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Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens' feed efficiency.

Zhou N, Lee WR, Abasht B - BMC Genomics (2015)

Bottom Line: Differential expression analysis identified 1,059 genes (FDR < 0.05) that significantly divergently expressed in breast muscle between the high- and low-FE chickens.This study provides novel insights into transcriptional differences in breast muscle between high- and low-FE broiler chickens.Our results show that feed efficiency is associated with breast muscle growth in these birds; furthermore, some physiological changes, e.g., inflammatory response and oxidative stress, may occur in the breast muscle of the high-FE chickens, which may be of concern for continued selection for both of these traits together in modern broiler chickens.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA. nanzhou@udel.edu.

ABSTRACT

Background: Advanced selection technologies have been developed and continually optimized to improve traits of agricultural importance; however, these methods have been primarily applied without knowledge of underlying biological changes that may be induced by selection. This study aims to characterize the biological basis of differences between chickens with low and high feed efficiency (FE) with a long-term goal of improving the ability to select for FE.

Results: High-throughput RNA sequencing was performed on 23 breast muscle samples from commercial broiler chickens with extremely high (n = 10) and low (n = 13) FE. An average of 34 million paired-end reads (75 bp) were produced for each sample, 80% of which were properly mapped to the chicken reference genome (Ensembl Galgal4). Differential expression analysis identified 1,059 genes (FDR < 0.05) that significantly divergently expressed in breast muscle between the high- and low-FE chickens. Gene function analysis revealed that genes involved in muscle remodeling, inflammatory response and free radical scavenging were mostly up-regulated in the high-FE birds. Additionally, growth hormone and IGFs/PI3K/Akt signaling pathways were enriched in differentially expressed genes, which might contribute to the high breast muscle yield in high-FE birds and partly explain the FE advantage of high-FE chickens.

Conclusions: This study provides novel insights into transcriptional differences in breast muscle between high- and low-FE broiler chickens. Our results show that feed efficiency is associated with breast muscle growth in these birds; furthermore, some physiological changes, e.g., inflammatory response and oxidative stress, may occur in the breast muscle of the high-FE chickens, which may be of concern for continued selection for both of these traits together in modern broiler chickens.

No MeSH data available.


Related in: MedlinePlus

Upstream regulator JUN and FOS. A. Transcription factor JUN is predicted to be activated in the high-FE chickens with P-value = 1.70E-08 and Z-score = 2.923. B. FOS is predicted to be activated in the high-FE chickens with P-value = 7.64E-07 and Z-score = 2.277. Edges connecting the nodes are colored with orange when upstream regulators have activating effects on their target genes, blue when upstream regulators inhibit their downstream genes. Yellow edges indicate that the states of downstream genes are inconsistent with the prediction based on previous findings.
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Fig6: Upstream regulator JUN and FOS. A. Transcription factor JUN is predicted to be activated in the high-FE chickens with P-value = 1.70E-08 and Z-score = 2.923. B. FOS is predicted to be activated in the high-FE chickens with P-value = 7.64E-07 and Z-score = 2.277. Edges connecting the nodes are colored with orange when upstream regulators have activating effects on their target genes, blue when upstream regulators inhibit their downstream genes. Yellow edges indicate that the states of downstream genes are inconsistent with the prediction based on previous findings.

Mentions: Muscle inflammation is a key step in muscle remodeling, which can clean disrupted muscle cells and promote muscle regeneration by releasing growth factors [82]. A variety of circumstances (e.g., muscle injury, exercise and obesity) can activate transcription factors NF-kB and c-Jun/FOS in muscle cells, resulting in the expression and secretion of several factors [83]. These factors, including cytokines and other non-protein mediators, can either directly attract circulating immune cells to the muscle or activate resident immune cells, providing chemotactic signals for recruitment [84]. As a consequence, a number of immune cells are recruited to the muscle, phagocytizing the cellular debris and producing cytokines affecting muscle cells [83,85]. The IPA upstream regulator analysis predicts that transcription factors JUN and FOS are activated in the breast muscle of the high-FE birds (Figure 6). Protein encoded by JUN and FOS are components of activator protein 1 (AP-1), which is an important transcription factor responding to various physiological and pathological stimuli [86]. Overall, our results suggest that, compared with the low-FE birds, the high-FE birds experienced a more intense muscle restructuring and higher inflammatory responses in the breast muscle.Figure 6


Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens' feed efficiency.

Zhou N, Lee WR, Abasht B - BMC Genomics (2015)

Upstream regulator JUN and FOS. A. Transcription factor JUN is predicted to be activated in the high-FE chickens with P-value = 1.70E-08 and Z-score = 2.923. B. FOS is predicted to be activated in the high-FE chickens with P-value = 7.64E-07 and Z-score = 2.277. Edges connecting the nodes are colored with orange when upstream regulators have activating effects on their target genes, blue when upstream regulators inhibit their downstream genes. Yellow edges indicate that the states of downstream genes are inconsistent with the prediction based on previous findings.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4414306&req=5

Fig6: Upstream regulator JUN and FOS. A. Transcription factor JUN is predicted to be activated in the high-FE chickens with P-value = 1.70E-08 and Z-score = 2.923. B. FOS is predicted to be activated in the high-FE chickens with P-value = 7.64E-07 and Z-score = 2.277. Edges connecting the nodes are colored with orange when upstream regulators have activating effects on their target genes, blue when upstream regulators inhibit their downstream genes. Yellow edges indicate that the states of downstream genes are inconsistent with the prediction based on previous findings.
Mentions: Muscle inflammation is a key step in muscle remodeling, which can clean disrupted muscle cells and promote muscle regeneration by releasing growth factors [82]. A variety of circumstances (e.g., muscle injury, exercise and obesity) can activate transcription factors NF-kB and c-Jun/FOS in muscle cells, resulting in the expression and secretion of several factors [83]. These factors, including cytokines and other non-protein mediators, can either directly attract circulating immune cells to the muscle or activate resident immune cells, providing chemotactic signals for recruitment [84]. As a consequence, a number of immune cells are recruited to the muscle, phagocytizing the cellular debris and producing cytokines affecting muscle cells [83,85]. The IPA upstream regulator analysis predicts that transcription factors JUN and FOS are activated in the breast muscle of the high-FE birds (Figure 6). Protein encoded by JUN and FOS are components of activator protein 1 (AP-1), which is an important transcription factor responding to various physiological and pathological stimuli [86]. Overall, our results suggest that, compared with the low-FE birds, the high-FE birds experienced a more intense muscle restructuring and higher inflammatory responses in the breast muscle.Figure 6

Bottom Line: Differential expression analysis identified 1,059 genes (FDR < 0.05) that significantly divergently expressed in breast muscle between the high- and low-FE chickens.This study provides novel insights into transcriptional differences in breast muscle between high- and low-FE broiler chickens.Our results show that feed efficiency is associated with breast muscle growth in these birds; furthermore, some physiological changes, e.g., inflammatory response and oxidative stress, may occur in the breast muscle of the high-FE chickens, which may be of concern for continued selection for both of these traits together in modern broiler chickens.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA. nanzhou@udel.edu.

ABSTRACT

Background: Advanced selection technologies have been developed and continually optimized to improve traits of agricultural importance; however, these methods have been primarily applied without knowledge of underlying biological changes that may be induced by selection. This study aims to characterize the biological basis of differences between chickens with low and high feed efficiency (FE) with a long-term goal of improving the ability to select for FE.

Results: High-throughput RNA sequencing was performed on 23 breast muscle samples from commercial broiler chickens with extremely high (n = 10) and low (n = 13) FE. An average of 34 million paired-end reads (75 bp) were produced for each sample, 80% of which were properly mapped to the chicken reference genome (Ensembl Galgal4). Differential expression analysis identified 1,059 genes (FDR < 0.05) that significantly divergently expressed in breast muscle between the high- and low-FE chickens. Gene function analysis revealed that genes involved in muscle remodeling, inflammatory response and free radical scavenging were mostly up-regulated in the high-FE birds. Additionally, growth hormone and IGFs/PI3K/Akt signaling pathways were enriched in differentially expressed genes, which might contribute to the high breast muscle yield in high-FE birds and partly explain the FE advantage of high-FE chickens.

Conclusions: This study provides novel insights into transcriptional differences in breast muscle between high- and low-FE broiler chickens. Our results show that feed efficiency is associated with breast muscle growth in these birds; furthermore, some physiological changes, e.g., inflammatory response and oxidative stress, may occur in the breast muscle of the high-FE chickens, which may be of concern for continued selection for both of these traits together in modern broiler chickens.

No MeSH data available.


Related in: MedlinePlus