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Functional genomics of the digestive tract in broilers

Background The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider vari... Full description

Journal Title: BMC Genomics 2018, Vol.19
Main Author: Juanchich, Amélie
Other Authors: Hennequet-Antier, Christelle , Cabau, Cédric , Duclos, Michel , Mignon-Grasteau, Sandrine , Narcy, Agnès
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 14712164 ; DOI: 10.1186/s12864-018-5344-z
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title: Functional genomics of the digestive tract in broilers
format: Article
creator:
  • Juanchich, Amélie
  • Hennequet-Antier, Christelle
  • Cabau, Cédric
  • Duclos, Michel
  • Mignon-Grasteau, Sandrine
  • Narcy, Agnès
subjects:
  • Feeds
  • Muscles
  • Bioinformatics
  • Animals
  • Poultry Farming
  • Genes
  • Bioinformatics
  • Transcription
  • Enrichment
  • Sustainability
  • Genomes
  • Genomics
  • Bioinformatics
  • Digestive Tract
  • Efficiency
  • Breeding
  • Gene Expression
  • Gene Expression
  • Bioinformatics
  • Tissues
  • Enrichment
  • Functional Analysis
  • Muscle Contraction
  • Jejunum
  • Wildfowl
  • Gene Expression
  • Poultry Farming
  • Sustainable Agriculture
  • Poultry
  • Chickens
  • Motility
  • Gizzard
  • Ribonucleic Acid–RNA
  • Ribonucleic Acid–RNA
  • Chicken
  • Broiler
  • Digestive Tract
  • Transcriptome
  • Gizzard
  • Intestine
ispartof: BMC Genomics, 2018, Vol.19
description: Background The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. The aim of the project was to improve the understanding of genes involved in digestive functions by characterizing the transcriptome of different sections of the digestive tract: the junction between the proventriculus and the gizzard, the gizzard, the gastroduodenal junction, and the jejunum. Results Total RNA from the four tissues were sequenced on a HiSeq2500 for six 23-day-old chickens from a second generation (F2) cross between two lines that were divergent for their digestive efficiency (D+/D-). Bioinformatics and biostatistics analyses of the RNA-seq data showed a total of 11,040 differentially expressed transcripts between the four tissues. In total, seven clusters of genes with markedly different expression profiles were identified. Functional analysis on gene groups was performed using “Gene Ontology” and semantic similarity. It showed a significant enrichment of body immune defenses in the jejunum, and an enrichment of transcriptional activity in the gizzard. Moreover, an interesting enrichment for neurohormonal control of muscle contraction was found for the two gizzard’s junctions. Conclusion This analysis allows us to draw the first molecular portrait of the different sections of the digestive tract, which will serve as a basis for future studies on the genetic and physiological control of the response of the animal to feed variations.
language: eng
source:
identifier: E-ISSN: 14712164 ; DOI: 10.1186/s12864-018-5344-z
fulltext: fulltext_linktorsrc
issn:
  • 14712164
  • 1471-2164
url: Link


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titleFunctional genomics of the digestive tract in broilers
creatorJuanchich, Amélie ; Hennequet-Antier, Christelle ; Cabau, Cédric ; Duclos, Michel ; Mignon-Grasteau, Sandrine ; Narcy, Agnès
ispartofBMC Genomics, 2018, Vol.19
identifierE-ISSN: 14712164 ; DOI: 10.1186/s12864-018-5344-z
subjectFeeds ; Muscles ; Bioinformatics ; Animals ; Poultry Farming ; Genes ; Bioinformatics ; Transcription ; Enrichment ; Sustainability ; Genomes ; Genomics ; Bioinformatics ; Digestive Tract ; Efficiency ; Breeding ; Gene Expression ; Gene Expression ; Bioinformatics ; Tissues ; Enrichment ; Functional Analysis ; Muscle Contraction ; Jejunum ; Wildfowl ; Gene Expression ; Poultry Farming ; Sustainable Agriculture ; Poultry ; Chickens ; Motility ; Gizzard ; Ribonucleic Acid–RNA ; Ribonucleic Acid–RNA ; Chicken ; Broiler ; Digestive Tract ; Transcriptome ; Gizzard ; Intestine
descriptionBackground The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. The aim of the project was to improve the understanding of genes involved in digestive functions by characterizing the transcriptome of different sections of the digestive tract: the junction between the proventriculus and the gizzard, the gizzard, the gastroduodenal junction, and the jejunum. Results Total RNA from the four tissues were sequenced on a HiSeq2500 for six 23-day-old chickens from a second generation (F2) cross between two lines that were divergent for their digestive efficiency (D+/D-). Bioinformatics and biostatistics analyses of the RNA-seq data showed a total of 11,040 differentially expressed transcripts between the four tissues. In total, seven clusters of genes with markedly different expression profiles were identified. Functional analysis on gene groups was performed using “Gene Ontology” and semantic similarity. It showed a significant enrichment of body immune defenses in the jejunum, and an enrichment of transcriptional activity in the gizzard. Moreover, an interesting enrichment for neurohormonal control of muscle contraction was found for the two gizzard’s junctions. Conclusion This analysis allows us to draw the first molecular portrait of the different sections of the digestive tract, which will serve as a basis for future studies on the genetic and physiological control of the response of the animal to feed variations.
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descriptionBackground The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. The aim of the project was to improve the understanding of genes involved in digestive functions by characterizing the transcriptome of different sections of the digestive tract: the junction between the proventriculus and the gizzard, the gizzard, the gastroduodenal junction, and the jejunum. Results Total RNA from the four tissues were sequenced on a HiSeq2500 for six 23-day-old chickens from a second generation (F2) cross between two lines that were divergent for their digestive efficiency (D+/D-). Bioinformatics and biostatistics analyses of the RNA-seq data showed a total of 11,040 differentially expressed transcripts between the four tissues. In total, seven clusters of genes with markedly different expression profiles were identified. Functional analysis on gene groups was performed using “Gene Ontology” and semantic similarity. It showed a significant enrichment of body immune defenses in the jejunum, and an enrichment of transcriptional activity in the gizzard. Moreover, an interesting enrichment for neurohormonal control of muscle contraction was found for the two gizzard’s junctions. Conclusion This analysis allows us to draw the first molecular portrait of the different sections of the digestive tract, which will serve as a basis for future studies on the genetic and physiological control of the response of the animal to feed variations.
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authorJuanchich, Amélie ; Hennequet-Antier, Christelle ; Cabau, Cédric ; Duclos, Michel ; Mignon-Grasteau, Sandrine ; Narcy, Agnès
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11Digestive Tract
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abstractBackground The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. The aim of the project was to improve the understanding of genes involved in digestive functions by characterizing the transcriptome of different sections of the digestive tract: the junction between the proventriculus and the gizzard, the gizzard, the gastroduodenal junction, and the jejunum. Results Total RNA from the four tissues were sequenced on a HiSeq2500 for six 23-day-old chickens from a second generation (F2) cross between two lines that were divergent for their digestive efficiency (D+/D-). Bioinformatics and biostatistics analyses of the RNA-seq data showed a total of 11,040 differentially expressed transcripts between the four tissues. In total, seven clusters of genes with markedly different expression profiles were identified. Functional analysis on gene groups was performed using “Gene Ontology” and semantic similarity. It showed a significant enrichment of body immune defenses in the jejunum, and an enrichment of transcriptional activity in the gizzard. Moreover, an interesting enrichment for neurohormonal control of muscle contraction was found for the two gizzard’s junctions. Conclusion This analysis allows us to draw the first molecular portrait of the different sections of the digestive tract, which will serve as a basis for future studies on the genetic and physiological control of the response of the animal to feed variations.
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