies that allow an increase in the quality of the prediction and the saving of resources in the spatial and temporal sampling. This work proposes a new analytical methodology in the study of temporal structure. As a result, a model for estimating annual levels of urban traffic noise was proposed. The average errors are less than one decibel in all acoustics indicators. A new working methodology of urban noise has begun. Additionally, a general application can be found for the study of the impacts of pollution associated with traffic, with implications for urban design and possibly in economic and sociological aspects.