Josep M Folch

Josep M Folch
Autonomous University of Barcelona | UAB · Department of Animal and Food Science

About

355
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Introduction
Josep M Folch currently works at the Centre for Research in Agricultural Genomics (CRAG) and is professor at the Department of Animal and Food Science , Autonomous University of Barcelona. Josep does research in Molecular Biology, Biotechnology, Genetics and Genomics applied to animal breeding. In the last years he has focussed in the analysis of quantitative traits (QTLs), genes and gene networks affecting economically relevant traits in pigs.

Publications

Publications (355)
Preprint
Full-text available
Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify candi...
Article
Full-text available
Weaning is a critical period in the life of pigs with repercussions on their health and welfare and on the economy of the swine industry. This study aimed to assess the effect of the commercial early weaning on gut microbiota, intestinal gene expression and serum metabolomic response via an integrated-omic approach combining 16S rRNA gene sequencin...
Article
Full-text available
This research aims to determine whether a specific blend of phytogenic compounds (BPC) supplemented in gestating hyperprolific sow diets can promote prenatal maternal effects in terms of piglet gut function and morphology. Twenty-eight (Landrace × Yorkshire) gilts and sows (parity 0 to 7) were randomly distributed by parity number and body weight i...
Article
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There is a high interest on gut health in poultry with special focus on consequences of the intestinal diseases, such as coccidiosis and C . perfringens -induced necrotic enteritis (NE). We developed a custom gene expression panel, which could provide a snapshot of gene expression variation under challenging conditions. Ileum gene expression studie...
Article
Full-text available
The aim of this study was to determine the possible impact of early socialization and an enriched neonatal environment to improve adaptation of piglets to weaning. We hypothesized that changes in the microbiota colonization process and in their metabolic response and intestinal functionality could help the animals face weaning stress. A total of 48...
Article
Full-text available
mir-33a and mir-33b are co-transcribed with the SREBF2 and SREBF1 transcription factors, respectively. The main role of SREBF1 is the regulation of genes involved in fatty acid metabolism, while SREBF2 regulates genes participating in cholesterol biosynthesis and uptake. Our objective was to study the expression of both miR-33a and miR-33b, togethe...
Article
Full-text available
This study was conducted to investigate the effects of dietary supplementation of porcine digestible peptides (PDP), spray-dried plasma (SDP), or a combination of both, on growth performance and the expression of genes related to intestinal function of weaned pigs. A total of 180 piglets (trial 1) and 198 piglets (trial 2) were used to evaluate the...
Article
Full-text available
Meat quality has an important genetic component and can be modified by the fatty acid (FA) composition and the amount of fat contained in adipose tissue and muscle. The present study aimed to find genomic regions associated with the FA composition in backfat and muscle (longissimus dorsi) in 439 pigs with three different genetic backgrounds but hav...
Preprint
Full-text available
Background The improvement of sow prolificacy by breeding has increased the number of piglets produced per sow per year. However, intrauterine crowding and/or intrauterine growth restriction typically observed in hyperprolific sows impairs foetal growth which has decreased the average individual birthweight, with a larger proportion of low birthwei...
Preprint
Full-text available
Background: Porcine digestive peptides (PDP) have proven to be a valid substitute for other high-quality dietary protein sources for piglets, like spray-dried plasma (SDP), but knowledge about their influence on intestinal function is still scarce. This study was conducted to investigate the effects of PDP, SDP or a combination of both on growth pe...
Article
Full-text available
Intramuscular fat content and its fatty acid composition affect porcine meat quality and its nutritional value. The present work aimed to identify genomic variants regulating the expression in the porcine muscle (Longissimus dorsi) of 45 candidate genes for lipid metabolism and fatty acid composition in three experimental backcrosses based on the I...
Article
Full-text available
Phytogenic actives (PA) are plant-derived natural bioactive compounds that may promote livestock health and well-being, as well as improve growth performance and production efficiency. The current study aims to evaluate their effects on sows and their offspring. Eighty-one hyperprolific sows (up to parity 7) were assigned to 3 experimental treatmen...
Article
Full-text available
IGF2:g.3072G>A polymorphism has been described as the causal mutation of a maternally imprinted QTL for muscle growth and fat deposition in pigs. The objective of the current work was to study the association between the IGF2:g.3072G>A polymorphism and the IGF2 gene expression and its effect on fatty acid composition in adipose tissue in different...
Article
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The selection in commercial swine breeds for meat-production efficiency has been increasing among the past decades, reducing the intramuscular fat content, which has changed the sensorial and technological properties of pork. Through processes of natural adaptation and selective breeding, the accumulation of mutations has driven the genetic diverge...
Article
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The gut microbiota has been evolving with its host along the time creating a symbiotic relationship. In this study, we assess the role of the host genome in the modulation of the microbiota composition in pigs. Gut microbiota compositions were estimated through sequencing the V3-V4 region of the 16S rRNA gene from rectal contents of 285 pigs. A tot...
Article
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In addition to its value in meat production, the pig is an interesting animal model for human digestive tract studies due to its physiological similarities. The aim of this study was to describe the microbiome composition, distribution and interaction along the Iberian pig intestinal tract and its role in whole-body energy homeostasis. The V3-V4 re...
Article
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One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut...
Data
Haplotype description. Description for each common QTL region and segregation within the different datasets. (XLSX)
Data
List of candidate SNPs. SNPs selected from those SNPs identified in parallel RNA-Seq studies within positional and functional candidate genes. (XLSX)
Data
Results of the GWAS. Analysis carried out with the 650K genotyping chip data for the regions identified with the 60K porcine chip in the BC_DU backcross. (XLSX)
Data
Graphical representation of the minimum allele frequency (MAF). SNPs included in each of the datasets analyzed (BC_LD, BC_DI, BC_DU and Merged dataset). (TIF)
Data
Significant SNP associations (q-value <0.05) identified in the merged and backcross specific datasets for body weight at 150 days (BW150), backfat thickness at slaughter (BFTS), backfat thickness at 75 kg (BFT75), ham weight (HW), shoulder weight (SH), loin bone-in weight (LBW) and intramuscular fat (IMF): SNP ID, chromosome, position, reference al...
Article
Full-text available
The aim of this work was to study the genetic basis of the backfat expression of lipid-related genes associated with meat quality traits in pigs. We performed a genome-wide association study with the backfat gene expression measured in 44 genes by qPCR and the PorcineSNP60 BeadChip genotypes in 115 Iberian x Landrace backcross animals. A total of 1...
Article
The FABP4 and FABP5 genes, coding for fatty acid transport proteins, have long been studied as positional candidate genes for SSC4 QTL affecting fat deposition and composition traits in pigs. Polymorphisms in these genes, FABP4:g.2634_2635insC and FABP5:g.3000T>G, have previously been associated with fatness traits in an Iberian by Landrace cross (...
Article
Fatty acid composition and fat desaturation+ have profound effects on meat quality. One of the major enzymes participating in fatty acid metabolism is the stearoyl-CoA desaturase (SCD), which is the key enzyme involved in the fatty acid desaturation, in particular in the synthesis of C18:1 from C18:0 and C16:1 from C16:0. Previous studies have repo...
Article
Full-text available
Copy number variations (CNVs) are important genetic variants complementary to SNPs, and can be considered as biomarkers for some economically important traits in domestic animals. In the present study, a genomic analysis of porcine CNVs based on next-generation sequencing data was carried out to identify CNVs segregating in an Iberian x Landrace ba...
Data
Analysis by qPCR of CNVR112 (GPAT2). The y-axis represents the RQ quantitative measurement by qPCR for each sample and the x-axis shows the different samples. The baseline represents the calibrator. (TIFF)
Data
Analysis by qPCR of CNVR157 (CLCA4). The y-axis represents the RQ quantitative measurement by qPCR for each sample and the x-axis shows the different samples. The baseline represents the calibrator. (TIFF)
Data
Analysis by qPCR of CNVR298 (MOGAT2). The y-axis represents the RQ quantitative measurement by qPCR for each sample and the x-axis shows the different samples. The baseline represents the calibrator. (TIFF)
Data
Primers used for qPCR assays. (XLSX)
Data
Pathway analysis of genes identified in CNVRs. (XLSX)
Data
Analysis by qPCR of CNVR447 (PRKG1). The y-axis represents the RQ quantitative measurement by qPCR for each sample and the x-axis shows the different samples. The baseline represents the calibrator. (TIFF)
Data
Information of 540 identified CNVRs and gene annotation within the CNVRs retrieved from the Ensembl Genes 84 Database using the Biomart data management system. (XLSX)
Data
Duplication and deletion calls predicted by Control-FREEC software from all seven pigs. (XLSX)
Data
Association analysis between CNVRs and different phenotypic records in BC1_LD animals. (XLSX)
Article
Copy number variations (CNVs) are important genetic variants complementary to SNPs, and can be considered as biomarkers for some economically important traits in domestic animals. In the present study, a genomic analysis of porcine CNVs based on next-generation sequencing data was carried out to identify CNVs segregating in an Iberian x Landrace ba...
Article
Full-text available
In the present study, liver co-expression networks and expression Genome Wide Association Study (eGWAS) were performed to identify DNA variants and molecular pathways implicated in the functional regulatory mechanisms of meat quality traits in pigs. With this purpose, the liver mRNA expression of 44 candidates genes related with lipid metabolism wa...
Article
Full-text available
Genetical genomics approaches aim at identifying quantitative trait loci for molecular traits, also known as intermediate phenotypes, such as gene expression, that could link variation in genetic information to physiological traits. In the current study, an expression GWAS has been carried out on an experimental Iberian × Landrace backcross in orde...
Article
RNA-Seq technology is widely used in quantitative gene expression studies and identification of non-annotated transcripts. However this technology also can be used for polymorphism detection and RNA editing in transcribed regions in an efficient and cost-effective way. This study used SNP data from an RNA-Seq assay to identify genes and mutations u...
Article
Full-text available
The aim of this work is to better understand the genetic mechanisms determining two complex traits affecting porcine meat quality: intramuscular fat (IMF) content and its fatty acid (FA) composition. With this purpose, expression Genome-Wide Association Study (eGWAS) of 45 lipid-related genes associated with meat quality traits in swine muscle (Lon...
Article
APOA2 is a protein implicated in triglyceride, fatty acid and glucose metabolism. In pigs, the APOA2 gene is located on pig chromosome 4 (SSC4) in a QTL region affecting fatty acid composition, fatness and growth traits. In this study, we evaluated APOA2 as a candidate gene for meat quality traits in an Iberian × Landrace backcross population. The...
Article
Full-text available
Background In previous studies on an Iberian x Landrace cross, we have provided evidence that supported the porcine ELOVL6 gene as the major causative gene of the QTL on pig chromosome 8 for palmitic and palmitoleic acid contents in muscle and backfat. The single nucleotide polymorphism (SNP) ELOVL6:c.-533C > T located in the promoter region of ELO...
Article
Full-text available
Background Linkage maps are essential tools for the study of several topics in genome biology. High density linkage maps for the porcine autosomes have been constructed exploiting the high density data provided by the PorcineSNP60 BeadChip. However, a high density SSCX linkage map has not been reported up to date. The aim of the current study was t...