Effect of diets supplemented with linseed alone or combined with vitamin E and selenium or with plant extracts on Longissimus thoracis transcriptome in growing-finishing Italian Large White pigs
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ABSTRACT:
PROVIDER: PRJEB28465 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2775650_1.fastq.gz | Fastqsanger.gz | |||
| ERR2775650_2.fastq.gz | Fastqsanger.gz | |||
| ERR2775660_1.fastq.gz | Fastqsanger.gz | |||
| ERR2775660_2.fastq.gz | Fastqsanger.gz | |||
| ERR2775670_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Supplementing farm animals diet with functional ingredients may improve the nutritional quality of meat products. Diet composition has been also demonstrated to influence the gene expression with effect on biological processes and pathways. However, the knowledge on the effect of nutrients at the molecular level is scant. In particular, studies on the effects of antioxidants and polyphenols dietary supplementation have been investigated mainly in rodents, and only scarcely in farm animals so far. RNA-seq with next-generation sequencing (NGS) is increasingly the method of choice for studying changes in the transcriptome and it has been recently employed also in pig nutrigenomics studies to identify diet-induced changes in gene expression. The present study aimed to investigate the effect of diets enriched with functional ingredients (linseed, vitamin E and plant extracts) on the transcriptome of pig Longissimus thoracis to elucidate the role of these compounds in influencing genes involved in muscle physiology and metabolism compared to a standard diet. Results: 893 significant differentially expressed genes (DEGs) (FDR adjusted P-value < 0.05) were detected by RNA-seq analysis in the three diet comparisons (D2-D1, D3-D1, D4-D1). The functional analysis of DEGs showed that the diet enriched with n-3 PUFA from linseed (D2) mostly downregulated genes, compared to the standard diet (D1) included in pathways and biological processes (BPs) involved in muscle development, contraction, and glycogen metabolism. The diet supplemented with linseed and vitamin E/Selenium (D3) compared to D1 mostly downregulated genes linked to oxidative phosphorylation. Only few genes were upregulated by the D3 and involved in extracellular matrix (ECM) organization. Finally, the comparison D4-D1 showed that the diet supplemented with linseed and plant extracts (D4) upregulated the majority of genes compared to D1 that were included in a complex network of pathways and BPs all connected by hub genes. In particular, IGF2 was a hub gene connecting protein metabolism, ECM organization, immune system and lipid biosynthesis pathways. Conclusion: The supplementation of pig diet with n-3 PUFA from linseed, antioxidants and plant-derived polyphenols can influence the expression of a relevant number of genes in Longissimus thoracis muscle that are involved a variety of biochemical pathways linked to muscle function and metabolism.
2019-06-29 | E-MTAB-7131 | biostudies-arrayexpress
Project description:BackgroundSupplementing farm animals diet with functional ingredients may improve the nutritional quality of meat products. Diet composition has been also demonstrated to influence the gene expression with effect on biological processes and pathways. However, the knowledge on the effect of nutrients at the molecular level is scant. In particular, studies on the effects of antioxidants and polyphenols dietary supplementation have been investigated mainly in rodents, and only scarcely in farm animals so far. RNA-Seq with next-generation sequencing is increasingly the method of choice for studying changes in the transcriptome and it has been recently employed also in pig nutrigenomics studies to identify diet-induced changes in gene expression. The present study aimed to investigate the effect of diets enriched with functional ingredients (linseed, vitamin E and plant extracts) on the transcriptome of pig Longissimus thoracis to elucidate the role of these compounds in influencing genes involved in muscle physiology and metabolism compared to a standard diet.ResultsEight hundred ninety-three significant differentially expressed genes (DEGs) (FDR adjusted P-value ≤ 0.05) were detected by RNA-Seq analysis in the three diet comparisons (D2-D1, D3-D1, D4-D1). The functional analysis of DEGs showed that the diet enriched with n-3 PUFA from linseed (D2) mostly downregulated genes in pathways and biological processes (BPs) related to muscle development, contraction, and glycogen metabolism compared to the standard diet. The diet supplemented with linseed and vitamin E/Selenium (D3) showed to mostly downregulate genes linked to oxidative phosphorylation. Only few genes involved in extracellular matrix (ECM) organization were upregulated by the D3. Finally, the comparison D4-D1 showed that the diet supplemented with linseed and plant extracts (D4) upregulated the majority of genes compared to D1 that were involved in a complex network of pathways and BPs all connected by hub genes. In particular, IGF2 was a hub gene connecting protein metabolism, ECM organization, immune system and lipid biosynthesis pathways.ConclusionThe supplementation of pig diet with n-3 PUFA from linseed, antioxidants and plant-derived polyphenols can influence the expression of a relevant number of genes in Longissimus thoracis muscle that are involved in a variety of biochemical pathways linked to muscle function and metabolism.
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Project description:Animal nutrition considerably affects milk composition that influences its nutritional quality. Milk component synthesis and secretion by the mammary gland involve the expression of a large number of genes whose nutritional regulation remains poorly defined. In this study, 14 lactating goats received 3 experimental diets: 1- the basal diet with hay prepared from regrowth of natural grassland pasture offered ad libitum and a concentrate mixture (CTRL, n = 5)), the basal diet with 530 g/d extruded linseed (EL, n = 4) or with a combination of 340 g/d extruded linseed and 39 g/d of fish oil (ELFO, n = 5). To investigate the pathways regulated by nutrition, we examined the effect of EL and ELFO diets compared with CRTL diet and the effect of EL diet compared to ELFO diet on the expression of approximately 8400 genes in caprine mammary gland using a bovine oligonucleotide microarray.
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Project description:Arouquesa breed is an autochthonous Portuguese breed produced under a traditional mountain system. It is known for its Arouquesa PDO beef, a high-quality product with valued organoleptic characteristics. There is a need to improve production systems without affecting beef quality. The aim of this work is to compare the proteomics profile from the Longissimus thoracis muscle from Arouquesa animals produced under different systems. Sixty weaners were produced under the following systems: traditional (TF) and traditional with starter feed supplementation (TF+S1) with weaning and slaughtering at 8 months, the S1+S2 (weaning at 5 months and grower supplement until slaughter) and two rearing periods with finishing supplementation (TF+S3 and S3). Upon slaughter, samples of L. thoracis were taken and analyzed using a shotgun proteomics workflow. Several putative biomarkers of beef quality for the Arouquesa breed were identified: VIM, FSCN1, SERPINH1, ALDH1A1, NDUFB5, ANXA1, PDK4, CEMIP2, NDUFB9, PDLIM1, OXCT1, MYH4. These proteins were involved in actin binding, skeletal muscle development and in the mitochondrial respiratory chain and they can influence mostly meat tenderness and color. Our results demonstrate the link between production practices and putative meat quality signatures, that have potential to improve traceability of certified products.
2024-08-08 | PXD048338 | Pride
Project description:The aim of this study was to determine the effects of linseed dietary supplementation on gene expression in the mammary gland of grazing dairy cows. Milk composition and gene expression in the mammary gland tissue were evaluated in dairy cows supplemented with linseed. The linseed supplementation improves the health and nutrition quality aspects of dairy milk, but also affects the gene networks expression signature associated with cellular growth and proliferation, cell-death, signalling, nutrient metabolism, and immune response, and in turn, the mammary gland integrity and health.
2012-11-18 | GSE24200 | GEO
Project description:The goal of the study is to identify gene expression during seed development process in linseed flax.
2019-04-27 | GSE130378 | GEO
Project description:The aim of this study was to determine the effects of linseed dietary supplementation on gene expression in the mammary gland of grazing dairy cows. Milk composition and gene expression in the mammary gland tissue were evaluated in dairy cows supplemented with linseed. The linseed supplementation improves the health and nutrition quality aspects of dairy milk, but also affects the gene networks expression signature associated with cellular growth and proliferation, cell-death, signalling, nutrient metabolism, and immune response, and in turn, the mammary gland integrity and health. The experiment was carried out in a complete randomized blocked designed structure comprising 14 Holstein-Friesian cows (6 second parity, 2 third parity and 6 older cows), selected from a 550-cow herd. Cows were paired in 7 blocks on the basis of similarity in parity (second parity, third parity and older cows), expected date of calving, and milk performance in the previous lactation (in order of priority). Cows within each block were randomly allocated to one of two treatment groups, “Omega” or “Control”. The dietary Omega treatment consisted of a basal diet supplemented with a concentrate-mixture including linseed on a dry matter (DM) basis, whereas cows in treatment group Control were supplemented with a concentrate mixture without linseed. Linseed was chosen because it is rich in c9,c12,c15-18:3 (ALA). Concentrate mixtures were fed with a concentrate dispenser. Experimental treatments started 3 weeks before the expected calving date (wk -3) and lasted until 6 weeks after calving (wk 6).
2012-11-18 | E-GEOD-24200 | biostudies-arrayexpress
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Project description:The bovine transcriptome dynamics in logissimus muscle (LM) during the post-natal growth remain unknown. Biopsies of LM from Angus steers were harvested at 0, 60, 120, and 220 d from early-weaning. A 13,153 bovine oligonucleotide array was used for transcript profiling. Functional analysis of microarray data was performed using the Dynamic Impact Approach (DIA) by means of KEGG and DAVID databases. During the growing phase, most of the highly-impacted pathways (e.g. Ascorbate and aldarate metabolism, Drug metabolism - cytochrome P450 and Retinol metabolism) were inhibited. The finishing phase, was characterized with the most striking differences with 3,784 differentially expressed genes (DEG; FDR <0.01). The functional analysis of those DEG revealed that the most-impacted KEGG canonical pathway was “Glycosylphosphatidylinositol (GPI) - anchor biosynthesis”. The inhibition of this pathway suggested a unique role of GPI-anchor proteins in intracellular trafficking during the finishing phase. A mechanism regulating muscle growth during the finishing phase was uncovered in which inhibition of calpastatin and activation of tyrosine aminotransferase ubiquitination promote proteasomal degradation, while the concurrent activation of ribosomal proteins promotes protein synthesis, thus, the balance of these processes likely results in a steady state of protein turnover during the finishing phase. Overall, results underscored the importance of transcriptome dynamics in LM to support key biological functions during rapid growth.
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