Transcriptome architecture across tissues in the pig

Ferraz, André Luiz Julien; González-Ojeda, Alejandro; López‐Béjar, Manel; Fernandes, Lana Teixeira; Castelló, Anna; Folch, Josep María; Pérez‐Enciso, Miguel

doi:10.1186/1471-2164-9-173

Cited by 48 publications

(62 citation statements)

References 40 publications

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“…2A) is consistent with the previous results, which showed that the largest source of variability was tissue rather than sex or breed (Ferraz et al, 2008). The significant correlation coefficient and the GO term analysis of DEGs between brain and liver samples showed the differentially expressed genes to relate to different physiological functions and exhibited a strong correspondence to tissue functions.…”

Section: Discussionsupporting

confidence: 91%

“…From above, swine brain and liver are the important targeted tissues in the biomedical model system. Currently, although various swine tissue transcriptomic data have been obtained, more studies focused on muscle to gain insights into improving meat quality from the perspective of agricultural economy (Monego et al, 2005;Ferraz et al, 2008), the transcriptomic analysis of brains and livers in pig remains limited. The brain and liver are complementary and at the crossroads of many key neuroendocrine, metabolic and behavioral regulations.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptomic analysis of Rongchang pig brains and livers

Gan

Xie

Fu-yuan

et al. 2015

Gene

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis of Rongchang pig brains and livers

Gan

Xie

Fu-yuan

et al. 2015

Gene

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“…At the present time, there are no sequences from this breed on public sequence databases. On the other hand, data from Meishan and other breeds have already been described in more than one study (Tang et al, 2007;Ferraz et al, 2008). All ESTs were deposited in the dbEST database and will not only be a valuable addition to the current archived sequences from pig, but will also provide a major resource for the comparative analysis of gene expression profiles between commercial and naturalized breeds.…”

Section: Discussionmentioning

confidence: 99%

Transcript profiling of expressed sequence tags from semimembranosus muscle of commercial and naturalized pig breeds

Nascimento

Peixoto²,

Verardo³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. In general, genetic differences across different breeds of pig lead to variation in mature body size and slaughter age. The Commercial breeds Duroc and Large White and the local Brazilian breed Piau are ostensibly distinct in terms of growth and muscularity, commercial breeds are much leaner while local breeds grow much slower and are fat type pigs. However, the genetic factors that underlie such distinctions remain unclear. We used expressed sequence tags (ESTs) to characterize and compare transcript profiles in the semimembranosus muscle of these pig breeds. Our aim was to identify differences in breedrelated gene expression that might influence growth performance and meat quality. We constructed three non-normalized cDNA libraries from semimembranosus muscle, using two samples from each one, of these three breeds; 6902 high-quality ESTs were obtained. Cluster analysis was performed and these sequences were clustered into 3670 unique sequences; 24.7% of the sequences were categorized as contigs and 75.3% of the sequences were singletons. Based on homology searches against the Swiss-Prot protein database, we were able to assign a putative protein identity to only 1050 unique sequences. Among these, 58.5% were full-length protein sequences and 17.2% were pig-specific sequences. Muscle structural and cytoskeletal proteins, such as actin, and myosin, were the most abundant transcripts (16.7%) followed by those related to mitochondrial function (12.9%), and ribosomal proteins (12.4%). Furthermore, ESTs generated in this study provide a rich source for identification of novel genes and for the comparative analysis of gene expression patterns in divergent pig breeds.

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“…Notch signaling pathway and the WNT signaling pathway. Recent study on porcine microarray expression profi ling in 16 tissues revealed the interaction between gene and tissue for differentially expressed genes targeted differentially for each tissues's transcriptome (Ferraz et al, 2008). Evidence from the recently published transcriptomics based nutritional studies performed in livestock species suggests that, with appropriate study design, it is feasible to apply transcriptomic methods successfully in animal feed and nutritional research.…”

Section: Application Of Transcriptomics In Animal and Feed Sciencesmentioning

confidence: 99%

Application of nutrigenomics tools in animal feeding and nutritional research

Zduńczyk¹,

Pareek²

2009

J. Anim. Feed Sci.

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The development of nutrigenomic studies has brought about a number of new research tools (transcriptomics, proteomics and metabolomics), which are important in animal nutrition and food research. This review presents an overview on the application of nutrigenomics tools in this scientifi c area. The use of microarray technologies -the main tools of transcriptomics, has allowed new information concerning the physiological effect of different dietary proteins, of omega-3 polyunsaturated fatty acids and dietary conditioning of colon cancer, to be obtained. The use of proteomics tools (mainly two-dimensional electrophoresis) revealed new information concerning the protein composition of egg and poultry meat proteins, the effect of dietary methionine on breast-meat accretion, the toxicity of dioxin and the safe use of transgenic crops in animal nutrition. Metabolomic analysis allowed the detection of changes in the biochemical profi les of plasma and urine from pigs fed different diets and the determination of metabolite profi les in the liver of rats used as an animal model to characterize the toxicity of triazol fungicides. In livestock species, the microarray technology was discussed and reviewed as potential nutrigenomics tools, in context to its economic benefi ts and improvement of the food quality and safety in dairy and meat industries. However, the newly emerged nutrigenomics tools like -gene expression-based biomarker development still poses a major challenge. Finally, latest developments in the standardization of metobolomics data in relation to functional genomics, nutrigenomics and toxicology studies are discussed.

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Transcriptome architecture across tissues in the pig

Cited by 48 publications

References 40 publications

Transcriptomic analysis of Rongchang pig brains and livers

Transcriptomic analysis of Rongchang pig brains and livers

Transcript profiling of expressed sequence tags from semimembranosus muscle of commercial and naturalized pig breeds

Application of nutrigenomics tools in animal feeding and nutritional research

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