Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics.
Ontology highlight
ABSTRACT:
SUBMITTER: Ovilo C
PROVIDER: S-EPMC4070551 | biostudies-literature | 2014
REPOSITORIES: biostudies-literature
Publications
Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics.
Ovilo Cristina C Benítez Rita R Fernández Almudena A Núñez Yolanda Y Ayuso Miriam M Fernández Ana Isabel AI Rodríguez Carmen C Isabel Beatriz B Rey Ana Isabel AI López-Bote Clemente C Silió Luis L
BMC genomics 20140531
<h4>Background</h4>The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in piglets of both genetic types, in order to identify genes, pathways and regulatory factors responsible for their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DU ...[more]
Similar Datasets
Project description:Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth, and seven IB and 10 IBxDU at four months of age (growing period). Muscle transcriptome was analyzed on LD samples with RNA-Seq technology. We detected 261 differentially expressed genes between IB and IBxDU neonates and 113 at growth (p < 0.01 and Fold-Change > 1. 5). Newborns transcriptome reflected a highly proliferative developmental stage, while older pigs showed upregulation of catabolic and muscle functioning processes. Regarding the genetic type effect, IBxDU newborns showed enrichment of gene pathways involved in muscle growth, in agreement with the higher prenatal growth observed in these pigs. However, IB growing pigs showed enrichment of pathways involved in protein deposition and cellular growth, supporting the catch-up growth experienced by IB pigs during this period. Moreover, newborn and growing IB pigs showed more active glucose and lipid metabolism than IBxDU pigs.
2017-02-09 | GSE86441 | GEO
Project description:We studied the influence of genetic type (pure Iberian pigs vs crossbred with Duroc) on l.dorsi transcriptome Background: The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in young animals of both genetic types, in order to identify genes, pathways and transcription factors responsible of their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DUxIB) were generated. Piglets (14 from each genetic type) were sacrificed at weaning (28 days) and longissimus dorsi muscle was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays. Results: Loin muscle composition showed significant differences between genetic types in intramuscular fat content (6% vs. 4.2% in IB and DUxIB animals, respectively, P=0.009) and in saturated and monounsaturated fatty acid contents (P=0.019 and P=0.044, respectively). Statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR<0.10), 102 upregulated in IB and 154 upregulated in DUxIB. The size of the effects ranged between 1.2x and 7.8x. Transcript differences were validated for a subset of DE genes by qPCR. Some candidate genes with known effects on muscle growth were found among the DE genes upregulated in DUxIB (IGF2, collagens, integrins). Genes related to lipid metabolism and proteolysis were found among the genes upregulated in IB (ME1, ELOVL6, caspases, catepsins, ubiquitination proteins). We observed alteration in biological functions related to extracellular matrix organization, cellular adhesion, muscle growth and lipid metabolism. Transcription factors (TF) potentially involved in the expression differences found were identified by calculating the regulatory impact factors (RIF). Sixteen TF were found, some of them with known relationship with muscle development (MSTN, SIX4), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these TF and DE genes show relevant differences between genetic types. Conclusion: The results contribute valuable information about molecular mechanisms determining the phenotypic differences of growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. 28 male piglets were employed. 14 animals coming for pure Iberian parents and 14 coming from the crossing of Duroc boars with Iberian sows. Animals were sacrificed at 28 d of age. At the sacrifice, longissimus dorsi muscle tissue was sampled from each animal.
2014-06-11 | E-GEOD-53029 | biostudies-arrayexpress
Project description:We studied the influence of genetic type (pure Iberian pigs vs crossbred with Duroc) on l.dorsi transcriptome Background: The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in young animals of both genetic types, in order to identify genes, pathways and transcription factors responsible of their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DUxIB) were generated. Piglets (14 from each genetic type) were sacrificed at weaning (28 days) and longissimus dorsi muscle was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays. Results: Loin muscle composition showed significant differences between genetic types in intramuscular fat content (6% vs. 4.2% in IB and DUxIB animals, respectively, P=0.009) and in saturated and monounsaturated fatty acid contents (P=0.019 and P=0.044, respectively). Statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR<0.10), 102 upregulated in IB and 154 upregulated in DUxIB. The size of the effects ranged between 1.2x and 7.8x. Transcript differences were validated for a subset of DE genes by qPCR. Some candidate genes with known effects on muscle growth were found among the DE genes upregulated in DUxIB (IGF2, collagens, integrins). Genes related to lipid metabolism and proteolysis were found among the genes upregulated in IB (ME1, ELOVL6, caspases, catepsins, ubiquitination proteins). We observed alteration in biological functions related to extracellular matrix organization, cellular adhesion, muscle growth and lipid metabolism. Transcription factors (TF) potentially involved in the expression differences found were identified by calculating the regulatory impact factors (RIF). Sixteen TF were found, some of them with known relationship with muscle development (MSTN, SIX4), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these TF and DE genes show relevant differences between genetic types. Conclusion: The results contribute valuable information about molecular mechanisms determining the phenotypic differences of growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism.
2014-06-11 | GSE53029 | GEO
Project description:Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype*weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.
2020-01-07 | GSE140460 | GEO
Project description:Low protein diets supplied during the growing period of pigs can diminish their growth rate and increase the intramuscular fat (IMF) content which affects the sensorial and technological characteristics of the traits. In the present study, the effects of a low protein diet supplied during the growing diet of Duroc x Iberian crossbred pigs on several phenotypic traits and liver and longissimus dorsi transcriptome, were analysed 20 days after the differential treatment was started (EARLY) and at the end of it (FINAL). A total of 20 crossbred pigs were assigned to two different dietary treatments during the growing period: a control diet (C) and a low protein diet (LP) with the same energy and lower levels of raw protein (11%) and lysine (0.60%). The transcriptomes of liver and longissimus dorsi were quantified through RNAseq. A total of 134 differentially expressed annotated genes and new isoforms (DEGs) between C and LP diets in liver of EARLY animals; 480 DEGs in liver of LATE animals, and 128 DEGs and 68 DEGs in longissimus dorsi of EARLY and LATE animals were detected. The functional analyses revealed that low protein diet diminishes the expression in liver of genes codifying for proteins involved in immune system both in EARLY and LATE animals, affects the expression of genes involved in cholesterol homeostasis in liver and in the energy process and growth in longissimus dorsi. Pigs fed with LP diet had not higher IMF content than C ones, although some lipogenesis genes such as FASN, SCD or SREBF1 were higher expressed on their liver. A low protein diet supplied during growing period affects multiple biological process that could compromise the immune and energy state of the Duroc x Iberian crossbred pigs. These results point out that we should be very cautious before implementing this type of regime in Duroc x Iberian pigs.
2021-07-01 | GSE163513 | GEO
Project description:INGA FOOD S. A., as a Spanish company that produces and commercializes fattened pigs, has produced a hybrid Iberian sow called CASTÚA by crossing the Retinto and Entrepelado varieties. The selection of the parental populations is based on selection criteria calculated from purebred information, under the assumption that the genetic correlation between purebred and crossbred performance is high; however, these correlations can be less than one because of a GxE interaction or the presence of non-additive genetic effects. This study estimated the additive and dominance variances of the purebred and crossbred populations for litter size, and calculated the additive genetic correlations between the purebred and crossbred performances. The dataset consisted of 2030 litters from the Entrepelado population, 1977 litters from the Retinto population, and 1958 litters from the crossbred population. The individuals were genotyped with a GeneSeek® GGP Porcine70K HDchip. The model of analysis was a 'biological' multivariate mixed model that included additive and dominance SNP effects. The estimates of the additive genotypic variance for the total number born (TNB) were 0.248, 0.282 and 0.546 for the Entrepelado, Retinto and Crossbred populations, respectively. The estimates of the dominance genotypic variances were 0.177, 0.172 and 0.262 for the Entrepelado, Retinto and Crossbred populations. The results for the number born alive (NBA) were similar. The genetic correlations between the purebred and crossbred performance for TNB and NBA-between the brackets-were 0.663 in the Entrepelado and 0.881 in Retinto poplulations. After backsolving to obtain estimates of the SNP effects, the additive genetic variance associated with genomic regions containing 30 SNPs was estimated, and we identified four genomic regions that each explained > 2% of the additive genetic variance in chromosomes (SSC) 6, 8 and 12: one region in SSC6, two regions in SSC8, and one region in SSC12.
| S-EPMC8774905 | biostudies-literature
Project description:One of the most important determinants of meat quality is the intramuscular fat (IMF) content. The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the present study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for their IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq allowed identifying ∼10,000 of the 25,878 annotated genes in the analyzed samples. In addition to this, 42.46% of the identified transcripts corresponded to newly predicted isoforms. Differential expression analyses revealed a total of 221 DE annotated genes and 116 DE new isoforms. Functional analyses identified an enrichment of overexpressed genes involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC, and ADIPOQ) in animals with a higher content of IMF and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB, and SEMA4D) in the animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. Co-expression networks analyses revealed six long non-coding RNAs (lncRNAs) (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, and ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1, and CIDEC. Analyses of the regulatory impact factors (RIFs) revealed 301 transcriptionally regulatory factors involved in expression differences, with five of them involved in adipogenesis (ARID5B, CREB1, VDR, ATF6, and SP1) and other three taking part of myogenesis and development of skeletal muscle (ATF3, KLF11, and MYF6). The results obtained provide relevant insights about the genetic mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors for further identification of polymorphisms susceptible of being incorporated in a selection program.
| S-EPMC6288315 | biostudies-literature
Project description:This study takes pig longissimus dorsi muscle as the object. Through spatial transcriptome research, we clarified the gene expression distribution of different types of muscle fibers in the tissue, and their corresponding marker genes were identified.
2022-05-17 | GSE203094 | GEO
Project description:The two breeds, Mashen (MS; a northern China breed) and Large White (LW; a western lean breed) pigs, show important phenotypic differences in growth, adaptability, intramuscular fat (IMF) content, and energy metabolism since early developmental stage. The main aim of this study was the evaluation of longissimus thoracis muscle transcriptome profile of both genetic types to identify genes, pathways responsible for their differentiated phenotype. Longissimus thoracis of MS and LW pigs were sampled at 0 day (early stage), 90 days (middle stage), and 180 days (later stage) after birth. A total of 3,487 differentially expressed genes (DEGs) were identified at the three time points. Sample clustering analysis revealed the slower growth rate of MS than LW pigs. Gene expression pattern analysis revealed that multicellular organism growth genes (GHSR, EZR, FOXS1, DRD2, SH3PXD2B, CSF1, and TSHR) were involved in the fast growth rate of LW pigs at early stage. Furthermore, DEGs (ACACA, ACSF3, OXSM, CBR4, and HSD17B8) functionally related to fatty acid synthesis revealed that IMF accumulation occurred around 90 and up to 180 days. These DEGs provided valuable resource to study the phenotypic difference in longissimus thoracis muscle between MS and LW pigs.
| S-EPMC7717936 | biostudies-literature
Project description:Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences, transcriptional regulation and genetic polymorphisms that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth. Morphometric measures and blood samples were obtained and samples from Biceps femoris muscle were employed for compositional and transcriptome analysis by RNA-Seq technology. Phenotypic differences were evident at this early age, including greater body size and weight in IBxDU and greater Biceps femoris intramuscular fat and plasma cholesterol content in IB newborns. We detected 150 differentially expressed genes between IB and IBxDU neonates (p < 0.01 and Fold-Change > 1. 5). Several were related to adipose and muscle tissues development (DLK1, FGF21 or UBC). The functional interpretation of the transcriptomic differences revealed enrichment of functions and pathways related to lipid metabolism in IB and to cellular and muscle growth in IBxDU. Protein catabolism, cholesterol biosynthesis and immune system were functions enriched in both genotypes. We identified transcription factors potentially affecting the observed gene expression differences. Some of them have known functions on adipogenesis (CEBPA, EGRs), lipid metabolism (PPARGC1B) and myogenesis (FOXOs, MEF2D, MYOD1), which suggest a key role in the meat quality differences existing between IB and IBxDU hams. We also identified several polymorphisms showing differential segregation between IB and IBxDU pigs. Among them, non-synonymous variants were detected in several transcription factors as PPARGC1B gene, which could be associated to altered gene function. Taken together, these results provide information about candidate genes, metabolic pathways and genetic polymorphisms potentially involved in phenotypic differences between IB and IBxDU associated to meat quality and production traits.
2016-09-25 | GSE73566 | GEO