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Background: The composition and distribution of fatty acids (FA) are important factors determining the quality, flavor, and nutrient value of meat. In addition, FAs synthesized in the body participate in energy metabolism and are involved in different regulatory pathways in the form of signaling molecules or by acting as agonist or antagonist ligands of different nuclear receptors. Finally, synthesis and catabolism of FAs affect adaptive immunity by regulating lymphocyte metabolism. The present study performed genome-wide association studies using FA profiles of blood, liver, backfat and muscle from 432 commercial Duroc pigs., Results: Twenty-five genomic regions located on 15 Sus scrofa chromosomes (SSC) were detected. Annotation of the quantitative trait locus (QTL) regions identified 49 lipid metabolism-related candidate genes. Among these QTLs, four were identified in more than one tissue. The ratio of C20:4n-6/C20:3n-6 was associated with the region on SSC2 at 7.56-14.26 Mb for backfat, liver, and muscle. Members of the fatty acid desaturase gene cluster (FADS1, FADS2, and FADS3) are the most promising candidate genes in this region. Two QTL regions on SSC14 (103.81-115.64 Mb and 100.91-128.14 Mb) were identified for FA desaturation in backfat and muscle. In addition, two separate regions on SSC9 at 0 - 14.55 Mb and on SSC12 at 0-1.91 Mb were both associated with the same multiple FA traits for backfat, with candidate genes involved in de novo FA synthesis and triacylglycerol (TAG) metabolism, such as DGAT2 and FASN. The ratio C20:0/C18:0 was associated with the region on SSC5 at 64.84-78.32 Mb for backfat. Furthermore, the association of the C16:0 content with the region at 118.92-123.95 Mb on SSC4 was blood specific. Finally, candidate genes involved in de novo lipogenesis regulate T cell differentiation and promote the generation of palmitoleate, an adipokine that alleviates inflammation., Conclusions: Several SNPs and candidate genes were associated with lipid metabolism in blood, liver, backfat, and muscle. These results contribute to elucidating the molecular mechanisms implicated in the determination of the FA profile in different pig tissues and can be useful in selection programs that aim to improve health and energy metabolism in pigs., (© 2024. The Author(s).)

Obesity is a risk factor for highly prevalent age-related neurodegenerative diseases, the pathogenesis of whichinvolves mitochondrial dysfunction and protein oxidative damage. Lipoxidation, driven by high levels of peroxidizable unsaturated fatty acids and low antioxidant protection of the brain, stands out as a significant risk factor. To gain information on the relationship between obesity and brain molecular damage, in a porcine model of obesity we evaluated (1) the level of mitochondrial respiratory chain complexes, as the main source of free radical generation, by Western blot; (2) the fatty acid profile by gas chromatography; and (3) the oxidative modification of proteins by mass spectrometry. The results demonstrate a selectively higher amount of the lipoxidation-derived biomarker malondialdehyde-lysine (MDAL) (34% increase) in the frontal cortex, and positive correlations between MDAL and LDL levels and body weight. No changes were observed in brain fatty acid profile by the high-fat diet, and the increased lipid peroxidative modification was associated with increased levels of mitochondrial complex I (NDUFS3 and NDUFA9 subunits) and complex II (flavoprotein). Interestingly, introducing n3 fatty acids and a probiotic in the high-fat diet prevented the observed changes, suggesting that dietary components can modulate protein oxidative modification at the cerebral level and opening new possibilities in neurodegenerative diseases' prevention., Competing Interests: M.R.P. and J.A.M.M. are employees of Laboratorios Ordesa. The rest of the authors declare no conflicts of interest.

Preweaning piglet mortality (PWM), a trait highly related to litter size, is one of the main concerns associated with productive efficiency and animal welfare in commercial pig farms. The objectives of this work were to study piglet survival at the farm level, to establish a survival rate (SR) as a target indicator to be improved, and to model it based on other reproductive parameters. Analyzed data corresponded to 580 Spanish commercial farms with a total inventory of 809,768 sows. These farms showed a mean SR of 85.70% piglets born alive (BA), which decreased to 81.81% when total piglets born (TB) were considered. The SR was strongly associated with prolificacy (P < 0.01), the parities with the highest prolificacy being those that had the lowest SR. Thus, the highest correlations were for the SR of piglets BA in the third and fourth parities (r = -0.460 and r = -0.452, respectively, P < 0.01), and for the SR of piglets TB in the fourth parity (r = -0.546, P < 0.01), which was the one with the highest prolificacy. The values corresponding to the quartile of farms with the highest SR within the most productive farms were established as targets to be improved, which were ≥88.5% of piglets BA and 83.2% of piglets TB. Nevertheless, the direct associations shown between the piglet's survival and prolificacy and other productive factors, such as the age of piglets at weaning, the farrowings per sow and year and the farrowing interval, suggest the convenience of modeling the risk of PWM on farms to have its own target of survival index to be improved., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model., (© 2024. The Author(s).)

Background: Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments., Results: Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene., Conclusions: In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems., (© 2023. The Author(s).)

Weaned piglets, being immature, demand careful handling to mitigate post-weaning stress in order to avoid immunosuppression and the use of antimicrobials to palliate the effects of disease outbreaks due to poor management. The objective of this work is to design a quick scan calculator or multi-criteria evaluation model of management for weaned piglets, founded on 10 critical indices covering post-weaning management aspects based on hygienic measures and management of facilities and animals. These include pre-weaning handling, batch management, biosecurity, water management, feed management, health program, stockmen training, temperature, ventilation, and floor conditions and density to relate handling and hygiene practices with farm performance and the consumption of veterinary medication. Each index carries a maximum score of ten, with evaluations derived from different management factors that make up each index (from three to eight factors were evaluated per index). Their cumulative score reflects the degree of adequacy of on-farm management. Therefore, a perfectly managed farm would achieve 100 points. The calculator underwent testing on 23 intensive farms with a total population of close to 16,000 sows and more than 400,000 weaned piglets, revealing the highest mean scores in floor conditions and density (8.03 out of 10) and pre-weaning handling and health programs (6.87 and 6.28, respectively). Conversely, the lowest scores corresponded to temperature, ventilation, water management, and stockmen training (4.08, 4.32, 4.81, and 4.93, respectively). The assessed farms averaged a global score of 56.12 out of 100 (from 37.65 to 76.76). The calculator's global score correlated with key post-weaning productivity and piglet health indicators, such as the feed conversion ratio, mortality rate, and piglet production cost, with r values of -0.442, -0.437, and -0.435, respectively ( p < 0.05). Additionally, it negatively correlated with medication costs per piglet (r = -0.414; p < 0.05) and positively with annual farm productivity (r = 0.592; p < 0.01). To enhance management, hygiene, and prevention, farms should prioritize addressing indices with the lowest scores, thereby reducing medication consumption and enhancing productivity and health outcomes. Additionally, this quick scan calculator can be used for benchmarking purposes.

C-reactive protein (CRP) is an evolutionary highly conserved protein. Like humans, CRP acts as a major acute phase protein in pigs. While CRP regulatory mechanisms have been extensively studied in humans, little is known about the molecular mechanisms that control pig CRP gene expression. The main goal of the present work was to study the regulatory mechanisms and identify functional genetic variants regulating CRP gene expression and CRP blood levels in pigs. The characterization of the porcine CRP proximal promoter region revealed a high level of conservation with both cow and human promoters, sharing binding sites for transcription factors required for CRP expression. Through genome-wide association studies and fine mapping, the most associated variants with both mRNA and protein CRP levels were localized in a genomic region 39.3 kb upstream of CRP . Further study of the region revealed a highly conserved putative enhancer that contains binding sites for several transcriptional regulators such as STAT3, NF-kB or C/EBP-β. Luciferase reporter assays showed the necessity of this enhancer-promoter interaction for the acute phase induction of CRP expression in liver, where differences in the enhancer sequences significantly modified CRP activity. The associated polymorphisms disrupted the putative binding sites for HNF4α and FOXA2 transcription factors. The high correlation between HNF4α and CRP expression levels suggest the participation of HNF4α in the regulatory mechanism of porcine CRP expression through the modification of its binding site in liver. Our findings determine, for the first time, the relevance of a distal regulatory element essential for the acute phase induction of porcine CRP in liver and identify functional polymorphisms that can be included in pig breeding programs to improve immunocompetence., Competing Interests: Author MCAMB was employed by the company Hendrix Genetics. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Hernández-Banqué, Jové-Juncà, Crespo-Piazuelo, González-Rodríguez, Ramayo-Caldas, Esteve-Codina, Mercat, Bink, Quintanilla and Ballester.)

Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms (SNPs) and the gut microbiota, but little is known about the relationship between structural variants and fecal microbial traits. The main goal of this study was to explore the association between porcine genome copy number variants (CNVs) and the diversity and composition of pig fecal microbiota. For this purpose, we used whole-genome sequencing data to undertake a comprehensive identification of CNVs followed by a genome-wide association analysis between the estimated CNV status and the fecal bacterial diversity in a commercial Duroc pig population. A CNV predicted as gain (DUP) partially harboring ABCC2-DNMBP loci was associated with richness ( P  = 5.41 × 10 -5 , false discovery rate [FDR] = 0.022) and Shannon α-diversity ( P  = 1.42 × 10 -4 , FDR = 0.057). The in silico predicted gain of copies was validated by real-time quantitative PCR (qPCR), and its segregation, and positive association with the richness and Shannon α-diversity of the porcine fecal bacterial ecosystem was confirmed in an unrelated F1 (Duroc × Iberian) cross. Our results advise the relevance of considering the role of host-genome structural variants as potential modulators of microbial ecosystems and suggest the ABCC2-DNMBP CNV as a host-genetic factor for the modulation of the diversity and composition of the fecal microbiota in pigs. IMPORTANCE A better understanding of the environmental and host factors modulating gut microbiomes is a topic of greatest interest. Recent evidence suggests that genetic variation in the pig genome partially controls the composition of porcine gut microbiota. However, since previous studies have been focused on the association between single nucleotide polymorphisms and the fecal microbiota, little is known about the relationship between other sources of genetic variation, like the structural variants and microbial traits. Here, we identified, experimentally validated, and replicated in an independent population a positive link between the gain of copies of ABCC2-DNMBP loci and the diversity and composition of pig fecal microbiota. Our results advise the relevance of considering the role of host-genome structural variants as putative modulators of microbial ecosystems and open the possibility of implementing novel holobiont-based management strategies in breeding programs for the simultaneous improvement of microbial traits and host performance., Competing Interests: The authors declare no conflict of interest.

Background: Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available., Methods: We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70 k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only., Results: Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy., Conclusions: Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default., (© 2023. The Author(s).)

In general, the relationship between the predicted functional consequences of missense mutations mapping to genes known to be involved in human diseases and the severity of disease manifestations is weak. In this study, we tested in pigs whether missense single nucleotide polymorphisms (SNPs), predicted to have consequences on the function of genes related to lipid metabolism are associated with lipid phenotypes. Association analysis demonstrated that nine out of 72 nominally associated SNPs were classified as "highly" or "very highly consistent" in silico-predicted functional mutations and did not show association with lipid traits expected to be affected by inactivation of the corresponding gene. Although the lack of endophenotypes and the limited sample size of certain genotypic classes might have limited to some extent the reach of the current study, our data indicate that present-day bioinformatic tools have a modest ability to predict the impact of missense mutations on complex phenotypes., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Pig industry is facing new challenges that make necessary to reorient breeding programs to produce more robust and resilient pig populations. The aim of the present work was to study the genetic determinism of lymphocyte subpopulations in the peripheral blood of pigs and identify genomic regions and biomarkers associated to them. For this purpose, we stained peripheral blood mononuclear cells to measure ten immune-cell-related traits including the relative abundance of different populations of lymphocytes, the proportions of CD4 + T cells and CD8 + T cells, and the ratio of CD4 + /CD8 + T cells from 391 healthy Duroc piglets aged 8 weeks. Medium to high heritabilities were observed for the ten immune-cell-related traits and significant genetic correlations were obtained between the proportion of some lymphocytes populations. A genome-wide association study pointed out 32 SNPs located at four chromosomal regions on pig chromosomes SSC3, SSC5, SSC8, and SSCX as significantly associated to T-helper cells, memory T-helper cells and γδ T cells. Several genes previously identified in human association studies for the same or related traits were located in the associated regions, and were proposed as candidate genes to explain the variation of T cell populations such as CD4, CD8A, CD8B, KLRC2, RMND5A and VPS24 . The transcriptome analysis of whole blood samples from animals with extreme proportions of γδ T, T-helper and memory T-helper cells identified differentially expressed genes ( CAPG, TCF7L1, KLRD1 and CD4 ) located into the associated regions. In addition, differentially expressed genes specific of different T cells subpopulations were identified such as SOX13 and WC1 genes for γδ T cells. Our results enhance the knowledge about the genetic control of lymphocyte traits that could be considered to optimize the induction of immune responses to vaccines against pathogens. Furthermore, they open the possibility of applying effective selection programs for improving immunocompetence in pigs and support the use of the pig as a very reliable human biomedical model., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Ballester, Jové-Juncà, Pascual, López-Serrano, Crespo-Piazuelo, Hernández-Banqué, González-Rodríguez, Ramayo-Caldas and Quintanilla.)

The contribution of microRNAs (miRNAs) to mRNA post-transcriptional regulation has often been explored by the post hoc selection of downregulated genes and determining whether they harbor binding sites for miRNAs of interest. This approach, however, does not discriminate whether these mRNAs are also downregulated at the transcriptional level. Here, we have characterized the transcriptional and post-transcriptional changes in mRNA expression in two porcine tissues: gluteus medius muscle of fasted and fed Duroc gilts and adipose tissue of lean and obese Duroc-Göttingen minipigs. Exon-intron split analysis of RNA-seq data allowed us to identify downregulated mRNAs with high post-transcriptional signals in fed or obese states, and we assessed whether they harbor binding sites for upregulated miRNAs in any of these two physiological states. We found 26 downregulated mRNAs with high post-transcriptional signals in the muscle of fed gilts and 21 of these were predicted targets of miRNAs upregulated in fed pigs. For adipose tissue, 44 downregulated mRNAs in obese minipigs displayed high post-transcriptional signals, and 25 of these were predicted targets of miRNAs upregulated in the obese state. These results suggest that the contribution of miRNAs to mRNA repression is more prominent in the skeletal muscle system. Finally, we identified several genes that may play relevant roles in the energy homeostasis of the pig skeletal muscle (DKK2 and PDK4) and adipose (SESN3 and ESRRG) tissues. By differentiating transcriptional from post-transcriptional changes in mRNA expression, exon-intron split analysis provides a valuable view of the regulation of gene expression, complementary to canonical differential expression analyses., (© 2022 Stichting International Foundation for Animal Genetics.)

Introduction: In patients with urinary continent channel (UCC) and Malone Antegrade Continent Enema (MACE) procedures, two separate abdominal stomas are needed. The umbilicus is a preferred site for single channel stomas given the ability to conceal the stoma. However, there are no studies describing outcomes of both stomas being created in the umbilicus. We aimed to describe our experience in patients who underwent UCC and MACE stomas both placed in the umbilicus., Methods: A retrospective review from 2009 to 2020 was performed in our institution for patients who underwent the creation of UCC and MACE stomas simultaneously in the umbilicus. The variation in the technique involves two V-skin shaped flaps in the umbilicus; the MACE and UCC stomas are delivered from both flaps and placed at the right and left side respectively. Patients with greater than 3 months of follow-up were included in the study., Results: There were 17 patients identified with the median age of 13.5 years and a median follow-up of 32.8 months. The mean BMI percentile was 89.5%. Monti technique and split appendix with cecal extension were utilized in 8 (47.1%) and 7 (41.2%) patients respectively and 13 (76.5%) patients required concurrent urological procedures. All channel-related complications occurred within a mean time of 15.7 months. Skin-level stenosis in the MACE occurred in 5 (29.4%) events, and all were successfully managed by placing an indwelling catheter for up to two weeks. There were 2 (11.8%) complications related to UCC, which required subfascial minor surgical revision. The rate of patients with symptomatic UTI decreased 35.3% postoperatively, and no new onset of UTI occurred in patients without a prior history of UTI. During follow-up, all patients remained dry between CIC, however one had occasional leakage related to delay in catheterization. Total fecal continence was achieved in 14 (82.3%) patients. Additionally, 3 (16.6%) patients experienced improvement in fecal continence with sporadic soiling episodes., Comments: Placement of UCC and MACE stomas in the umbilicus demonstrate a percentage of complication of 7/34 (20.6%) with only 2 patients requiring surgical intervention, comparable to the standard. UTI rate decreased in patients with a prior history of UTI. We believe the patients' perspective and degree of satisfaction will fully determine the benefits of this technique., Conclusions: Simultaneous UCC and MACE stomas placed at the umbilicus showed good functional outcomes and similar complication rates to traditional approach where stomas were placed separately in the abdominal wall., (Copyright © 2022. Published by Elsevier Ltd.)

Prcis: Glaucoma cascade screening in first-degree relatives (FDRs) of young Haitian glaucoma patients had high yield for diagnosing manifest and suspected glaucoma in 30.8% of those screened despite modest participation., Purpose: To evaluate the outcomes of glaucoma cascade screening in FDRs (parents, siblings, and offspring) of Haitian juvenile open-angle glaucoma (JOAG) patients., Patients and Methods: Consecutive index patients (Haitians with JOAG) were identified, and the number/type of FDRs residing in South Florida were recorded. These FDRs were invited for free glaucoma screening, which included a comprehensive ophthalmic exam, gonioscopy, automated visual field testing and optical coherence tomographic analysis of the retinal nerve fiber layers. FDR characteristics and clinical findings from screening are reported., Results: A total of 77 FDRs were invited, 26 (33.8%) agreed to undergo screening (18 females, 9 males), which revealed 2 (7.7%) with manifest glaucoma (mean age 77.5 y; one of whom was previously unaware of his glaucoma diagnosis), 6 (23.1%) with suspected glaucoma (mean age 29.8±18.3 y), and 18 (69.2%) without manifest or suspected glaucoma (mean age 37.2±21.8 y). Siblings of index patients were least likely to participate in cascade glaucoma screening when compared with index patients' parents or offspring. FDR eyes with manifest glaucoma had significantly worse best-corrected visual acuities, higher intraocular pressures, thinner central corneal thicknesses, and thinner circumferential papillary retinal nerve fiber layer thicknesses than those without glaucoma., Conclusion: Glaucoma cascade screening of Haitian JOAG patients' FDRs revealed that 30.8% had suspected or manifest glaucoma. Future efforts centered on provider-initiated recruitment and improving public glaucoma awareness and education may increase screening participation., Competing Interests: Disclosure: The authors declare no conflict of interest., (Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc.)

Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products., (© 2022. The Author(s).)

In recent years, the increase in awareness of antimicrobial resistance together with the societal demand of healthier meat products have driven attention to health-related traits in livestock production. Previous studies have reported medium to high heritabilities for these traits and described genomic regions associated with them. Despite its genetic component, health- and immunity-related traits are complex and its study by association analysis with genomic markers may be missing some information. To analyse multiple phenotypes and gene-by-gene interactions, systems biology approaches, such as the association weight matrix (AWM), allows combining genome wide association study results with network inference algorithms. The present study aimed to identify gene networks, key regulators and candidate genes associated to immunocompetence in pigs by integrating multiple health-related traits, enriched for innate immune phenotypes, using the AWM approach. The co-association network analysis unveiled a network comprised of 3,636 nodes (genes) and 451,407 edges (interactions), including a total of 246 regulators. From these, five genes ( ARNT2 , BRMS1L , MED12L , SUPT3H and TRIM25 ) were selected as key regulators as they were associated with the maximum number of genes with the minimum overlapping (1,827 genes in total). The five regulators were involved in pathways related to immunity such as lymphocyte differentiation and activation, platelet activation and degranulation, megakaryocyte differentiation, FcγR-mediated phagocytosis and response to nitric oxide, among others, but also in immunometabolism. Furthermore, we identified genes co-associated with the key regulators previously reported as candidate genes (e.g., ANGPT1, CD4, CD36, DOCK1 , PDE4B, PRKCE, PTPRC and SH2B3 ) for immunity traits in humans and pigs, but also new candidate ones (e.g., ACSL3 , CXADR , HBB , MMP12 , PTPN6 , WLS ) that were not previously described. The co-association analysis revealed new regulators associated with health-related traits in pigs. This approach also identified gene-by-gene interactions and candidate genes involved in pathways related to cell fate and metabolic and immune functions. Our results shed new light in the regulatory mechanisms involved in pig immunity and reinforce the use of the pig as biomedical model., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Crespo-Piazuelo, Ramayo-Caldas, González-Rodríguez, Pascual, Quintanilla and Ballester.)

Background: The gut microbiota influences host performance playing a relevant role in homeostasis and function of the immune system. The aim of the present work was to identify microbial signatures linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs., Results: To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and the relative abundance of gut bacterial communities in 389 pigs genotyped for 70K SNPs. The heritability (h 2 ; proportion of phenotypic variance explained by the host genetics) and microbiability (m 2 ; proportion of variance explained by the microbial composition) showed similar values for most of the analyzed immunity traits, except for both IgM and IgG in plasma that was dominated by the host genetics, and the haptoglobin in serum which was the trait with larger m 2 (0.275) compared to h 2 (0.138). Results from the MWAS suggested a polymicrobial nature of the immunocompetence in pigs and revealed associations between pigs gut microbiota composition and 15 of the analyzed traits. The lymphocytes phagocytic capacity (quantified as mean fluorescence) and the total number of monocytes in blood were the traits associated with the largest number of taxa (6 taxa). Among the associations identified by MWAS, 30% were confirmed by an information theory network approach. The strongest confirmed associations were between Fibrobacter and phagocytic capacity of lymphocytes (r = 0.37), followed by correlations between Streptococcus and the percentage of phagocytic lymphocytes (r = -0.34) and between Megasphaera and serum concentration of haptoglobin (r = 0.26). In the interaction network, Streptococcus and percentage of phagocytic lymphocytes were the keystone bacterial and immune-trait, respectively., Conclusions: Overall, our findings reveal an important connection between gut microbiota composition and immunity traits in pigs, and highlight the need to consider both sources of information, host genome and microbial levels, to accurately characterize immunocompetence in pigs., (© 2021. The Author(s).)

Background: Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3'UTR binding sites can disrupt canonical conserved miRNA-mRNA pairings, and thus modify gene expression patterns. However, to date such polymorphic sites in miRNA genes and their association with gene expression phenotypes and complex traits are poorly characterized in pigs., Results: By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we identified 285 single nucleotide polymorphisms (SNPs) that map to miRNA loci, and 109,724 SNPs that are located in predicted 7mer-m8 miRNA binding sites within porcine 3'UTR. In porcine miRNA genes, SNP density is reduced compared with their flanking non-miRNA regions. By sequencing the genomes of five Duroc boars, we identified 12 miRNA SNPs that were subsequently genotyped in their offspring (N = 345, Lipgen population). Association analyses of miRNA SNPs with 38 lipid-related traits and hepatic and muscle microarray expression phenotypes recorded in the Lipgen population were performed. The most relevant detected association was between the genotype of the rs319154814 (G/A) SNP located in the apical loop of the ssc-miR-326 hairpin precursor and PPP1CC mRNA levels in the liver (q-value = 0.058). This result was subsequently confirmed by qPCR (P-value = 0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits., Conclusions: Our findings show a reduced variability of porcine miRNA genes, which is consistent with strong purifying selection, particularly in the seed region that plays a critical role in miRNA binding. Although it is generally assumed that SNPs mapping to the seed region are those with the most pronounced consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is significantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confirmation of such an interaction is reported in humans but not in pigs, this result highlights the need to further investigate the functional effects of miRNA polymorphisms that are located outside the seed region on gene expression in pigs.

Background: Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical "single-gene-single-trait" approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately., Results: In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP-P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance., Conclusions: Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits. Video Abstract.

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a "One Health" perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a "One Health" perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.

The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., prediction of a phenotype of interest) from taxonomic abundances has become increasingly common in the microbiome field. However, a gap exists between supervised and classical unsupervised analyses, based on computing ecological dissimilarities for visualization or clustering. Despite this, both approaches face common challenges, like the compositional nature of next-generation sequencing data or the integration of the spatial and temporal dimensions. Here we propose a kernel framework to place on a common ground the unsupervised and supervised microbiome analyses, including the retrieval of microbial signatures (taxa importances). We define two compositional kernels (Aitchison-RBF and compositional linear) and discuss how to transform non-compositional beta-dissimilarity measures into kernels. Spatial data is integrated with multiple kernel learning, while longitudinal data is evaluated by specific kernels. We illustrate our framework through a single point soil dataset, a human dataset with a spatial component, and a previously unpublished longitudinal dataset concerning pig production. The proposed framework and the case studies are freely available in the kernInt package at https://github.com/elies-ramon/kernInt., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Ramon, Belanche-Muñoz, Molist, Quintanilla, Perez-Enciso and Ramayo-Caldas.)

Aggression behaviour has several negative consequences on the performance and welfare of pigs. Here, the Social Network Analysis (SNA) approach was employed to (1) identify individual traits that describe the role of each animal in the aggression; (2) investigate the association of these traits with performance and feeding behaviour traits. The study was conducted on 326 Duroc pigs reared in 29 pens. Several individual centrality traits were identified and used to calculate the Social Rank Index. The Dominant, Subordinate, and Isolated animals represented 21.1%, 57.5% and 21.4%, respectively. No significant correlations were observed between out-degree (number of initiated agonistic behaviours) and growth traits, indicating the similarity of growth patterns for dominant and non-dominant animals. Furthermore, out-degree was correlated positively with average daily occupation time (time at the feeder/day) and average daily feeding frequency (number of visits to the feeder/day) but negatively with average daily feeding rate (gr/min). This may indicate the ability of non-dominant pigs to modify their behaviour to obtain their requirements. The Hamming distances between networks showed that there is no common behaviour pattern between pens. In conclusion, SNA showed the potential for extracting behaviour traits that could be used to improve pig performance and welfare.

The inclusion of health-related traits, or functionally associated genetic markers, in pig breeding programs could contribute to produce more robust and disease resistant animals. The aim of the present work was to study the genetic determinism and genomic regions associated to global immunocompetence and health in a Duroc pig population. For this purpose, a set of 30 health-related traits covering immune (mainly innate), haematological, and stress parameters were measured in 432 healthy Duroc piglets aged 8 weeks. Moderate to high heritabilities were obtained for most traits and significant genetic correlations among them were observed. A genome wide association study pointed out 31 significantly associated SNPs at whole-genome level, located in six chromosomal regions on pig chromosomes SSC4, SSC6, SSC17 and SSCX, for IgG, γδ T-cells, C-reactive protein, lymphocytes phagocytic capacity, total number of lymphocytes, mean corpuscular volume and mean corpuscular haemoglobin. A total of 16 promising functionally-related candidate genes, including CRP, NFATC2, PRDX1, SLA, ST3GAL1, and VPS4A, have been proposed to explain the variation of immune and haematological traits. Our results enhance the knowledge of the genetic control of traits related with immunity and support the possibility of applying effective selection programs to improve immunocompetence in pigs.

As obesity incidence is alarmingly rising among young individuals, we aimed to characterize an experimental model of this situation, considering the similarity between human and porcine physiology. For this reason, we fed prepubertal (63 days old) Duroc breed females (n=21) either with a standard growth diet (3800 kcal/day) or one with a high-calorie content (5200 kcal/day) during 70 days. Computerized tomography, mass-spectrometry-based metabolomics and lipidomics, as well as peripheral blood mononuclear cell transcriptomics, were applied to define traits linked to high-calorie intake. Samples from a human cohort confirmed potential lipidomic markers. Compared to those fed a standard growth diet, pigs fed a high-calorie diet showed an increased weight gain (13%), much higher adiposity (53%), hypertriacylglyceridemia and hypercholesterolemia in parallel to insulin resistance. This diet induced marked changes in the circulating lipidome, particularly in phosphatidylethanolamine-type molecules. Also, circulating specific diacylglycerol and monoacylglycerol contents correlated with visceral fat and intrahepatic triacylglycerol concentrations. Specific lipids associated with obesity in swine (mainly belonging to glycerophospholipid, triacylglyceride and sterol classes) were also linked with obesity traits in the human cohort, reinforcing the usefulness of the chosen approach. Interestingly, no overt inflammation in plasma or adipose tissue was evident in this model. The presented model is useful as a preclinical surrogate of prepubertal obesity in order to ascertain the pathophysiology interactions between energy intake and obesity development., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Background: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (H P ) and fixation index (F ST )] and group-based F ST approaches, which compare groups of breeds defined according to external traits and use/specialization/type., Results: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars., Conclusions: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.

Background: The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight., Results: Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight., Conclusions: Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.

Despite the broad variety of available microRNA (miRNA) prediction tools, their application to the discovery and annotation of novel miRNA genes in domestic species is still limited. In this study we designed a comprehensive pipeline (eMIRNA) for miRNA identification in the yet poorly annotated porcine genome and demonstrated the usefulness of implementing a motif search positional refinement strategy for the accurate determination of precursor miRNA boundaries. The small RNA fraction from gluteus medius skeletal muscle of 48 Duroc gilts was sequenced and used for the prediction of novel miRNA loci. Additionally, we selected the human miRNA annotation for a homology-based search of porcine miRNAs with orthologous genes in the human genome. A total of 20 novel expressed miRNAs were identified in the porcine muscle transcriptome and 27 additional novel porcine miRNAs were also detected by homology-based search using the human miRNA annotation. The existence of three selected novel miRNAs (ssc-miR-483, ssc-miR484 and ssc-miR-200a) was further confirmed by reverse transcription quantitative real-time PCR analyses in the muscle and liver tissues of Göttingen minipigs. In summary, the eMIRNA pipeline presented in the current work allowed us to expand the catalogue of porcine miRNAs and showed better performance than other commonly used miRNA prediction approaches. More importantly, the flexibility of our pipeline makes possible its application in other yet poorly annotated non-model species., Competing Interests: Conflict of interest The authors declare no conflict of interest., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Global prevalence of obesity has increased to epidemic proportions over the past 40 years, with childhood obesity reaching alarming rates. In this study, we determined changes in liver and adipose tissue transcriptomes of a porcine model for prepubertal early obesity induced by a high-calorie diet and supplemented with bioactive ingredients. A total of 43 nine-weeks-old animals distributed in four pens were fed with four different dietary treatments for 10 weeks: a conventional diet; a western-type diet; and a western-type diet with Bifidobacterium breve and rice hydrolysate, either adding or not omega-3 fatty acids. Animals fed a western-type diet increased body weight and total fat content and exhibited elevated serum concentrations of cholesterol, whereas animals supplemented with bioactive ingredients showed lower body weight gain and tended to accumulate less fat. An RNA-seq experiment was performed with a total of 20 animals (five per group). Differential expression analyses revealed an increase in lipogenesis, cholesterogenesis and inflammatory processes in animals on the western-type diet while the supplementation with bioactive ingredients induced fatty acid oxidation and cholesterol catabolism, and decreased adipogenesis and inflammation. These results reveal molecular mechanisms underlying the beneficial effects of bioactive ingredient supplementation in an obese pig model.

Background: The role of non-coding RNAs in the porcine muscle metabolism is poorly understood, with few studies investigating their expression patterns in response to nutrient supply. Therefore, we aimed to investigate the changes in microRNAs (miRNAs), long intergenic non-coding RNAs (lincRNAs) and mRNAs muscle expression before and after food intake., Results: We measured the miRNA, lincRNA and mRNA expression levels in the gluteus medius muscle of 12 gilts in a fasting condition (AL-T0) and 24 gilts fed ad libitum during either 5 h. (AL-T1, N  = 12) or 7 h. (AL-T2, N  = 12) prior to slaughter. The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced, whereas lincRNA and mRNA expression data were already available. In terms of mean and variance, the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs. Food intake induced the differential expression of 149 (AL-T0/AL-T1) and 435 (AL-T0/AL-T2) mRNAs, 6 (AL-T0/AL-T1) and 28 (AL-T0/AL-T2) miRNAs and none lincRNAs, while the number of differentially dispersed genes was much lower. Among the set of differentially expressed miRNAs, we identified ssc-miR-148a-3p, ssc-miR-22-3p and ssc-miR-1, which play key roles in the regulation of glucose and lipid metabolism. Besides, co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding. One case example was represented by seven miRNAs (ssc-miR-148a-3p, ssc-miR-151-3p, ssc-miR-30a-3p, ssc-miR-30e-3p, ssc-miR-421-5p, ssc-miR-493-5p and ssc-miR-503) which putatively interact with the PDK4 mRNA, one of the master regulators of glucose utilization and fatty acid oxidation., Conclusions: As a whole, our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (© The Author(s). 2020.)

Background: Feed efficiency (FE) has a major impact on the economic sustainability of pig production. We used a systems-based approach that integrates single nucleotide polymorphism (SNP) co-association and gene-expression data to identify candidate genes, biological pathways, and potential predictors of FE in a Duroc pig population., Results: We applied an association weight matrix (AWM) approach to analyse the results from genome-wide association studies (GWAS) for nine FE associated and production traits using 31K SNPs by defining residual feed intake (RFI) as the target phenotype. The resulting co-association network was formed by 829 SNPs. Additive effects of this SNP panel explained 61% of the phenotypic variance of RFI, and the resulting phenotype prediction accuracy estimated by cross-validation was 0.65 (vs. 0.20 using pedigree-based best linear unbiased prediction and 0.12 using the 31K SNPs). Sixty-eight transcription factor (TF) genes were identified in the co-association network; based on the lossless approach, the putative main regulators were COPS5, GTF2H5, RUNX1, HDAC4, ESR1, USP16, SMARCA2 and GTF2F2. Furthermore, gene expression data of the gluteus medius muscle was explored through differential expression and multivariate analyses. A list of candidate genes showing functional and/or structural associations with FE was elaborated based on results from both AWM and gene expression analyses, and included the aforementioned TF genes and other ones that have key roles in metabolism, e.g. ESRRG, RXRG, PPARGC1A, TCF7L2, LHX4, MAML2, NFATC3, NFKBIZ, TCEA1, CDCA7L, LZTFL1 or CBFB. The most enriched biological pathways in this list were associated with behaviour, immunity, nervous system, and neurotransmitters, including melatonin, glutamate receptor, and gustation pathways. Finally, an expression GWAS allowed identifying 269 SNPs associated with the candidate genes' expression (eSNPs). Addition of these eSNPs to the AWM panel of 829 SNPs did not improve the accuracy of genomic predictions., Conclusions: Candidate genes that have a direct or indirect effect on FE-related traits belong to various biological processes that are mainly related to immunity, behaviour, energy metabolism, and the nervous system. The pituitary gland, hypothalamus and thyroid axis, and estrogen signalling play fundamental roles in the regulation of FE in pigs. The 829 selected SNPs explained 61% of the phenotypic variance of RFI, which constitutes a promising perspective for applying genetic selection on FE relying on molecular-based prediction.

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.

The genetic factors determining the phenotypic variation of porcine fatness phenotypes are still largely unknown. We investigated whether the polymorphism of eight genes (MIGA2, CRY2, NPAS2, CIART, ARNTL2, PER1, PER2 and PCK1), which display differential expression in the skeletal muscle of fasted and fed sows, is associated with the variation of lipid and mRNA expression phenotypes in Duroc pigs. The performance of an association analysis with the GEMMA software demonstrated that the rs330779504 SNP in the MIGA2 gene is associated with LDL concentration at 190 days (LDL 2 , corrected P-value = 0.057). Moreover, the rs320439526 SNP of the CRY2 gene displayed a significant association with stearic acid content in the longissimus dorsi muscle (LD C18:0, corrected P-value = 0.015). Both SNPs were also associated with the mRNA levels of the corresponding genes in the gluteus medius skeletal muscle. From a biological perspective these results are meaningful because MIGA2 protein plays an essential role in mitochondrial fusion, a process tightly connected with the energy status of the cell, while CRY2 is a fundamental component of the circadian clock. However, inclusion of these two SNPs in chromosome-wide association analyses demonstrated that they are not located at the peaks of significance for the two traits under study (LDL 2 for rs330779504 and LD C18:0 for rs320439526), thus implying that these two SNPs do not have causal effects.

Background: To date, the molecular mechanisms that underlie residual feed intake (RFI) in pigs are unknown. Results from different genome-wide association studies and gene expression analyses are not always consistent. The aim of this research was to use machine learning to identify genes associated with feed efficiency (FE) using transcriptomic (RNA-Seq) data from pigs that are phenotypically extreme for RFI., Methods: RFI was computed by considering within-sex regression on mean metabolic body weight, average daily gain, and average backfat gain. RNA-Seq analyses were performed on liver and duodenum tissue from 32 high and 33 low RFI pigs collected at 153 d of age. Machine-learning algorithms were used to predict RFI class based on gene expression levels in liver and duodenum after adjusting for batch effects. Genes were ranked according to their contribution to the classification using the permutation accuracy importance score in an unbiased random forest (RF) algorithm based on conditional inference. Support vector machine, RF, elastic net (ENET) and nearest shrunken centroid algorithms were tested using different subsets of the top rank genes. Nested resampling for hyperparameter tuning was implemented with tenfold cross-validation in the outer and inner loops., Results: The best classification was obtained with ENET using the expression of 200 genes in liver [area under the receiver operating characteristic curve (AUROC): 0.85; accuracy: 0.78] and 100 genes in duodenum (AUROC: 0.76; accuracy: 0.69). Canonical pathways and candidate genes that were previously reported as associated with FE in several species were identified. The most remarkable pathways and genes identified were NRF2-mediated oxidative stress response and aldosterone signalling in epithelial cells, the DNAJC6, DNAJC1, MAPK8, PRKD3 genes in duodenum, and melatonin degradation II, PPARα/RXRα activation, and GPCR-mediated nutrient sensing in enteroendocrine cells and SMOX, IL4I1, PRKAR2B, CLOCK and CCK genes in liver., Conclusions: ML algorithms and RNA-Seq expression data were found to provide good performance for classifying pigs into high or low RFI groups. Classification was better with gene expression data from liver than from duodenum. Genes associated with FE in liver and duodenum tissue that can be used as predictive biomarkers for this trait were identified.

Background: Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression and the genetic determinism of IMF traits in the porcine gluteus medius (GM) and longissimus dorsi (LD) muscles., Results: A comparative analysis of the mRNA expression profiles of the pig GM and LD muscles in 16 Duroc pigs with available microarray mRNA expression measurements revealed the existence of 106 differentially expressed probes (fold-change > 1.5 and q-value < 0.05). Amongst the genes displaying the most significant differential expression, several loci belonging to the Hox transcription factor family were either upregulated (HOXA9, HOXA10, HOXB6, HOXB7 and TBX1) or downregulated (ARX) in the GM muscle. Differences in the expression of genes with key roles in carbohydrate and lipid metabolism (e.g. FABP3, ORMDL1 and SLC37A1) were also detected. By performing a GWAS for IMF content and composition traits recorded in the LD and GM muscles of 350 Duroc pigs, we identified the existence of one region on SSC14 (110-114 Mb) displaying significant associations with C18:0, C18:1(n-7), saturated and unsaturated fatty acid contents in both GM and LD muscles. Moreover, we detected several genome-wide significant associations that were not consistently found in both muscles. Further studies should be performed to confirm whether these associations are muscle-specific. Finally, the performance of an eQTL scan for 74 genes, located within GM QTL regions and with available microarray measurements of gene expression, made possible to identify 14 cis-eQTL regulating the expression of 14 loci, and six of them were confirmed by RNA-Seq., Conclusions: We have detected significant differences in the mRNA expression patterns of the porcine LD and GM muscles, evidencing that the transcriptomic profile of the skeletal muscle tissue is affected by anatomical, metabolic and functional factors. A highly significant association with IMF composition on SSC14 was replicated in both muscles, highlighting the existence of a common genetic determinism, but we also observed the existence of a few associations whose magnitude and significance varied between LD and GM muscles.

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships., Competing Interests: The authors have declared that no competing interests exist, excepting that the corresponding author Cristina Óvilo is a PLOS ONE Editorial Board member. However, this does not alter the authors’ adherence to all the PLOS ONE policies.

In a previous study, we observed that circadian clock genes are differentially expressed in the skeletal muscle of fasting and fed sows. The goal of the current work was to investigate if these genes are also differentially expressed in tissues containing the central (hypothalamus) and peripheral (duodenum, dorsal fat, muscle, and liver) clocks. As animal material, we used 12 sows that fasted 12 h before slaughtering (T0) and 12 sows that were fed ad libitum 7 h prior slaughtering (T2). Tissue samples were collected immediately after slaughter and total RNA was subsequently extracted. The expression of the ARNTL, BHLHE40, CRY2, NPAS2, NR1D1, PER1, PER2 , and SIK1 genes was measured by quantitative reverse transcription PCR. The numbers of clock genes showing differential expression before and after feeding varied depending on the tissue i.e., four in dorsal fat and duodenum, six in skeletal muscle, and seven in the liver. In contrast, none of the eight analysed genes displayed a significant differential expression in hypothalamus, the tissue where the central clock resides. This result supports that the differential expression of clock genes in the four tissues mentioned above is probably induced by nutrition and not by the central clock entrained by light. Moreover, we have observed that the NPAS2 and ARNTL genes display positive log 2 (FC) values in the five tissues under analysis, whilst the CRY2, PER1 (except dorsal fat) and PER2 (except hypothalamus) genes generally show negative log 2 (FC) values. Such result might be explained by the existence of a negative feedback loop between the ARNTL/NPAS2 and CRY/PER genes. Collectively, these results support that nutrition plays an important role in modulating the timing of porcine peripheral circadian clocks. Such regulation could be essential for coordinating the subsequent metabolic response to nutrient supply.

In the current study the collagen, texture, and sensory characteristics of meat from 712 yearling males of 10 local Spanish and French beef breeds raised in their typical production systems were described. The breed-production system affected collagen and texture variables but affected sensory variables only slightly. There was a large amount of intra breed-production system variation for all the variables. French breeds had lower values for collagen solubility (~12%) than Spanish breeds (~40%). Stress (WB) varied from 36 N/cm 2 in Casina to 44 N/cm 2 in Salers, whereas compression stress at 80% ranged from 35 N/cm 2 in Asturiana de los Valles to 40 N/cm 2 in Salers. Oven cooking resulted in higher cooking losses (24%) than cooking on a grill (12%). Cooking losses increased as the grill temperature increased. Numerous significant correlations were found among variables. Carcass weight is associated with all the collagen and texture variables. Correlation coefficients among texture and collagen variables were statistically significant and these correlation coefficients were in general higher for solubility percentage than for total collagen content, highlighting the importance of the solubility of collagen rather than total collagen in determining meat textural properties., Practical Applications: To differentiate a product in the market, it is necessary to define its characteristics. Differentiation allows increasing the added value of products and, therefore, income of the farmers. In addition, it guarantees to the consumers that the product they purchase has the intrinsic and extrinsic quality features that they seek. For consumers, beef texture is one of the most important quality attributes sought, therefore, studying factors that can affect beef texture is a major interest for the industry., (© 2018 Wiley Periodicals, Inc.)

Background: The molecular basis of compensatory growth in monogastric animals has not yet been fully explored. Herewith, in this study we aim to determine changes in the pig skeletal muscle transcriptome profile during compensatory growth following a feed restriction period. A RNA-Seq experiment was performed with a total of 24 females belonging to a Duroc commercial line. Half of the animals received either a restricted (RE) or ad libitum (AL) diet during the first fattening period (60-125 d of age). After that, all gilts were fed ad libitum for a further ~30 d until the age of ~155 d, when animals were slaughtered and samples of gluteus medius muscle were harvested to perform RNA-Seq analyses and intramuscular fat content determination., Results: During the period following food restriction, RE animals re-fed ad libitum displayed compensatory growth, showed better feed conversion rate and tended to deposit more subcutaneous fat than AL fed animals. Animals were slaughtered in the phase of accelerated growth, when RE animals had not completely compensated the performance of AL group, showing lower live and carcass weights. At intramuscular level, RE gilts showed a higher content of polyunsaturated fatty acids during the compensatory growth phase. The comparison of RE and AL expression profiles allowed the identification of 86 (ǀlog 2 Fold-Changeǀ > 1, p adj  < 0.05) differentially expressed (DE) genes. A functional categorization of these DE genes identified AMPK Signaling as the most significantly enriched canonical pathway. This kinase plays a key role in the maintenance of energy homeostasis as well as in the activation of autophagy. Among the DE genes identified as components of AMPK Signaling pathway, five out of six genes were downregulated in RE pigs., Conclusions: Animals re-fed after a restriction period exhibited a less oxidative metabolic profile and catabolic processes in muscle than animals fed ad libitum. The downregulation of autophagy observed in the skeletal muscle of pigs undergoing compensatory growth may constitute a mechanism to increase muscle mass thus ensuring an accelerated growth rate. These results reveal that the downregulation of AMPK Signaling plays an important role in compensatory growth in pigs.

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 log 2 fold-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 log 2 fold-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.

This study aims identifying candidate genes and pathways associated with feed efficiency (FE) in pigs. Liver and duodenum transcriptomes of 37 gilts showing high and low residual feed intake (RFI) were analysed by RNA-Seq. Gene expression data was explored through differential expression (DE) and weighted gene co-expression network analyses. DE analysis revealed 55 and 112 differentially regulated genes in liver and duodenum tissues, respectively. Clustering genes according to their connectivity resulted in 23 (liver) and 25 (duodenum) modules of genes with a co-expression pattern. Four modules, one in liver (with 444 co-expressed genes) and three in duodenum (gathering 37, 126 and 41 co-expressed genes), were significantly associated with FE indicators. Intra-module analyses revealed tissue-specific candidate genes; 12 of these genes were also identified as DE between individuals with high and low RFI. Pathways enriched by the list of genes showing DE and/or belonging to FE co-expressed modules included response to oxidative stress, inflammation, immune response, lipid metabolism and thermoregulation. Low overlapping between genes identified in duodenum and liver tissues was observed but heat shock proteins were associated to FE in both tissues. Our results suggest tissue-specific rather than common transcriptome regulatory processes associated with FE in pigs.

Background: Improving feed efficiency ([Formula: see text]) is a key factor for any pig breeding company. Although this can be achieved by selection on an index of multi-trait best linear unbiased prediction of breeding values with optimal economic weights, considering deviations of feed intake from actual needs ([Formula: see text]) should be of value for further research on biological aspects of [Formula: see text]. Here, we present a random regression model that extends the classical definition of [Formula: see text] by including animal-specific needs in the model. Using this model, we explore the genetic determinism of several [Formula: see text] components: use of feed for growth ([Formula: see text]), use of feed for backfat deposition ([Formula: see text]), use of feed for maintenance ([Formula: see text]), and unspecific efficiency in the use of feed ([Formula: see text]). Expected response to alternative selection indexes involving different components is also studied., Results: Based on goodness-of-fit to the available feed intake ([Formula: see text]) data, the model that assumes individual (genetic and permanent) variation in the use of feed for maintenance, [Formula: see text] and [Formula: see text] showed the best performance. Joint individual variation in feed allocation to maintenance, growth and backfat deposition comprised 37% of the individual variation of [Formula: see text]. The estimated heritabilities of [Formula: see text] using the model that accounts for animal-specific needs and the traditional [Formula: see text] model were 0.12 and 0.18, respectively. The estimated heritabilities for the regression coefficients were 0.44, 0.39 and 0.55 for [Formula: see text], [Formula: see text] and [Formula: see text], respectively. Estimates of genetic correlations of [Formula: see text] were positive with amount of feed used for [Formula: see text] and [Formula: see text] but negative for [Formula: see text]. Expected response in overall efficiency, reducing [Formula: see text] without altering performance, was 2.5% higher when the model assumed animal-specific needs than when the traditional definition of [Formula: see text] was considered., Conclusions: Expected response in overall efficiency, by reducing [Formula: see text] without altering performance, is slightly better with a model that assumes animal-specific needs instead of batch-specific needs to correct [Formula: see text]. The relatively small difference between the traditional [Formula: see text] model and our model is due to random intercepts (unspecific use of feed) accounting for the majority of variability in [Formula: see text]. Overall, a model that accounts for animal-specific needs for [Formula: see text], [Formula: see text] and [Formula: see text] is statistically superior and allows for the possibility to act differentially on [Formula: see text] components.

Background: The genetic basis of muscle fat deposition in pigs is not well known. So far, we have only identified a limited number of genes involved in the absorption, transport, storage and catabolism of lipids. Such information is crucial to interpret, from a biological perspective, the results of genome-wide association analyses for intramuscular fat content and composition traits. Herewith, we have investigated how the ingestion of food changes gene expression in the gluteus medius muscle of Duroc pigs., Results: By comparing the muscle mRNA expression of fasted pigs (T0) with that of pigs sampled 5 h (T1) and 7 h (T2) after food intake, we have detected differential expression (DE) for 148 (T0-T1), 520 (T0-T2) and 135 (T1-T2) genes (q-value <0.05 and a |FC| > of 1.5). Many of these DE genes were transcription factors, suggesting that we have detected the coordinated response of the skeletal muscle to nutrient supply. We also found DE genes with a dual role in oxidative stress and angiogenesis (THBS1, THBS2 and TXNIP), two biological processes that are probably activated in the post-prandial state. Finally, we have identified several loci playing a key role in the modulation of circadian rhythms (ARNTL, PER1, PER2, BHLHE40, NR1D1, SIK1, CIART and CRY2), a result that indicates that the porcine muscle circadian clock is modulated by nutrition., Conclusion: We have shown that hundreds of genes change their expression in the porcine skeletal muscle in response to nutrient intake. Many of these loci do not have a known metabolic role, a result that suggests that our knowledge about the genetic basis of muscle energy homeostasis is still incomplete.

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 (pH 24 ), 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 significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects 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 pH 24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism.

Current statistical approaches to investigate the nature and magnitude of transmission ratio distortion (TRD) are scarce and restricted to the most common experimental designs such as F2 populations and backcrosses. In this article, we describe a new Bayesian approach to check TRD within a given biallelic genetic marker in a diploid species, providing a highly flexible framework that can accommodate any kind of population structure. This model relies on the genotype of each offspring and thus integrates all available information from either the parents' genotypes or population-specific allele frequencies and yields TRD estimates that can be corroborated by the calculation of a Bayes factor (BF). This approach has been evaluated on simulated data sets with appealing statistical performance. As a proof of concept, we have also tested TRD in a porcine population with five half-sib families and 352 offspring. All boars and piglets were genotyped with the Porcine SNP60 BeadChip, whereas genotypes from the sows were not available. The SNP-by-SNP screening of the pig genome revealed 84 SNPs with decisive evidences of TRD (BF > 100) after accounting for multiple testing. Many of these regions contained genes related to biological processes (e.g., nucleosome assembly and co-organization, DNA conformation and packaging, and DNA complex assembly) that are critically associated with embryonic viability. The implementation of this method, which overcomes many of the limitations of previous approaches, should contribute to fostering research on TRD in both model and nonmodel organisms., (Copyright © 2014 by the Genetics Society of America.)

Background: The genetic determinism of blood lipid concentrations, the main risk factor for atherosclerosis, is practically unknown in species other than human and mouse. Even in model organisms, little is known about how the genetic determinants of lipid traits are modulated by age-specific factors. To gain new insights into this issue, we have carried out a genome-wide association study (GWAS) for cholesterol (CHOL), triglyceride (TRIG) and low (LDL) and high (HDL) density lipoprotein concentrations measured in Duroc pigs at two time points (45 and 190 days)., Results: Analysis of data with mixed-model methods (EMMAX, GEMMA, GenABEL) and PLINK showed a low positional concordance between trait-associated regions (TARs) for serum lipids at 45 and 190 days. Besides, the proportion of phenotypic variance explained by SNPs at these two time points was also substantially different. The four analyses consistently detected two regions on SSC3 (124 Mb, CHOL and LDL at 190 days) and SSC6 (135 Mb, CHOL and TRIG at 190 days) with highly significant effects on the porcine blood lipid profile. Moreover, we have found that SNP variation within SSC3, SSC6, SSC10, SSC13 and SSC16 TARs is associated with the expression of several genes mapping to other chromosomes and related to lipid metabolism., Conclusions: Our data demonstrate that the effects of genomic determinants influencing lipid concentrations in pigs, as well as the amount of phenotypic variance they explain, are influenced by age-related factors.

Background: The main goal of the present study was to analyse the genetic architecture of mRNA expression in muscle, a tissue with an outmost economic importance for pig breeders. Previous studies have used F(2) crosses to detect porcine expression QTL (eQTL), so they contributed with data that mostly represents the between-breed component of eQTL variation. Herewith, we have analysed eQTL segregation in an outbred Duroc population using two groups of animals with divergent fatness profiles. This approach is particularly suitable to analyse the within-breed component of eQTL variation, with a special emphasis on loci involved in lipid metabolism., Methodology/principal Findings: GeneChip Porcine Genome arrays (Affymetrix) were used to determine the mRNA expression levels of gluteus medius samples from 105 Duroc barrows. A whole-genome eQTL scan was carried out with a panel of 116 microsatellites. Results allowed us to detect 613 genome-wide significant eQTL unevenly distributed across the pig genome. A clear predominance of trans- over cis-eQTL, was observed. Moreover, 11 trans-regulatory hotspots affecting the expression levels of four to 16 genes were identified. A Gene Ontology study showed that regulatory polymorphisms affected the expression of muscle development and lipid metabolism genes. A number of positional concordances between eQTL and lipid trait QTL were also found, whereas limited evidence of a linear relationship between muscle fat deposition and mRNA levels of eQTL regulated genes was obtained., Conclusions/significance: Our data provide substantial evidence that there is a remarkable amount of within-breed genetic variation affecting muscle mRNA expression. Most of this variation acts in trans and influences biological processes related with muscle development, lipid deposition and energy balance. The identification of the underlying causal mutations and the ascertainment of their effects on phenotypes would allow gaining a fundamental perspective about how complex traits are built at the molecular level.

Background: Selection for increasing intramuscular fat content would definitively improve the palatability and juiciness of pig meat as well as the sensorial and organoleptic properties of cured products. However, evidences obtained in human and model organisms suggest that high levels of intramuscular fat might alter muscle lipid and carbohydrate metabolism. We have analysed this issue by determining the transcriptomic profiles of Duroc pigs with divergent phenotypes for 13 fatness traits. The strong aptitude of Duroc pigs to have high levels of intramuscular fat makes them a valuable model to analyse the mechanisms that regulate muscle lipid metabolism, an issue with evident implications in the elucidation of the genetic basis of human metabolic diseases such as obesity and insulin resistance., Results: Muscle gene expression profiles of 68 Duroc pigs belonging to two groups (HIGH and LOW) with extreme phenotypes for lipid deposition and composition traits have been analysed. Microarray and quantitative PCR analysis showed that genes related to fatty acid uptake, lipogenesis and triacylglycerol synthesis were upregulated in the muscle tissue of HIGH pigs, which are fatter and have higher amounts of intramuscular fat than their LOW counterparts. Paradoxically, lipolytic genes also showed increased mRNA levels in the HIGH group suggesting the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Several genes related to the insulin-signalling pathway, that is usually impaired in obese humans, were also upregulated. Finally, genes related to antigen-processing and presentation were downregulated in the HIGH group., Conclusion: Our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to to elucidate the effects of lipid deposition on muscle metabolism in pigs.

The fine mapping of polymorphisms influencing cholesterol (CT), triglyceride (TG), and lipoprotein serum levels in human and mouse has provided a wealth of knowledge about the complex genetic architecture of these traits. The extension of these genetic analyses to pigs would be of utmost importance since they constitute a valuable biological and clinical model for the study of coronary artery disease and myocardial infarction. In the present work, we performed a whole genome scan for serum lipid traits in a half-sib Duroc pig population of 350 individuals. Phenotypic registers included total CT, TG, and low (LDL)- and high (HDL)-density lipoprotein serum concentrations at 45 and 190 days of age. This approach allowed us to identify two genomewide significant quantitative trait loci (QTL) for HDL-to-LDL ratio at 45 days (SSC6, 84 cM) and for TG at 190 days (SSC4, 23 cM) as well as a number of chromosomewide significant QTL. The comparison of QTL locations at 45 and 190 days revealed a notable lack of concordance at these two time points, suggesting that the effects of these QTL are age specific. Moreover, we have observed a considerable level of correspondence among the locations of the most significant porcine lipid QTL and those identified in humans. This finding might suggest that, in mammals, diverse polymorphisms located in a common set of genes are involved in the genetic variation of serum lipid levels.