Integrated Transcriptomics Profiling in Chahua and Digao Chickens' Breast for Assessment Molecular Mechanism of Meat Quality Traits

Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.

Transcriptome-based analysis of early post-mortem formation of pale, soft, and exudative (PSE) pork

Pale, soft, and exudative (PSE) meat can cause consumer dissatisfaction and economic losses. This study determined meat quality, glycolytic enzyme activity, and differential gene expression in the longissimus lumborum (LL) and semimembranosus (SM) of normal and PSE pork carcasses. The SM did not result in PSE meat. Hexokinase, lactate dehydrogenase, and pyruvate kinase activities were lower in the SM of PSE carcasses than in the normal carcasses. Functional enrichment analysis revealed that immune, inflammatory, and muscle fibre genes were significantly enriched in PSE pork. More specifically, PPP1R3G and MSS51 may be key genes regulating pork quality in the SM. Meanwhile, the differential expression of PLVAB, ADIPOQ, LEP, MYH4, MYH7, MYL3, MYL6B, FOS, ATF3, and HSPA6 may induce PSE formation in the LL. These results may provide insights into PSE pork formation mechanisms and reveal candidate genes for improving meat quality after validation.

Phosphorylation state of pyruvate dehydrogenase and metabolite levels in turkey skeletal muscle in normal and pale, soft, exudative meats

1. Turkey production has increased dramatically as genetic selection has succeeded in increasing body weight and muscle yield to fulfil increasing consumer demand. However, producing fast-growing, heavily muscled birds is linked to increased heat stress susceptibility and can result in pale, soft, exudative (PSE) meat. Previous studies indicated that pyruvate dehydrogenase kinase 4 (PDK4) is significantly reduced in PSE samples, suggesting this as a candidate gene associated with the development of this problem.2. The objective of this study was to determine whether pre-market thermal challenge results in PSE meat as a result of differential expression of PDK4. Two genetic lines of turkeys were used in this study; the Randombred Control Line 2 (RBC2) and a commercial line. Turkeys were exposed to a pre-market thermal challenge of 12 h at 35°C followed by 12 h at 27°C for 5 d. Birds were slaughtered and processed according to industry standards. Pectoralis major samples were categorised as PSE or normal based on marinade uptake and cook loss indicators. In the first experiment, the relative expression of pyruvate dehydrogenase (PDH) and the phosphorylation state of PDH in normal and PSE turkey meat were analysed by western blotting. In the second experiment, the same samples were used to measure metabolite levels at 5 min post-mortem, comparing the normal to the PSE samples.3. The results of the first experiment showed that PSE samples had significantly lower total PDH (P = 0.029) compared to normal meat. However, there was no significant difference in the degree of phosphorylation of sites 1, 2 or 3. In the second experiment, there were no significant differences in glycogen, lactate, glycolytic potential or ATP when comparing PSE to control samples.4. These results suggested that a reduction in PDK4 expression alone does not explain the development of PSE meat.

Prospect of early vascular tone and satellite cell modulations on white striping muscle myopathy

Polyphasic myodegeneration potentially causes severe physiological and metabolic disorders in the breast muscle of fast-growing broiler chickens. To date, the etiology of recent muscle myopathies, such as the white striping (WS) phenotype, is still unknown. White striping–affected breast meats compromise the water holding capacity and predispose muscle to poor vascular tone, leading to the deterioration of meat qualities. Herein, this review article provides insight on the complexities around chicken breast myopathies: (i) the etiologies of WS occurrence in chicken; (ii) the metabolic changes that occur in WS defect in pectoralis major; and (iii) the interactions between breast muscle physiology and vascular tone. It also addressed the effects of nutritional supplements on muscle myopathies on chicken breast meats. Moreover, the review explored breast muscle biology focusing on the early preparation of satellite and vascular cells in fast-growth chicken breeds. Transcriptomics and histological analyses revealed poor vascularity in breast muscle of fast growth chickens. Thus, we suggest in ovo feeding of nutrients promoting vascularization and satellite cells replenishment as a potential strategy to enhance endothelium-derived nitric oxide availability to promote vascularization in the pectoralis major muscle region.

Functional contexts of adipose and gluteal muscle tissue gene co-expression networks in the domestic horse

A gene's response to an environment is tightly bound to the underlying genetic variation present in an individual's genome and varies greatly depending on the tissue it is being expressed in. Gene co-expression networks provide a mechanism to understand and interpret the collective transcriptional responses of genes. Here, we use the Camoco co-expression network framework to characterize the transcriptional landscape of adipose and gluteal muscle tissue in 83 domestic horses (Equus caballus) representing 5 different breeds. In each tissue, gene expression profiles, capturing transcriptional response due to variation across individuals, were used to build two separate, tissue-focused, genotypically-diverse gene co-expression networks. The aim of our study was to identify significantly co-expressed clusters of genes in each tissue, then compare the clusters across networks to quantify the extent that clusters were found in both networks as well as to identify clusters found in a single network. The known and unknown functions for each network were quantified using complementary, supervised and unsupervised approaches. First, supervised ontological enrichment was utilized to quantify biological functions represented by each network. Curated ontologies (GO and KEGG) were used to measure the known biological functions present in each tissue. Overall, a large percentage of terms (40.3% of GO and 41% of KEGG) were co-expressed in at least one tissue. Many terms were co-expressed in both tissues, however a small proportion of terms exhibited single tissue co-expression suggesting functional differentiation based on curated, functional annotation. To complement this, an unsupervised approach not relying on ontologies was employed. Strongly co-expressed sets of genes defined by Markov clustering identified sets of unannotated genes showing similar patterns of co-expression within a tissue. We compared gene sets across tissues and identified clusters of genes the either segregate in co-expression by tissue or exhibit high levels of co-expression in both tissues. Clusters were also integrated with GO and KEGG ontologies to identify gene sets containing previously curated annotations versus unannotated gene sets indicating potentially novel biological function. Coupling together these transcriptional datasets, we mapped the transcriptional landscape of muscle and adipose setting up a generalizable framework for interpreting gene function for additional tissues in the horse and other species.

RNA-seq-based quanitative transcriptome analysis of meat color and taste from chickens administered by eucalyptus leaf polyphenols extract

To evaluate how eucalyptus leaf polyphenol extract (EPE) affects chicken meat color and taste, we added different levels of EPE (0%, 0.06%, 0.09%, and 0.12%) to chicken feed. The redness (a^* value) and the myoglobin content of breast muscle in EPE group were remarkably higher. Furthermore, the guanosine monophosphate, histidine, and glycine muscle contents were also enhanced. Transcriptome analysis showed that 10 candidate genes related to meat quality were affected by EPE treatment. The identified genes, with functions critical to chicken meat color and taste, will help to determine the molecular mechanisms of EPE.

Absolute expressions of hypoxia-inducible factor-1 alpha (HIF1A) transcript and the associated genes in chicken skeletal muscle with white striping and wooden breast myopathies

Development of white striping (WS) and wooden breast (WB) in broiler breast meat have been linked to hypoxia, but their etiologies are not fully understood. This study aimed at investigating absolute expression of hypoxia-inducible factor-1 alpha subunit (HIF1A) and genes involved in stress responses and muscle repair using a droplet digital polymerase chain reaction. Total RNA was isolated from pectoralis major collected from male 6-week-old medium (carcass weight ≤ 2.5 kg) and heavy (carcass weight > 2.5 kg) broilers. Samples were classified as “non-defective” (n = 4), “medium-WS” (n = 6), “heavy-WS” (n = 7) and “heavy-WS+WB” (n = 3) based on abnormality scores. The HIF1A transcript was up-regulated in all of the abnormal groups. Transcript abundances of genes encoding 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (PFKFB4), lactate dehydrogenase-A (LDHA), and phosphorylase kinase beta subunit (PHKB) were increased in heavy-WS but decreased in heavy-WS+WB. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was up-regulated in non-defective samples. The muscle-specific mu-2 isoform of glutathione S-transferases (GSTM2) was up-regulated in the abnormal samples, particularly in the heavy groups. The genes encoding myogenic differentiation (MYOD1) and myosin light chain kinase (MYLK) exhibited similar expression pattern, of which medium-WS and heavy-WS significantly increased compared to non-defective whereas expression in heavy-WS+WB was not different from either non-defective or WS-affected group. The greatest and the lowest levels of calpain-3 (CAPN3) and delta-sarcoglycan (SCGD) were observed in heavy-WS and heavy-WS+WB, respectively. Based on micrographs, the abnormal muscles primarily comprised fibers with cross-sectional areas ranging from 2,000 to 3,000 μm². Despite induced glycolysis at the transcriptional level, lower stored glycogen in the abnormal muscles corresponded with the reduced lactate and higher pH within their meats. The findings support hypoxia within the abnormal breasts, potentially associated with oversized muscle fibers. Between WS and WB, divergent glucose metabolism, cellular detoxification and myoregeneration at the transcriptional level could be anticipated.

Early differential gene expression in beef Longissimus thoracis muscles from carcasses with normal (<5.8) and high (>5.9) ultimate pH

The objective of this study was to investigate early postmortem (0.5 h) gene expression in beef Longissimus thoracis (LT) muscles from carcasses with NORMAL (<5.8) and HIGH (>5.9) ultimate pH (pH_u). A total of 53 transcripts were differentially expressed (P-value <.05): 40 showed up-regulation and 13 showed down-regulation in HIGH pH_u carcasses. Four up-regulated (PDK4, GADD45B, MAOA, METTL21C) genes were confirmed (P < .05) by q-PCR. HIGH pH_u samples resulted with lower values in glycolytic potential and AMP-activated protein kinase activity compared to NORMAL at 0.5 and 24 h postmortem (P < .05). Functional pathway analysis showed that calcium transport and GADD45 signaling pathways are associated with the development of HIGH pH meat. Genes involved in stress-related signaling, such as GADD45B, METTL21C and MAOA were overexpressed. These genes are involved in stress signaling that might be affecting Ca²⁺ transport and oxidative metabolism pathways in HIGH pH muscles.

Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils

BACKGROUND

Essential oil (EO) dietary supplementation is a new strategy to improve animal health. EO compounds have antiparasitic, antimicrobial, antiviral, antimycotic, antioxidant and anti-inflammatory proprieties. Nutrigenomics investigations represent innovative approaches in understanding the relation between diet effect and gene expression related to the animal performance. Few nutrigenomics studies have used a high-throughput RNA-Sequencing (RNA-Seq) approach, despite great potential of RNA-Seq data in gene expression quantification and in co-expression network analyses. Our aim is to use the potential of RNA-Sequencing data in order to evaluate the effect of an EO supplementary diet on gene expression in both lamb liver and muscle.

RESULTS

Using a treatment and sex interaction model, 13 and 4 differentially expressed genes were identified in liver and muscle respectively. Sex-specific differentially expressed (DE) genes were identified in both sexes. Using network based analysis, different clusters of co-expressed genes that were highly correlated to the diet were detected in males vs. females, in agreement with DE analysis. A total of five regulatory genes in liver tissue associated to EO diet were identified: DNAJB9, MANF, UFM1, CTNNLA1 and NFX1. Our study reveals a sex-dependent effect of EO diet in both tissues, and an influence on the expression of genes mainly involved in immune, inflammatory and stress pathway.

CONCLUSION

Our analysis suggests a sex-dependent effect of the EO dietary supplementation on the expression profile of both liver and muscle tissues. We hypothesize that the presence of EOs could have beneficial effects on wellness of male lamb and further analyses are needed to understand the biological mechanisms behind the different effect of EO metabolites based on sex. Using lamb as a model for nutrigenomics studies, it could be interesting to investigate the effects of EO diets in other species and in humans.

Muscle structure and gene expression in pectoralis major muscle in response to deep pectoral myopathy induction in fast- and slow-growing commercial broilers

1. The objective of this study was to determine muscle structure and gene expression in pectoralis major (p. major) muscle of broilers in response to deep pectoral myopathy (DPM) induction. 2. A total of 160 chickens from slow- and fast-growing broilers were raised under same conditions. Half of the broilers from each strain were encouraged to wing flap when they reached 2800 g body weight. Pectoralis minor (p. minor) muscle of the broilers was inspected for the occurrence of DPM and p. major samples were collected from broilers with or without DPM. The muscle fibre area and number, capillary number and the signalling pathways of vascular development (vascular endothelial growth factor A, VEGFA) and muscle contraction regulation (actin alpha 1, ACTA1; myosin light chain kinase 2, MYLK2 and ATPase Ca⁺² transporting gene 1, ATP2A1) were studied in p. major muscle. 3. DPM induction increased fibre area of p. major muscle with a greater rate in the slow-growing strain compared with fast-growing line. Although the capillary number was higher in slow-growing compared with fast-growing broilers, in the case of DPM induction, the number of capillaries was similar between strains. 4. Expression of VEGFA, MYLK2 and ATP2A1 was greater in slow- than in fast-growing broilers. DPM induction increased expression of ACTA1, VEGFA and ATP2A1 in p. major muscle of broilers from both strains; however, MYLK2 expression was downregulated. 5. Changes in capillary density and expression of VEGFA found in the p. major muscle of broilers with DPM suggest increased blood flow to increase oxygen availability. The upregulation of ATP2A1 by DPM induction could be attributable to alterations in calcium ion transportation from the cytoplasm into the sarcoplasmic reticulum. 6. The results are evidence of changes in muscle structure and gene expression pathways in p. major muscle of broilers with DPM.

Different oxidative status and expression of calcium channel components in stress-induced dysfunctional chicken muscle

The objective of this study was to assess the effects of transport stress at high ambient temperatures on the oxidation status and the expression of essential elements responsible for the Ca transport (sarco- (endo-) plasmic reticulum Ca-ATPase (SERCA1) and the ryanodine receptor (RyR) in (PM) muscles of broilers. Briefly, Arbor Acres broiler chickens ( = 112) were randomly categorized into 2 treatments: unstressed control (C) and 0.5 h transport (T). Each treatment consisted of 8 replicates of 7 birds each. Birds were transported according to a designed protocol. PM muscle samples in T group were collected and classified as normal (T-NOR) or pale, soft, and exudative-like (T-PSE) using meat quality parameters. The results indicated that production of corticosterone (CORT) and reactive oxygen species (ROS) increased significantly after transportation ( < 0.05). Thiobarbituric acid reactive substance values and carbonyl contents increased significantly in the T group ( < 0.05). Moreover, the extent of lipid peroxidation and protein oxidation was more severe in the T-PSE group compared to the T-NOR group ( < 0.05). The mRNA and protein expression of SERCA1 and αRyR increased in the T-NOR group but decreased significantly in the T-PSE group compared to the CON group ( < 0.05). The mRNA expression of βRyR was found to be enhanced in the T-NOR group compared to the CON group, whereas there was no difference in the T-PSE group ( < 0.05). The results indicate that short-distance transport of broilers affects their physiological responses and biochemical changes which may lead to different oxidative states and, importantly, to different expressions of SERCA and RyR. These induced changes in abnormal sarcoplasmic Ca homeostasis have significant implications for the development of PSE-like meat.

Calcium Homeostasis and Muscle Energy Metabolism Are Modified in HspB1-Null Mice

Hsp27—encoded by HspB1—is a member of the small heat shock proteins (sHsp, 12–43 kDa (kilodalton)) family. This protein is constitutively present in a wide variety of tissues and in many cell lines. The abundance of Hsp27 is highest in skeletal muscle, indicating a crucial role for muscle physiology. The protein identified as a beef tenderness biomarker was found at a crucial hub in a functional network involved in beef tenderness. The aim of this study was to analyze the proteins impacted by the targeted invalidation of HspB1 in the Tibialis anterior muscle of the mouse. Comparative proteomics using two-dimensional gel electrophoresis revealed 22 spots that were differentially abundant between HspB1-null mice and their controls that could be identified by mass spectrometry. Eighteen spots were more abundant in the muscle of the mutant mice, and four were less abundant. The proteins impacted by the absence of Hsp27 belonged mainly to calcium homeostasis (Srl and Calsq1), contraction (TnnT3), energy metabolism (Tpi1, Mdh1, PdhB, Ckm, Pygm, ApoA1) and the Hsp proteins family (HspA9). These data suggest a crucial role for these proteins in meat tenderization. The information gained by this study could also be helpful to predict the side effects of Hsp27 depletion in muscle development and pathologies linked to small Hsps.

Relationship of Skeletal Muscle Development and Growth to Breast Muscle Myopathies: A Review

Selection in meat-type birds has focused on growth rate, muscling, and feed conversion. These strategies have made substantial improvements but have affected muscle structure, repair mechanisms, and meat quality, especially in the breast muscle. The increase in muscle fiber diameters has reduced available connective tissue spacing, reduced blood supply, and altered muscle metabolism in the breast muscle. These changes have increased muscle fiber degeneration and necrosis but have limited muscle repair mechanisms mediated by the adult myoblast (satellite cell) population of cells, likely resulting in the onset of myopathies. This review focuses on muscle growth mechanisms and how changes in the cellular development of the breast muscle may be associated with breast muscle myopathies occurring in meat-type birds.

Disorder of endoplasmic reticulum calcium channel components is associated with the increased apoptotic potential in pale, soft, exudative pork

Eight pale, soft and exudative (PSE) and eight reddish-pink, firm and non-exudative (RFN) porcine longissimus muscle samples were selected based on pH and L* at 1h postmortem (PM), and drip loss at 24h PM, and used to evaluate the cellular calcium and apoptosis status. We found that SERCA1 was decreased, while IP3R was decreased in PSE meat (P<0.05), indicative of the overloaded sarcoplasmic calcium status. In PSE meat, the pro-apoptotic factor BAX was increased while the anti-apoptotic factor Bcl-2 was decreased (P<0.05). The significantly increased activity of caspase 3 and the expression of its cleavage fragment suggested higher apoptotic potential in PSE meat compared with RFN meat (P<0.05). Moreover, the significantly higher expression level of cytochrome C (P<0.05) suggests the important role of mitochondria during apoptosis appearance in PSE meat. Taken together, our data inferred that the calcium channel disorder present in PSE meat was associated with the increased apoptotic potential.

Monitoring of Chicken RNA Integrity as a Function of Prolonged Postmortem Duration

Gene expression profiling has offered new insights into postmortem molecular changes associated with meat quality. To acquire reliable transcript quantification, high quality RNA is required. The objective of this study was to analyze integrity of RNA isolated from chicken skeletal muscle (pectoralis major) and its capability of serving as the template in quantitative real-time polymerase chain reaction (qPCR) as a function of postmortem intervals representing the end-points of evisceration, carcass chilling and aging stages in chicken abattoirs. Chicken breast muscle was dissected from the carcasses (n = 6) immediately after evisceration, and one-third of each sample was instantly snap-frozen and labeled as 20 min postmortem. The remaining muscle was stored on ice until the next rounds of sample collection (1.5 h and 6 h postmortem). The delayed postmortem duration did not significantly affect A260/A280 and A260/A230 (p≥0.05), suggesting no altered purity of total RNA. Apart from a slight decrease in the 28s:18s ribosomal RNA ratio in 1.5 h samples (p<0.05), the value was not statistically different between 20 min and 6 h samples (p≥0.05), indicating intact total RNA up to 6 h. Abundance of reference genes encoding beta-actin (ACTB), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), hypoxanthine-guanine phosphoribosyltransferase (HPRT), peptidylprolylisomerase A (PPIA) and TATA box-binding protein (TBP) as well as meat-quality associated genes (insulin-like growth factor 1 (IGF1), pyruvate dehydrogenase kinase isozyme 4 (PDK4), and peroxisome proliferator-activated receptor delta (PPARD) were investigated using qPCR. Transcript abundances of ACTB, GAPDH, HPRT, and PPIA were significantly different among all postmortem time points (p<0.05). Transcript levels of PDK4 and PPARD were significantly reduced in the 6 h samples (p<0.05). The findings suggest an adverse effect of a prolonged postmortem duration on reliability of transcript quantification in chicken skeletal muscle. For the best RNA quality, chicken skeletal muscle should be immediately collected after evisceration or within 20 min postmortem, and rapidly preserved by deep freezing.

Improvement of turkey breast meat quality and cooked gel functionality using hot-boning, quarter sectioning, crust-freeze-air-chilling and cold-batter-mincing technologies

The effect of rapid carcass chilling on breast meat quality was evaluated using commercial (COMM) and random-bred (RB) turkeys. Immediately after slaughter, 48 turkeys from COMM or RB line were randomly subjected to one of four chilling methods: 1) water-immersion chilling (WIC) of the carcasses at 0°C ice slurry, 2) WIC after temperature abuse (TA) of the carcasses at 40°C for 30 min (TA-WIC), 3) hot-boning, quarter sectioning, and crust-freeze-air-chilling (HB-(1)/4CFAC) of breast fillets at -12°C, and 4) HB-(1)/4CFAC of fillets after TA of carcasses (TA-HB-(1)/4CFAC). The TA increased carcass and fillet temperatures by ∼1.3 and ∼4.1°C, respectively, regardless of turkey line, whereas HB-(1)/4CFAC of fillets required 28 and 33% of carcass chilling time for COMM and RB, respectively. During chilling, COMM breast pH rapidly reduced from 6.04 to 5.82, resulting in a significantly lower pH than RB after chilling (P < 0.05), whereas COMM R-value sharply increased from 1.17 to 1.43, causing no difference from RB (P > 0.05). Significantly higher L* value and cooking yield (P < 0.05) were seen in the samples of TA and WIC than those of no TA and HB-(1)/4CFAC, respectively, with no difference observed between COMM and RB fillets (P > 0.05). Higher values of hardness, gumminess, and chewiness were found for RB, no TA, and HB-(1)/4CFAC gels than COMM, TA, and WIC, respectively. These results generally indicated that protein quality and textural properties of turkey fillets were improved, regardless of strains or temperature abuse, using HB-(1)/4CFAC technology.

Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing

Background

Improvements in poultry production within the past 50 years have led to increased muscle yield and growth rate, which may be contributing to an increased rate and development of new muscle disorders in chickens. Previously reported muscle disorders and conditions are generally associated with poor meat quality traits and have a significant negative economic impact on the poultry industry. Recently, a novel myopathy phenotype has emerged which is characterized by palpably “hard” or tough breast muscle. The objective of this study is to identify the underlying biological mechanisms that contribute to this emerging muscle disorder colloquially referred to as “Wooden Breast”, through the use of RNA-sequencing technology.

Methods

We constructed cDNA libraries from five affected and six unaffected breast muscle samples from a line of commercial broiler chickens. After paired-end sequencing of samples using the Illumina Hiseq platform, we used Tophat to align the resulting sequence reads to the chicken reference genome and then used Cufflinks to find significant changes in gene transcript expression between each group. By comparing our gene list to previously published histology findings on this disorder and using Ingenuity Pathways Analysis (IPA®), we aim to develop a characteristic gene expression profile for this novel disorder through analyzing genes, gene families, and predicted biological pathways.

Results

Over 1500 genes were differentially expressed between affected and unaffected birds. There was an average of approximately 98 million reads per sample, across all samples. Results from the IPA analysis suggested “Diseases and Disorders” such as connective tissue disorders, “Molecular and Cellular Functions” such as cellular assembly and organization, cellular function and maintenance, and cellular movement, “Physiological System Development and Function” such as tissue development, and embryonic development, and “Top Canonical Pathways” such as, coagulation system, axonal guidance signaling, and acute phase response signaling, are associated with the Wooden Breast disease.

Conclusions

There is convincing evidence by RNA-seq analysis to support localized hypoxia, oxidative stress, increased intracellular calcium, as well as the possible presence of muscle fiber-type switching, as key features of Wooden Breast Disease, which are supported by reported microscopic lesions of the disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1623-0) contains supplementary material, which is available to authorized users.