A porcine gluteus medius muscle genome-wide transcriptome analysis: dietary effects of omega-6 and omega-3 fatty acids on biological mechanisms

Ogłuszka, Magdalena; Szostak, Agnieszka; Pas, M.F.W. te; Poławska, Ewa; Urbański, Paweł; Blicharski, Tadeusz; Pareek, Chandra Shekhar; Juszczuk-Kubiak, Edyta; Dunkelberger, Jenelle; Horbańczuk, J.O.; Pierzchała, M.

doi:10.1186/s12263-017-0552-8

Cited by 20 publications

(23 citation statements)

References 39 publications

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“…Aim of the presented study was to investigate the liver transcriptome and to explore the genetic variability in terms of SNPs/SNVs in the Polish Landrace pigs fed with PUFAs diets. Our results provide novel cSNP transcriptomic data (https://www.ncbi.nlm.nih.gov/sra) of Polish Landrace breed to explain the regulatory mechanisms of the liver tissue's biological response to increased concentration of PUFAs diets [22]. Related studies showed that consumption of PUFAs and other fatty acids diets were genetically regulated the growth performance and immune system in pigs [23].…”

Section: Discussionmentioning

confidence: 71%

“…Research materials: The liver tissues samples of Polish Landrace pigs for RNA-seq based NGS experiment were selected on the basis of fatty acid profiles in order to compare the liver transcriptomes characterized by low (control groups) and high (PUFAs enriched diet groups) omega-6/ omega-3 fatty acids ratio in Polish Landrace pigs. The threshold value of < 7 for low and > 7 for high omega-6/omega-3 fatty acids ratio was used in accordance to previous study [22]. After slaughtering, the liver tissues were collected at the Institute IGHZ, Jastrzębiec and were frozen in liquid nitrogen and stored at − 80°C for further RNA extraction.…”

Section: Methodsmentioning

confidence: 99%

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RNA-seq based SNP discovery in liver transcriptome of Polish Landrace pigs

Pierzchała¹,

Ogłuszka²,

Goluch³

et al. 2019

TRVS

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Background: RNA-seq technology is most commonly used in quantitative measurement of gene expression levels and identification of non-annotated transcripts. It is also used for the coding SNPs (cSNPs) discoveries in an efficient and cost-effective way. The aim of this study was to identify the putative genetic cSNPs variants in liver transcriptome of Polish Landrace pigs fed with high and low (normal) omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) diets.Methods. RNA-seq based NGS experiment was performed on Polish Landrace pigs fed with high and low diets. Total RNA were isolated from liver tissues ofPUFAs dietary of Polish Landrace pigs. The RNA-seq libraries preparations were performed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control (QC) of raw RNA-seq data of liver transcriptome was performed using the Trimmomatic and FastQC tools. The paired-end mapping of the liver transcriptome RNA-seq data (n=12) was performed on the reference genome Sus scrofa v.10.2, followed by cSNPs discovery using GATK and SAMtools bioinformatics SNPs caller tools. RNA-seq based SNP discovery in liver transcriptome TRANSLATioNAL ReSeARch iN VeTeRiNARy ScieNceVol 2, No 1, 2019Conclusions. Study concluded that identification of cSNPs dataset representing the liver transcriptome of Polish Landrace pigs fed with a control diet (low) and pigs fed with a PUFAs diet (high) may be helpful to develop a new set of genetic markers for trait-associated studies (viz., growth and metabolic traits) specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in the genetic improvement of the pig production traits using the genome-wide association studies (GWAS) and to finally implement on marker assisted selection (MAS) and genomics selection (GS) program in active breeding population of Polish Landrace pigs in Poland.

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Section: Discussionmentioning

confidence: 71%

Section: Methodsmentioning

confidence: 99%

RNA-seq based SNP discovery in liver transcriptome of Polish Landrace pigs

Pierzchała¹,

Ogłuszka²,

Goluch³

et al. 2019

TRVS

Self Cite

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show abstract

“…Our results provide novel cSNP transcriptomic data (https://www. ncbi.nlm.nih.gov/sra) of Polish Landrace breed to explain the regulatory mechanisms of the muscle tissue's biological response to increased concentration of omega-6 and omega-3 fatty acids (PUFAs) diets [22]. Recent studies have reported that consumption of PUFAs and other fatty acids diets were genetically regulated the growth performance and immune system in pigs [23].…”

Section: Discussionmentioning

confidence: 99%

“…The gluteus medius muscle samples of Polish Landrace pigs for RNA-seq based NGS experiment were selected based on fatty acid profiles in order to compare muscle transcriptomes characterized by low (control groups) and high (PUFAs enriched diet groups) omega-6/omega-3 fatty acids ratio in Polish Landrace pigs. The threshold value of < 7 for low and > 7 for high omega-6/omega-3 fatty acids ratio was used in this study [22]. After slaughtering the gluteus medius muscle tissues were collected at the Institute IGHZ, Jastrzębiec and were frozen in liquid nitrogen and stored at − 80 °C for further RNA extraction.…”

Section: Animalsmentioning

confidence: 99%

RNA-seq based SNP discovery in gluteus medius muscle of Polish Landrace pigs

Pierzchała

Ogłuszka

Poławska

et al. 2019

TRVS

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Background: Single nucleotide polymorphisms (SNPs) are the well-known molecular markers in genetics and breeding studies applied to veterinary sciences and livestock production. Advancement of next generation sequencing (NGS) provides a high-throughput means of potential putative SNP discovery. The aim of the study was to identify the putative genetic variants in gluteus medius muscle transcriptome of Polish Landrace pigs.Methods. RNA-seq based NGS experiment was performed on Polish Landrace pigs fed with omega-6 and omega-3 polyunsaturated fatty acids (and normal diets. Isolation of total RNA from gluteus medius muscle was performed PUFAs dietary of Polish Landrace pigs. The RNA-seq libraries were constructed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control of raw RNA-seq data was performed using the Trimmomatic and FastQC tools. High QC pairedend RNA-seq data of gluteus medius muscle transcriptome were mapped to the reference genome Sus scrofa v.10.2. Finally, the SNPs discovery was performed using GATK and SAMtools bioinformatics SNPs caller tools. Results:The Fastq RNA-seq data generated from two pooled paired-end libraries (151bp) of gluteus medius muscle tissue of Polish Landrace pigs were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Study identified a total of 50.5 million pairedend reads (32.5 million low PUFAs dietary group and 18 million reads high PUFAs dietary group) of gluteus medius muscle transcriptome of Polish Landrace pigs. SNP discovery identified a total of 35436 homozygous and 28644 heterozygous cSNPs in gluteus medius muscle transcriptomes representing both dietary groups of Polish Landrace pig. Moreover, a total of 25187 and 5488 cSNP were identified as synonymous SNPs, and 18005 and 4780 cSNP were identified as nonsynonymous SNPs. Finally, single nucleotide variation (SNV) representing substitutions of all four possibilities (A,T,G,C) were identified ranging 2935 to 3227 SNVs (high PUFAs) and 3528 to 3882 SNVs (low PUFAs) for the heterozygous cSNPs and 2712 to 4058 (high PUFAs) and 4169 to 5692 SNVs (low PUFAs) for the heterozygous SNPs in gluteus medius muscle transcriptomes of Polish Landrace pigs. Conclusions.Study concluded that identification of cSNPs dataset representing the gluteus medius muscle transcriptome of Polish Landrace pigs fed with a control diet (low) and pigs fed with a PUFAs diet (high) may be helpful to develop a new set of genetic markers specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in genome-wide association studies (GWAS) and to finally implement on marker assisted selection (MAS) and genomics selection (GS) program in active breeding population of Polish Landrace pigs in Poland.

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“…Another suggested mechanism is that through its ability to increase muscle cell membrane lipid content/composition and fluidity, LCn-3PUFAs supplementation may modulate key substrates along the anabolic signaling cascades such as the activating protein kinase C (PKC) pathway, which leads to increased translational activity and protein synthesis (Smith et al, 2011b). More importantly, several studies in human and other animal models (Castillero et al, 2009;Ogluszka et al, 2017;Yoshino et al, 2016) support that LCn-3PUFAs supplementation leads to transcriptional regulation of skeletal muscle metabolism thus contributing to the aforementioned mechanisms. For instance, Yoshino et al (2016) found that the beneficial effects of LCn-3PUFAs on muscle mass, strength, and function in older adults may be in part transcriptionally regulated and involve gene set pathways related to mitochondrial function, structural support, anabolic signaling, and both calpainand ubiquitin-mediated proteolysis.…”

Section: Skeletal Muscle Condition Is Critical To Survival In Variomentioning

confidence: 99%

The role of omega-3 fatty acids in skeletal muscle anabolism, strength, and function in healthy and diseased states

et al. 2017

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Omega‐3 fatty acids (LCn‐3PUFAs) have become increasingly successful and important components of diet regimens used for improving and/or maintaining muscle mass, strength, and functional ability, especially in older adults, for certain illnesses or during traumatic injury. Using data from human, cell culture and animal model‐based studies, various investigators suggest that LCn‐3PUFAs are extremely potent in either directly stimulating muscle protein anabolism or reducing muscle and plasma levels of pro‐inflammatory cytokines. However, a few others report that such benefits from LCn‐3PUFAs are at best minimal. In recognition of the growing importance of LCn‐3PUFAs in nutritional strategies aimed at maintaining adequate muscle mass, strength, and function during various circumstances, this work provides an examination of available data, reviews certain limitations of available studies on this theme, and suggests areas of focus for future research. Practical applications As the largest tissue in the body, skeletal muscle metabolism has a substantial impact on an individual's overall health, thus dietary strategies are critical to help optimize its metabolic functions. This review will contribute toward increasing awareness of the growing efforts and strategies to incorporate LCn‐3PUFAs in diet regimens and supplements used to counteract diminishing muscle mass, strength, and function due to sarcopenia and other muscle impairment conditions such as cancers, traumatic injury, and infection (sepsis). More research is needed in this area to address issues such as the minimum dose of LCn‐3PUFAs supplementation required to maintain and/or increase muscle protein synthesis or lean body mass, and what ratio of administered LCn‐3PUFAs is absorbed into the blood.

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A porcine gluteus medius muscle genome-wide transcriptome analysis: dietary effects of omega-6 and omega-3 fatty acids on biological mechanisms

Cited by 20 publications

References 39 publications

RNA-seq based SNP discovery in liver transcriptome of Polish Landrace pigs

RNA-seq based SNP discovery in liver transcriptome of Polish Landrace pigs

RNA-seq based SNP discovery in gluteus medius muscle of Polish Landrace pigs

The role of omega-3 fatty acids in skeletal muscle anabolism, strength, and function in healthy and diseased states

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