Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K microarray. II. Differentially expressed focus genes

Bottje, Walter; Kong, Byung-Whi; Song, Joon Jin; Lee, J.Y.; Hargis, Billy M.; Lassiter, Kentu; Wing, T.; Hardiman, J.

doi:10.3382/ps.2012-02204

Cited by 37 publications

(65 citation statements)

References 83 publications

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“…Additionally, increased expression of adipose genes showed that PeM muscles may retain increased mass of adipose tissues, where the wooden breast myopathy showed increased occurrence of irregular adipose tissue throughout the muscle [19]. Higher expression of NOXO1 (NADPH oxidase organizer 1) indicates that oxidative stress and scavenging antioxidants are closely associated with feed efficiency, which has been reported previously [2, 3, 5]. PCSK1 (proprotein convertase subtilisin/kexin type 1) is not restricted to the expression in muscle tissues, and its functions in glucose and lipid metabolism [20, 21] implies that PeM muscle has more active cellular pathways for energy metabolism.…”

Section: Resultsmentioning

confidence: 71%

RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line

Kong¹,

Hudson

Seo³

et al. 2017

BMC Genomics

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BackgroundModern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations accumulated in modern broiler breeder lines during selective breeding conducted over several decades.MethodsTo identify genes important in determining muscle growth and feed efficiency in broilers, RNA sequencing (RNAseq) was conducted with breast muscle in modern pedigree male (PeM) broilers (n = 6 per group), and with an unselected foundation broiler line (Barred Plymouth Rock; BPR). The RNAseq analysis was carried out using Ilumina Hiseq (2 x 100 bp paired end read) and raw reads were assembled with the galgal4 reference chicken genome. With normalized RPM values, genes showing >10 average read counts were chosen and genes showing <0.05 p-value and >1.3 fold change were considered as differentially expressed (DE) between PeM and BPR. DE genes were subjected to Ingenuity Pathway Analysis (IPA) for bioinformatic functional interpretation.ResultsThe results indicate that 2,464 DE genes were identified in the comparison between PeM and BPR. Interestingly, the expression of genes encoding mitochondrial proteins in chicken are significantly biased towards the BPR group, suggesting a lowered mitochondrial content in PeM chicken muscles compared to BPR chicken. This result is inconsistent with more slow muscle fibers bearing a lower mitochondrial content in the PeM. The molecular, cellular and physiological functions of DE genes in the comparison between PeM and BPR include organismal injury, carbohydrate metabolism, cell growth/proliferation, and skeletal muscle system development, indicating that cellular mechanisms in modern broiler lines are tightly associated with rapid growth and differential muscle fiber contents compared to the unselected BPR line. Particularly, PDGF (platelet derived growth factor) signaling and NFE2L2 (nuclear factor, erythroid 2-like 2; also known as NRF2) mediated oxidative stress response pathways appear to be activated in modern broiler compared to the foundational BPR line. Upstream and network analyses revealed that the MSTN (myostatin) –FST (follistatin) interactions and inhibition of AR (androgen receptor) were predicted to be effective regulatory factors for DE genes in modern broiler line. PRKAG3 (protein kinase, AMP-activated, gamma 3 non-catalytic subunit) and LIPE (lipase E) are predicted as core regulatory factors for myogenic development, nutrient and lipid metabolism.ConclusionThe highly upregulated genes in PeM may represent phenotypes of subclinical myopathy commonly observed in the commercial broiler breast tissue, that can lead to muscle hardening, named as woody breast. By investigating global gene expression in a highly selected pedigree broiler line and a foundational breed (Barred Plymouth Rock), the results provide insight into cellular mechanisms that re...

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Section: Resultsmentioning

confidence: 71%

RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line

Kong¹,

Hudson

Seo³

et al. 2017

BMC Genomics

View full text Add to dashboard Cite

show abstract

“…Altogether, this suggests diminished oxidative stress in more efficient pigs. In agreement with this assumption, research in broilers has consistently shown that muscle mitochondria from high efficient birds produce less hydrogen peroxide [37]. In addition, others have shown that ROS production in muscle and RFI values were positively correlated, although no difference in electron leakage was seen in mitochondria prepared from livers of low and high RFI pig lines [38].…”

Section: Discussionmentioning

confidence: 76%

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

et al. 2017

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BackgroundAnimal’s efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI).ResultsPigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis and efflux in liver and perirenal fat were also differentially regulated in pigs from the low vs high RFI lines.ConclusionsNon-productive functions such as immunity, defense against pathogens and oxidative stress contribute likely to inter-individual variations in feed efficiency.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3639-0) contains supplementary material, which is available to authorized users.

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“…A specific example of this includes the UQCRQ gene, which was identified as differentially expressed in the muscle tissue from these animals and displayed the same direction of expression in all cohorts [5]. Oxidative stress has been proposed in many other studies as a factor that affects feed efficiency in swine, poultry, and beef cattle [25][26][27][28][29][30].…”

Section: Genes/pathways Identified For Gainmentioning

confidence: 95%

Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers

et al. 2020

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Mesenteric fat is a visceral fat depot that increases with cattle maturity and can be influenced by diet. There may be a relationship between the accumulation of mesenteric fat and feed efficiency in beef cattle. The purpose of this study was to identify genes that may be differentially expressed in steers with high and low BW gain and feed intake. RNA-Seq was used to evaluate the transcript abundance of genes in the mesenteric fat from a total of 78 steers collected over 5 different cohorts. A meta-analysis was used to identify genes involved with gain, feed intake or the interaction of both phenotypes. The interaction analysis identified 11 genes as differentially expressed. For the main effect of gain, a total of 87 differentially expressed genes (DEG) were identified (P ADJ <0.05), and 24 were identified in the analysis for feed intake. Genes identified for gain were involved in functions and pathways including lipid metabolism, stress response/protein folding, cell proliferation/growth, axon guidance and inflammation. The genes for feed intake did not cluster into pathways, but some of the DEG for intake had functions related to inflammation, immunity, and/or signal transduction (JCHAIN, RIPK1, LY86, SPP1, LYZ, CD5, CD53, SRPX, and NF2). At P ADJ <0.1, only 4 genes (OLFML3, LOC100300716, MRPL15, and PUS10) were identified as differentially expressed in two or more cohorts, highlighting the importance of evaluating the transcriptome of more than one group of animals and incorporating a meta-analysis. This meta-analysis has produced many mesenteric fat DEG that may be contributing to gain and feed intake in cattle. OPEN ACCESSCitation: Lindholm-Perry AK, Freetly HC, Oliver WT, Rempel LA, Keel BN (2020) Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers. PLoS ONE 15(1): e0227154. https://

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Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K microarray. II. Differentially expressed focus genes

Cited by 37 publications

References 83 publications

RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line

RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers

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