Differential expression and co-expression gene network analyses reveal molecular mechanisms and candidate biomarkers involved in breast muscle myopathies in chicken

Proteomic analyses on chicken breast meat with white striping myopathy

White striping (WS) is an emerging myopathy that results in significant economic losses as high as $1 billion (combined with losses derived from other breast myopathies including woody breast and spaghetti meat) to the global poultry industry. White striping is detected as the occurrence of white lines on raw poultry meat. The exact etiologies for WS are still unclear. Proteomic analyses of co-expressed WS and woody breast phenotypes previously demonstrated dysfunctions in carbohydrate metabolism, protein synthesis, and calcium buffering capabilities in muscle cells. In this study, we conducted shotgun proteomics on chicken breast fillets exhibiting only WS that were collected at approximately 6 h postmortem. After determining WS severity, protein extractions were conducted from severe WS meat with no woody breast (WB) condition (n = 5) and normal non-affected (no WS) control meat (n = 5). Shotgun proteomics was conducted by Orbitrap Lumos, tandem mass tag (TMT) analysis. As results, 148 differentially abundant proteins (|fold change|>1.4; p-value < 0.05) were identified in the WS meats compared with controls. The significant canonical pathways included BAG2 signaling pathway, glycogen degradation II, isoleucine degradation I, aldosterone signaling in epithelial cells, and valine degradation I. The potential upstream regulators include LIPE, UCP1, ATP5IF1, and DMD. The results of this study provide additional insights into the cellular mechanisms on the WS myopathy and meat quality.

Genetic architecture of white striping in turkeys (Meleagris gallopavo)

White striping (WS) is a myopathy of growing concern to the turkey industry. It is rising in prevalence and has negative consequences for consumer acceptance and the functional properties of turkey meat. The objective of this study was to conduct a genome-wide association study (GWAS) and functional analysis on WS severity. Phenotypic data consisted of white striping scored on turkey breast fillets (N = 8422) by trained observers on a 0-3 scale (none to severe). Of the phenotyped birds, 4667 genotypic records were available using a proprietary 65 K single nucleotide polymorphism (SNP) chip. The SNP effects were estimated using a linear mixed model with a 30-SNP sliding window approach used to express the percentage genetic variance explained. Positional candidate genes were those located within 50 kb of the top 1% of SNP windows explaining the most genetic variance. Of the 95 positional candidate genes, seven were further classified as functional candidate genes because of their association with both a significant gene ontology and molecular function term. The results of the GWAS emphasize the polygenic nature of the trait with no specific genomic region contributing a large portion to the overall genetic variance. Significant pathways relating to growth, muscle development, collagen formation, circulatory system development, cell response to stimulus, and cytokine production were identified. These results help to support published biological associations between WS and hypoxia and oxidative stress and provide information that may be useful for future-omics studies in understanding the biological associations with WS development in turkeys.

Spatial transcriptomics reveals alterations in perivascular macrophage lipid metabolism in the onset of Wooden Breast myopathy in broiler chickens

This study aims to use spatial transcriptomics to characterize the cell-type-specific expression profile associated with the microscopic features observed in Wooden Breast myopathy. 1 cm3 muscle sample was dissected from the cranial part of the right pectoralis major muscle from three randomly sampled broiler chickens at 23 days post-hatch and processed with Visium Spatial Gene Expression kits (10X Genomics), followed by high-resolution imaging and sequencing on the Illumina Nextseq 2000 system. WB classification was based on histopathologic features identified. Sequence reads were aligned to the chicken reference genome (Galgal6) and mapped to histological images. Unsupervised K-means clustering and Seurat integrative analysis differentiated histologic features and their specific gene expression pattern, including lipid laden macrophages (LLM), unaffected myofibers, myositis and vasculature. In particular, LLM exhibited reprogramming of lipid metabolism with up-regulated lipid transporters and genes in peroxisome proliferator-activated receptors pathway, possibly through P. Moreover, overexpression of fatty acid binding protein 5 could enhance fatty acid uptake in adjacent veins. In myositis regions, increased expression of cathepsins may play a role in muscle homeostasis and repair by mediating lysosomal activity and apoptosis. A better knowledge of different cell-type interactions at early stages of WB is essential in developing a comprehensive understanding.

Transcriptomic Profiles of Pectoralis major Muscles Affected by Spaghetti Meat and Woody Breast in Broiler Chickens

Spaghetti meat (SM) and woody breast (WB) are breast muscle myopathies of broiler chickens, characterized by separation of myofibers and by fibrosis, respectively. This study sought to investigate the transcriptomic profiles of breast muscles affected by SM and WB. Targeted sampling was conducted on a flock to obtain 10 WB, 10 SM, and 10 Normal Pectoralis major muscle samples from 37-day-old male chickens. Total RNA was extracted, cDNA was used for pair-end sequencing, and differentially expressed genes (DEGs) were determined by a false discovery rate of <0.1 and a >1.5-fold change. Principal component and heatmap cluster analyses showed that the SM and WB samples clustered together. No DEGs were observed between SM and WB fillets, while a total of 4018 and 2323 DEGs were found when comparing SM and WB, respectively, against Normal samples. In both the SM and WB samples, Gene Ontology terms associated with extracellular environment and immune response were enriched. The KEGG analysis showed enrichment of cytokine-cytokine receptor interaction and extracellular matrix-receptor interaction pathways in both myopathies. Although SM and WB are macroscopically different, the similar transcriptomic profiles suggest that these conditions may share a common pathogenesis. This is the first study to compare the transcriptomes of SM and WB, and it showed that, while both myopathies had profiles different from the normal breast muscle, SM and WB were similar, with comparable enriched metabolic pathways and processes despite presenting markedly different macroscopic features.

Time course evaluation of collagen type IV in Pectoralis major muscles of broiler chickens selected for different growth-rates

Collagen type IV (COL4) is one of the major components of animals' and humans' basement membranes of several tissues, such as skeletal muscles and vascular endothelia. Alterations in COL4 assembly and secretion are associated to muscular disorders in humans and animals among which growth-related abnormalities such as white striping and wooden breast affecting Pectoralis major muscles (PMs) in modern fast-growing (FG) chickens. Considering the high prevalence of these myopathies in FG broilers and that a worsening is observed as the bird slaughter age is increased, the present study was intended to evaluate the distribution and the expression level of COL4 protein and its coding genes in PMs of FG broilers at different stages of muscle development (i.e., 7, 14, 21, 28, 35, and 42 d of age). Medium-growing (MG) chickens have been considered as the control group in consideration of the lower selection pressure on breast muscle growth rate and hypertrophy. Briefly, 5 PM/sampling time/genotype were selected for western blot, immunohistochemistry (IHC), and gene expression analyses. The normalized expression levels of COL4 coding genes showed an overexpression of COL4A2 in FG than MG at d 28, as well as a significant decrease in its expression over their rearing period. Overall, results obtained through the gene expression analysis suggested that selection for the hypertrophic growth of FG broilers may have led to an altered regulation of fibroblast proliferation and COL4 synthesis. Moreover, western blot and IHC analyses suggested an altered secretion and/or degradation of COL4 protein in FG broilers, as evidenced by the fluctuating trend of 2 bands observed in FG over time. In view of the above, the present research supports the evidence about a potential aberrant synthesis and/or degradation of COL4 and corroborates the hypothesis regarding a likely involvement of COL4 in the series of events underlying the growth-related abnormalities in modern FG broilers.

Hypoxia promotes proliferation and inhibits myogenesis in broiler satellite cells

Breast muscle myopathies in broilers compromise meat quality and continue to plague the poultry industry. Broiler breast muscle myopathies are characterized by impaired satellite cell (SC)-mediated repair, and localized tissue hypoxia and dysregulation of oxygen homeostasis have been implicated as contributing factors. The present study was designed to test the hypothesis that hypoxia disrupts the ability of SC to differentiate and form myotubes, both of which are key components of myofiber repair, and to determine the extent to which effects are reversed by restoration of oxygen tension. Primary SC were isolated from pectoralis major of young (5 d) Cobb 700 chicks and maintained in growth conditions or induced to differentiate under normoxic (20% O2) or hypoxic (1% O2) conditions for up to 48 h. Hypoxia enhanced SC proliferation while inhibiting myogenic potential, with decreased fusion index and suppressed myotube formation. Reoxygenation after hypoxia partially reversed effects on both proliferation and myogenesis. Western blotting showed that hypoxia diminished myogenin expression, activated AMPK, upregulated proliferation markers, and increased molecular signaling of cellular stress. Hypoxia also promoted accumulation of lipid droplets in myotubes. Targeted RNAseq identified numerous differentially expressed genes across differentiation under hypoxia, including several genes that have been associated with myopathies in vivo. Altogether, these data demonstrate localized hypoxia may influence SC behavior in ways that disrupt muscle repair and promote the formation of myopathies in broilers.

The hypoxia-inducible factor 1 pathway plays a critical role in the development of breast muscle myopathies in broiler chickens: a comprehensive review

In light of the increased worldwide demand for poultry meat, genetic selection efforts have intensified to produce broiler strains that grow at a higher rate, have greater breast meat yield (BMY), and convert feed to meat more efficiently. The increased selection pressure for these traits, BMY in particular, has produced multiple breast meat quality defects collectively known as breast muscle myopathies (BMM). Hypoxia has been proposed as one of the major mechanisms triggering the onset and occurrence of these myopathies. In this review, the relevant literature on the causes and consequences of hypoxia in broiler breast muscles is reviewed and discussed, with a special focus on the hypoxia-inducible factor 1 (HIF-1) pathway. Muscle fiber hypertrophy induced by selective breeding for greater BMY reduces the space available in the perimysium and endomysium for blood vessels and capillaries. The hypoxic state that results from the lack of circulation in muscle tissue activates the HIF-1 pathway. This pathway alters energy metabolism by promoting anaerobic glycolysis, suppressing the tricarboxylic acid cycle and damaging mitochondrial function. These changes lead to oxidative stress that further exacerbate the progression of BMM. In addition, activating the HIF-1 pathway promotes fatty acid synthesis, lipogenesis, and lipid accumulation in myopathic muscle tissue, and interacts with profibrotic growth factors leading to increased deposition of matrix proteins in muscle tissue. By promoting lipidosis and fibrosis, the HIF-1 pathway contributes to the development of the distinctive phenotypes of BMM, including white striations in white striping-affected muscles and the increased hardness of wooden breast-affected muscles.

Dietary inositol-stabilized arginine silicate numerically reduced woody breast severity in male Ross 708 broilers without altering growth

The woody breast (WB) myopathy is an unintended outcome of fast broiler chicken growth and high breast muscle yields. Myodegeneration and fibrosis in the living tissue are results of hypoxia and oxidative stress driven by lack of blood supply to muscle fibers. The study aim was to titrate a vasodilator ingredient, inositol-stabilized arginine silicate (ASI), as a feed additive to improve blood flow and ultimately, breast meat quality. A total of 1,260 male Ross 708 broilers were assigned to: 1) a control basal diet, or the control diet plus increasing ASI: 2) 0.025% ASI, 3) 0.05% ASI, 4) 0.10% ASI, or 5) 0.15% ASI. At d 14, 28, 42, and 49, growth performance was measured on all broilers and serum from 12 broilers/diet was analyzed for creatine kinase and myoglobin presence. On d 42 and 49, 12 broilers/diet were measured for breast width, then left breast fillets were excised, weighed, palpated for WB severity, and visually scored for degree of white striping (WS). At 1 d postmortem, 12 raw fillets/treatment underwent compression force analysis, and at 2d postmortem, the same fillets were analyzed for water-holding capacity. mRNA was isolated from 6 right breasts/diet at both d 42 and 49 for qPCR quantification of myogenic gene expression. Birds fed the lowest dose of 0.025% ASI had a 5-point/3.25% feed conversion ratio reduction compared to birds fed 0.10% ASI over wk 4 to 6 and reduced serum myoglobin at 6-wk of age compared to the control. Breasts from birds fed 0.025% ASI received 42% greater normal WB scores at d 42 compared to control fillets. At d 49, breasts from broilers fed 0.10 and 0.15% ASI received 33% normal WB scores. At d 49, 0.025% AS-fed broiler breasts showed no severe WS. Increased myogenin expression was observed in 0.05 and 0.10% ASI breast samples on d 42 and myoblast determination protein-1 expression was upregulated in breasts from birds fed 0.10% ASI on d 49 compared to the control. Therefore, a dietary inclusion of 0.025, 0.10, or 0.15% ASI was beneficial in reducing WB and WS severity and promoting muscle growth factor gene expression at age of harvest without diminishing bird growth or breast muscle yields.

Breast muscle white striping and serum corticosterone reduced in broilers exposed to laser environmental enrichment

Genetic selection for breast yields and fewer days to market has inadvertent effects on broiler meat quality. Woody breast (WB) and white striping (WS) are pectoralis major myopathies prevalent in commercial broilers. Effects of voluntary exercise on these disorders, specifically, are unknown. A second-generation laser enrichment device shown to induce activity in Ross 308 and 708 birds was implemented using 1,360 Ross 708 broilers randomly assigned to laser enrichment or control for 49 d. Laser-enriched birds were exposed to 6-min laser periods 4 times daily. Seventy focal birds were gait and contact dermatitis scored weekly. Blood was collected wk 5 to 7 from 56 broilers for serum corticosterone, myoglobin, and troponin. Seventy broilers were sampled for breast muscle width, fillet dimensions, and WB and WS at wk 6 and 7. One and 2-day postmortem, fillet compression force and water-holding capacity were measured. Serum corticosterone was reduced by up to 21% in laser-enriched birds wk 5 to 7 (P < 0.01). Serum myoglobin was increased in laser-enriched broilers by 5% on wk 5 (P < 0.01) but increased in control birds wk 6 to 7 by up to 13% (P < 0.01). Serum troponin was reduced in laser-enriched broilers by 9% at wk 5 (P < 0.01). Laser exposure increased breast width and fillet weight at d 42 by 1.08 cm (P < 0.05) and 30 g (P < 0.05). At d 49, fillet height was increased 0.42 cm in laser-enriched birds (P < 0.05). Laser enrichment reduced severe WS incidence at d 42 by 24% (P < 0.05) and on d 49 by 15% (P < 0.10). Severe WB score was numerically reduced by 11% in laser enrichment on d 42 and 18% on d 49 (P > 0.05). Water-holding capacity was improved in laser-enriched breasts (P < 0.01) and expression of myostatin and insulin-like growth factor 2 were increased on d 49 (P ≤ 0.01. Laser enrichment reduced markers of stress and muscle damage while improving breast muscle quality and is therefore a potential effective enrichment for commercial broilers.

Cannabidiol and Nano-Selenium Increase Microvascularization and Reduce Degenerative Changes in Superficial Breast Muscle in C. perfringens-Infected Chickens

Here, we demonstrated the potential of Cannabis-derived cannabidiol (CBD) and nanosized selenium (nano-Se) for the modulation of microvascularization and muscle fiber lesions in superficial breast muscle in C. perfringens-challenged chickens. The administration of CBD resulted in a decreased number of atrophic fibers (3.13 vs. 1.13/1.5 mm²) compared with the control, whereas nano-Se or both substances resulted in a decreased split fiber number (4.13 vs. 1.55/1.5 mm²) and in a lower number of necrotic myofibers (2.38 vs. 0.69/1.5 mm²) in breast muscle than the positive control. There was a significantly higher number of capillary vessels in chickens in the CBD+Nano-Se group than in the control and positive control groups (1.31 vs. 0.97 and 0.98, respectively). Feeding birds experimental diets lowered the activity of DNA damage repair enzymes, including 3,N4-ethenodeoxycytosine (by 39.6%), 1,N6-ethenodeoxyadenosine (by 37.5%), 8-oxo-guanine (by 36.2%), formamidopyrimidine (fapy)-DNA glycosylase (by 56.2%) and human alkyl adenine DNA glycosylase (by 40.2%) in the ileal mucosa, but it did not compromise the blood mitochondrial oxygen consumption rate (-2.67 OD/min on average). These findings indicate a potential link between gut mucosa condition and histopathological changes in superficial pectoral muscle under induced inflammation and show the ameliorative effect of CBD and nano-Se in this cross-talk due to their protection from mucosal DNA damage.

Dietary vasodilator and vitamin C/L-arginine/choline blend improve broiler feed efficiency during finishing and reduce woody breast severity at 6 and 7 wks

Woody breast has become a considerable economic concern to the poultry industry. This myopathy presents rigid, pale breasts characterized by replacement of lean muscle protein with connective tissue, a result of hypoxia and oxidative stress in a metabolically starved muscle with inadequate circulation. Hence, the objectives were to supplement broiler diets with ingredients specifically aimed to improve circulation and oxidative status. About 1,344 male Ross 708 broilers were assigned to 1 of 4 diets: 1) a basal diet (control), 2) basal diet plus a blend of 0.2% supplemental L-arginine, 0.17% choline bitartrate, and 0.03% vitamin C (blend), 3) 0.1% vasodilator ingredient (vasodilator), or 4) 0.02% Astaxanthin ingredient (AsX). At d 14, 28, 42, and 49, performance outcomes were collected on all birds and serum from 16 broilers/diet (n = 64) was analyzed for creatine kinase and myoglobin. Once weekly beginning on d 28, a subset of 192 broilers were measured for breast width. On d 42 and 49, breast fillets from 16 broilers/diet (n = 64) were palpated for woody breast severity, weighed, and analyzed for compression force at 1-day postmortem and water-holding capacity at 2-day postmortem. mRNA was isolated from 15 breast fillets/timepoint for qPCR quantification of myogenic gene expression. Data were analyzed using Proc Mixed (SAS Version 9.4) with the fixed effect of diet. Feed conversion ratio was improved in the blend and vasodilator-fed birds d 42 to 49, each by over 2 points (P < 0.05). Breast width was increased in the control on d 42 compared to the vasodilator and AsX-fed broilers (P < 0.05). At d 42, there were 12% greater normal fillets in blend diet-fed birds and 13% more normal scores in vasodilator-fed birds at d 49 compared to the control. At d 49, myogenin expression was upregulated in the AsX diet compared to blend and control diets (P < 0.05), and muscle regulatory factor-4 expression was increased by 6.5% in the vasodilator diet compared to the blend and AsX diets (P < 0.05). Blend and vasodilator diets simultaneously improved feed efficiency in birds approaching market weight while reducing woody breast severity.

Embryonic transcriptome unravels mechanisms and pathways underlying embryonic development with respect to muscle growth, egg production, and plumage formation in native and broiler chickens

Background: Muscle development, egg production, and plumage colors are different between native and broiler chickens. The study was designed to investigate why improved Aseel (PD4) is colorful, stronger, and grew slowly compared with the control broiler (CB).

Methods: A microarray was conducted using the 7th-day embryo (7EB) and 18th-day thigh muscle (18TM) of improved Aseel and broiler, respectively. Also, we have selected 24 Gallus gallus candidate reference genes from NCBI, and total RNA was isolated from the broiler, improved Aseel embryo tissues, and their expression profiles were studied by real-time quantitative PCR (qPCR). Furthermore, microarray data were validated with qPCR using improved Aseel and broiler embryo tissues.

Results: In the differential transcripts screening, all the transcripts obtained by microarray of slow and fast growth groups were screened by fold change ≥ 1 and false discovery rate (FDR) ≤ 0.05. In total, 8,069 transcripts were differentially expressed between the 7EB and 18TM of PD4 compared to the CB. A further analysis showed that a high number of transcripts are differentially regulated in the 7EB of PD4 (6,896) and fewer transcripts are differentially regulated (1,173) in the 18TM of PD4 compared to the CB. On the 7th^- and 18th-day PD4 embryos, 3,890, 3,006, 745, and 428 transcripts were up- and downregulated, respectively. The commonly up- and downregulated transcripts are 91 and 44 between the 7th- and 18th-day of embryos. In addition, the best housekeeping gene was identified. Furthermore, we validated the differentially expressed genes (DEGs) related to muscle growth, myostatin signaling and development, and fatty acid metabolism genes in PD4 and CB embryo tissues by qPCR, and the results correlated with microarray expression data.

Conclusion: Our study identified DEGs that regulate the myostatin signaling and differentiation pathway; glycolysis and gluconeogenesis; fatty acid metabolism; Jak-STAT, mTOR, and TGF-β signaling pathways; tryptophan metabolism; and PI3K-Akt signaling pathways in PD4. The results revealed that the gene expression architecture is present in the improved Aseel exhibiting embryo growth that will help improve muscle development, differentiation, egg production, protein synthesis, and plumage formation in PD4 native chickens. Our findings may be used as a model for improving the growth in Aseel as well as optimizing the growth in the broiler.

Differential expression patterns of genes associated with metabolisms, muscle growth and repair in Pectoralis major muscles of fast- and medium-growing chickens

The aim of this study was to investigate the expression of genes related to muscle growth, hypoxia and oxidative stress responses, a multi-substrate serine/threonine-protein kinase (AMPK) and AMPK-related kinases, carbohydrate metabolism, satellite cells activities and fibro- adipogenic progenitors (FAPs) in fast-growing (FG) (n = 30) and medium-growing (MG) chickens (n = 30). Pectoralis major muscles were collected at 7d, 14d, 21d, 28d, 35d and 42d of age. According to their macroscopic features, the samples from FG up to 21d of age were classified as unaffected, while all samples collected at an older age exhibited macroscopic features ascribable to white striping and/or wooden breast abnormalities. In contrast, MG samples did not show any feature associated to muscle disorders. The absolute transcript abundance of 33 target genes was examined by droplet digital polymerase chain reaction. The results showed differential gene expression profiles between FG and MG chickens at different ages. While most genes remained unchanged in MG chickens, the expression patterns of several genes in FG were significantly affected by age. Genes encoding alpha 1, alpha 2, beta 2 and gamma 3 isoforms of AMPK, as well as AMPK-related kinases, were identified as differentially expressed between the two strains. The results support the hypothesis of oxidative stress-induced muscle damage with metabolic alterations in FG chickens. An increased expression of ANXA2, DES, LITAF, MMP14, MYF5 and TGFB1 was observed in FG strain. The results suggest the occurrence of dysregulation of FAP proliferation and differentiation occurring during muscle repair. FAPs could play an important role in defining the proliferation of connective tissue (fibrosis) and deposition of intermuscular adipose tissue which represents distinctive traits of muscle abnormalities. Overall, these findings demonstrate that dysregulated molecular processes associated with myopathic lesions in chickens are strongly influenced by growth rate, and, to some extent, by age.

Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

Background and aims

Treatment with tumor necrosis factor α (TNFα) antagonists in IBD patients suffers from primary non-response rates of up to 40%. Biomarkers for early prediction of therapy success are missing. We investigated the dynamics of gene expression and DNA methylation in blood samples of IBD patients treated with the TNF antagonist infliximab and analyzed the predictive potential regarding therapy outcome.

Methods

We performed a longitudinal, blood-based multi-omics study in two prospective IBD patient cohorts receiving first-time infliximab therapy (discovery: 14 patients, replication: 23 patients). Samples were collected at up to 7 time points (from baseline to 14 weeks after therapy induction). RNA-sequencing and genome-wide DNA methylation data were analyzed and correlated with clinical remission at week 14 as a primary endpoint.

Results

We found no consistent ex ante predictive signature across the two cohorts. Longitudinally upregulated transcripts in the non-remitter group comprised TH2- and eosinophil-related genes including ALOX15, FCER1A, and OLIG2. Network construction identified transcript modules that were coherently expressed at baseline and in non-remitting patients but were disrupted at early time points in remitting patients. These modules reflected processes such as interferon signaling, erythropoiesis, and platelet aggregation. DNA methylation analysis identified remission-specific temporal changes, which partially overlapped with transcriptomic signals. Machine learning approaches identified features from differentially expressed genes cis-linked to DNA methylation changes at week 2 as a robust predictor of therapy outcome at week 14, which was validated in a publicly available dataset of 20 infliximab-treated CD patients.

Conclusions

Integrative multi-omics analysis reveals early shifts of gene expression and DNA methylation as predictors for efficient response to anti-TNF treatment. Lack of such signatures might be used to identify patients with IBD unlikely to benefit from TNF antagonists at an early time point.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-022-01112-z.

The evolution of vimentin and desmin in Pectoralis major muscles of broiler chickens supports their essential role in muscle regeneration

Vimentin (VIM) and desmin (DES) are muscle-specific proteins having crucial roles in maintaining the lateral organization and alignment of the sarcomeric structure during myofibrils’ regeneration. The present experiment was designed to ascertain the evolution of VIM and DES in Pectoralis major muscles (PM) of fast-growing (FG) and medium-growing (MG) meat-type chickens both at the protein and gene levels. MG broilers were considered as a control group whereas the evolution of VIM and DES over the growth period was evaluated in FG by collecting samples at different developmental stages (7, 14, 21, 28, 35, and 42 days). After performing a preliminary classification of the samples based on their histological features, 5 PM/sampling time/genotype were selected for western blot, immunohistochemistry (IHC), and gene expression analyses. Overall, the findings obtained at the protein level mirrored those related to their encoding genes, although a potential time lag required to observe the consequences of gene expression was evident. The two- and 3-fold higher level of the VIM-based heterodimer observed in FG at d 21 and d 28 in comparison with MG of the same age might be ascribed to the beginning and progressive development of the regenerative processes. This hypothesis is supported by IHC highlighting the presence of fibers to co-expressing VIM and DES. In addition, gene expression analyses suggested that, unlike VIM common sequence, VIM long isoform may not be directly implicated in muscle regeneration. As for DES content, the fluctuating trends observed for both the native protein and its heterodimer in FG might be ascribed to its importance for maintaining the structural organization of the regenerating fibers. Furthermore, the higher expression level of the DES gene in FG in comparison with MG further supported its potential application as a marker of muscle fibers’ regeneration. In conclusion, the findings of the present research seem to support the existence of a relationship between the occurrence of muscle regeneration and the growth rate of meat-type chickens and corroborate the potential use of VIM and DES as molecular markers of these cellular processes.

Molecular Pathways and Key Genes Associated With Breast Width and Protein Content in White Striping and Wooden Breast Chicken Pectoral Muscle

Growth-related abnormalities affecting modern chickens, known as White Striping (WS) and Wooden Breast (WB), have been deeply investigated in the last decade. Nevertheless, their precise etiology remains unclear. The present study aimed at providing new insights into the molecular mechanisms involved in their onset by identifying clusters of co-expressed genes (i.e., modules) and key loci associated with phenotypes highly related to the occurrence of these muscular disorders. The data obtained by a Weighted Gene Co-expression Network Analysis (WGCNA) were investigated to identify hub genes associated with the parameters breast width (W) and total crude protein content (PC) of Pectoralis major muscles (PM) previously harvested from 12 fast-growing broilers (6 normal vs. 6 affected by WS/WB). W and PC can be considered markers of the high breast yield of modern broilers and the impaired composition of abnormal fillets, respectively. Among the identified modules, the turquoise (r = -0.90, p &lt; 0.0001) and yellow2 (r = 0.91, p &lt; 0.0001) were those most significantly related to PC and W, and therefore respectively named “protein content” and “width” modules. Functional analysis of the width module evidenced genes involved in the ubiquitin-mediated proteolysis and inflammatory response. GTPase activator activity, PI3K-Akt signaling pathway, collagen catabolic process, and blood vessel development have been detected among the most significant functional categories of the protein content module. The most interconnected hub genes detected for the width module encode for proteins implicated in the adaptive responses to oxidative stress (i.e., THRAP3 and PRPF40A), and a member of the inhibitor of apoptosis family (i.e., BIRC2) involved in contrasting apoptotic events related to the endoplasmic reticulum (ER)-stress. The protein content module showed hub genes coding for different types of collagens (such as COL6A3 and COL5A2), along with MMP2 and SPARC, which are implicated in Collagen type IV catabolism and biosynthesis. Taken together, the present findings suggested that an ER stress condition may underly the inflammatory responses and apoptotic events taking place within affected PM muscles. Moreover, these results support the hypothesis of a role of the Collagen type IV in the cascade of events leading to the occurrence of WS/WB and identify novel actors probably involved in their onset.

Prevalence of breast muscle myopathies (spaghetti meat, woody breast, white striping) and associated risk factors in broiler chickens from Ontario Canada

Spaghetti meat (SM), woody breast (WB), and white striping (WS) are myopathies that affect the pectoral muscle of fast-growing broiler chickens. The prevalence and possible risk factors of these myopathies have been reported in other countries, but not yet in Canada. Thus, the objective of this study was to assess the prevalence and risk factors associated with these myopathies in a representative population of Canadian broilers. From May 2019 to March 2020, 250 random breast fillets from each of 37 flocks (total, 9,250) were obtained from two processing plants and assessed for the presence and severity of myopathies. Demographic data (e.g., sex and average live weight), environmental conditions during the grow-out period (e.g., temperature), and husbandry parameters (e.g., vaccination) were collected for each flock. Associations between these factors and the myopathies were tested using logistic regression analyses. The prevalence of SM, severe WB, and mild or moderate WS was 36.3% (95% CI: 35.3–37.3), 11.8% (95% CI: 11.2–12.5), and 96.0% (95% CI: 95.6–96.4), respectively. Most (85.1%) of the fillets showed multiple myopathies. Regression analyses showed that the odds of SM increased with live weight (OR = 1.30, 95% CI 1.01–1.69) and higher environmental temperature during the grow-out period (OR = 1.75, 95% CI 1.31–2.34). The odds of WB increased with live weight (OR = 1.23, 95% CI 1.03–1.47) and when flocks were not vaccinated against coccidia (OR = 1.86, 95% CI 1.51–2.29). This study documents for the first time a high prevalence of myopathies in Ontario broilers, and suggests that these lesions may have a significant economic impact on the Canadian poultry industry. Our results indicate that environmental conditions and husbandry are associated with the development of breast myopathies, in agreement with the current literature. Future studies are needed to determine how risk factors can promote the occurrence of these conditions, in order to implement possible mitigating strategies.

Influences of Thermal Stress During Three Weeks Before Market Age on Histology and Expression of Genes Associated With Adipose Infiltration and Inflammation in Commercial Broilers, Native Chickens, and Crossbreeds

The objectives of this study were to examine the effects of cyclic thermal stress on histological characteristics of breast muscle and gene expression regarding adipose infiltration and inflammation in breast muscles collected from different breeds of chickens. The birds, from commercial broilers (CB, Ross 308, 3 weeks), native (NT, 100% Thai native Chee, 9 weeks), H75 (crossbred; 75% broiler and 25% NT, 5 weeks), and H50 (crossbred; 50% broiler and 50% NT, 7 weeks), were equally assigned into control or treatment groups. The control samples were reared under a constant temperature of 26 ± 1°C, while the treatment groups were exposed to 35 ± 1°C (6 h per day). After a 20-day thermal challenge, 12 male birds per treatment group were randomly collected for determination of live body weight, breast weight, numbers of growth-related myopathies, and breast meat chemical composition. Histological lesions were evaluated in the pectoralis major muscle immediately collected within 20 min postmortem based on hematoxylin and eosin staining. The results indicated that despite interaction between thermal stress and breed effects, thermal challenge significantly reduced feed intake, live body weight, and breast weight of the birds and increased moisture content in breast meat (p < 0.05). An interaction between the two main factors was found for protein content (p < 0.05) for which control CB showed less protein than the other groups. Heat stress decreased histological scores for adipose infiltration in CB (p < 0.05), but it did not significantly influence such scores in the other groups. CB received histological scores for adipose tissue at greater extent than those for the other groups. Differential absolute abundance of CD36, FABP4, LITAF, PDGFRA, PLIN1, PPARG, POSTN, SCD1, and TGFB1 in the muscle samples well-agreed with the trend of histological scores, suggesting potential involvement of dysregulated fibro-adipogenic progenitors together with imbalanced lipid storage and utilization in the breast muscle. The findings demonstrated that the cyclic thermal challenge restricted growth performance and breast mass of the birds, but such effects attenuated infiltration of adipose tissue and inflammatory cells in the CB breast muscle.

Laser Environmental Enrichment and Spirulina Algae Improve Broiler Growth Performance and Alter Myogenic Gene Expression and pectoralis major Dimensions

Sustainability in poultry production is evident in efforts to reduce inputs and a focus on bird welfare and livability. Dietary protein alternatives to traditional sources such as soybean meal aim to meet or exceed efficiency benchmarks and be cost-effective. Environmental enrichment encouraging activity may reduce the occurrence of the predominant breast muscle myopathy, woody breast (WB); interventions to minimize muscle damage and economic loss have yet to be established. The study objectives were to maintain or improve broiler performance and breast quality through environmental enrichment and partially replacing dietary soybean meal with Spirulina. Twelve hundred Ross 708 broilers were randomly assigned to enrichment (LASER; laser enrichment, or CON; no laser enrichment) and diet (algae; 2.5% Spirulina algae, or control) in a 2 × 2 factorial design for 49 days. The same 70 randomly selected birds were examined for contact dermatitis wk 1–6. Breast width was measured weekly on 200 growing broilers beginning on d22. On d42 and 49 slaughter, WB score was assigned using a tactile 0–3 scale and the right breast filet was weighed (n = 200). RNA isolated from 30 breast muscle samples each at d42 and 49 was analyzed using real-time qPCR. Laser enrichment increased body weight at all timepoints (d49: 0.148 kg, P &lt; 0.001). Feed conversion ratio was improved in LASER-enriched birds by 3 points in the starter period (P = 0.003). Breast width was increased at all timepoints in LASER-enriched birds compared to CON (d49: 0.47 cm, P &lt; 0.001). Algae inclusion increased body weight at d28 (0.059 kg, P = 0.005). At d42, 12% more LASER-enriched WB scores were 0 (normal) compared to CON, and at d49, 15% more enriched scores were 0. At d42, 5% more algae-fed broiler scores were 0 compared to control. LASER-enriched broiler breast tissue showed upregulated expression of myogenin, muscle regulatory factor 4, insulin-like growth factor 1, and myostatin compared to CON (P &lt; 0.01). Both laser enrichment and algae inclusion improved broiler performance without negatively impacting environmental or physiological outcomes. LASER enrichment decreased severity of WB score and positively shifted myogenic gene expression in the breast muscle at slaughter.

Metabolomic analysis indicates that higher drip loss may be related to the production of methylglyoxal as a by-product of glycolysis

The aim of the present study was to assess applicability of metabolomics analysis of exudate from chicken breast muscle to explanation of differences in drip loss. The research was carried out on the skinless breast fillets sourced from 60 broiler carcasses (7-wk-old male Ross broilers). In the meat samples the pH value, color parameters, drip loss, chemical composition, and sensory quality were evaluated. After measuring, the samples were divided into 2 groups taking into consideration the volume of drip loss (low ≤2% and high >2% drip loss). The muscle juice samples were collected during 24 h muscle storage and metabolomic analysis was performed. The results showed that chickens with higher drip loss were characterized by heavier carcasses. The meat with higher drip loss proved to be more acid, lighter, less red, and more yellow with higher level of glucose as well as glycolytic potential. That meat was also characterized by lower cooking loss, protein content and worse overall sensory quality as well as oxidation of lipids. The metabolomics analyses have shown that in the group with higher drip loss from muscle tissue the increase of metabolism of energy transformations taking place in muscle tissue after slaughter was observed and that differences between groups are related to 11 metabolic pathways, mainly carbohydrate metabolism (glycolysis, gluconeogenesis, pentose phosphate pathway) adenine and adenosine salvage, adenosine nucleotides degradation, arsenate detoxification, methylglyoxal degradation. Finally, the results indicate that in the group with higher drip loss and with deeper glycolysis, more methylglyoxal (as a by-product of carbohydrate metabolism) is produced which may lead to changes of muscle proteins properties and contribute to an increase in drip loss.

Deep sequencing microRNA profiles associated with wooden breast in commercial broilers

Wooden breast (WB) is a muscle disorder affecting modern commercial broiler chickens that leads to a palpable firm pectoralis major muscle and causes severe reduction in meat quality, resulting in substantial economic losses for the poultry industry. Most studies have focused on the regulatory mechanisms underlying this defect with respect to the gene and protein expression levels as well as the levels of metabolites. MicroRNAs (miRNAs) play critical roles in human muscular disorders, such as the Duchenne muscular dystrophy, by regulating the muscle regeneration or fibrosis processes. In this study, we investigated the miRNAs and related pathways that play important roles in the development of WB. We generated the miRNA expression profiles of the pectoralis major muscle samples from 3 WB-affected and 3 nonaffected chickens selected from a commercial broiler population via small RNA sequencing. A total of 578 miRNAs were identified in the chicken breast muscles from the initial analysis of the sequencing data. Of these, 23 miRNAs were significantly differentially expressed (false discovery rate [FDR] <0.05, log2|Foldchange| >1), including 20 upregulated and 3 downregulated miRNAs in the WB group compared to the normal group. Moreover, functional enrichment of the predicted target genes of differential miRNAs indicated that these miRNAs were involved in biological processes and pathways related to energy metabolism, apoptosis, focal adhesion, and development of blood vessels. Four differentially expressed miRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). We also highlighted several differentially expressed miRNAs, such as gga-miR-155, gga-miR-29c, and gga-miR-133, for their potential roles in the regulation of the development of WB. To the best of our knowledge, this is the first study investigating the miRNA expression profile of the breast muscle associated with WB. The findings of this study can be used to explore the potential molecular mechanisms of other muscle disorders in broilers and provide valuable information for chicken breeding.

Integrated Environmental and Genomic Analysis Reveals the Drivers of Local Adaptation in African Indigenous Chickens

Breeding for climate resilience is currently an important goal for sustainable livestock production. Local adaptations exhibited by indigenous livestock allow investigating the genetic control of this resilience. Ecological niche modeling (ENM) provides a powerful avenue to identify the main environmental drivers of selection. Here, we applied an integrative approach combining ENM with genome-wide selection signature analyses (XPEHH and Fst) and genotype-environment association (redundancy analysis), with the aim of identifying the genomic signatures of adaptation in African village chickens. By dissecting 34 agro-climatic variables from the ecosystems of 25 Ethiopian village chicken populations, ENM identified six key drivers of environmental challenges: One temperature variable-strongly correlated with elevation, three precipitation variables as proxies for water availability, and two soil/land cover variables as proxies of food availability for foraging chickens. Genome analyses based on whole-genome sequencing (n = 245), identified a few strongly supported genomic regions under selection for environmental challenges related to altitude, temperature, water scarcity, and food availability. These regions harbor several gene clusters including regulatory genes, suggesting a predominantly oligogenic control of environmental adaptation. Few candidate genes detected in relation to heat-stress, indicates likely epigenetic regulation of thermo-tolerance for a domestic species originating from a tropical Asian wild ancestor. These results provide possible explanations for the rapid past adaptation of chickens to diverse African agro-ecologies, while also representing new landmarks for sustainable breeding improvement for climate resilience. We show that the pre-identification of key environmental drivers, followed by genomic investigation, provides a powerful new approach for elucidating adaptation in domestic animals.

Woody breast myopathy broiler show age-dependent adaptive differential gene expression in Pectoralis major and altered in-vivo triglyceride kinetics in adipogenic tissues

A study was conducted to understand the differentially expressed genes in Pectoralis (P) major under woody breast (WB) myopathy condition in a high yielding broiler strain using RNA-sequencing at the growing (d 21) and finishing (d 42 and d 56) grow-out ages. Follow-up study was conducted to understand the in vivo triglyceride (TG) synthesis (d 49) occurring in adipogenic tissues using deuterium oxide (2H2O) as a metabolic tracer. Results indicated the top physiological systems affected in myopathy broiler were related to the musculo-skeletal system (d 21, 42, and 56) and cardiovascular system (d 42 and 56). Ubiquitin-specific proteases are expressed higher in myopathy broiler at d 21 (OTUD1) and d 42 (SACS) that potentially indicated higher degradation of muscle protein occurring at those ages. While genes related to transcription factors and muscle cell differentiation (ZNF234, BTG2) and muscle growth (IGF1) were upregulated with myopathy broiler suggesting concurrent muscle fiber regeneration. The downregulation of PYGB and MGAM genes related to carbohydrate transport and metabolism at d 42 potentially indicated nutrient-deficient state of myopathy affected fibers; whereas the nutrient-deficient physiological state of cells seemed to be counteracted by up-regulation of genes related to carbohydrate (ALDOB, GPD1L2) at d 56. There was a reduced (P < 0.05) in vivo TG synthesis in liver of the myopathy broiler (0.123 %/hr) compared to non-myopathy broiler (0.197 %/hr). The majority of TG synthesized in liver with myopathy broiler could conceivably be delivered to P. major (rather than to abdominal fat pad storage) to fulfil the increased energy need of muscle cells (via TG lipolysis and fatty acid [FA] oxidation). The increased utilization of FAs in the WB affected muscle could result in reduced secretion of FAs into blood circulation leading to sub-optimal availability of FAs for re-esterification for TG synthesis in liver. Results indicated that myopathy broiler at later age (d 56) of grow-out period were synchronously going through adaptive physiological processes of feedback responses to adverse cellular states.

Insights Into Transcriptome Profiles Associated With Wooden Breast Myopathy in Broilers Slaughtered at the Age of 6 or 7 Weeks

Transcriptomes associated with wooden breast (WB) were characterized in broilers at two different market ages. Breasts (Pectoralis major) were collected, 20-min postmortem, from male Ross 308 broilers slaughtered at 6 and 7 weeks of age. The breasts were classified as "non-WB" or "WB" based on palpation hardness scoring (non-WB = no abnormal hardness, WB = consistently hardened). Total RNA was isolated from 16 samples (n = 3 for 6 week non-WB, n = 3 for 6 week WB; n = 5 for 7 week non-WB, n = 5 for 7 week WB). Transcriptome was profiled using a chicken gene expression microarray with one-color hybridization technique, and compared between non-WB and WB samples of the same age. Among 6 week broilers, 910 transcripts were differentially expressed (DE) (false discovery rate, FDR < 0.05). Pathway analysis underlined metabolisms of glucose and lipids along with gap junctions, tight junction, and focal adhesion (FA) signaling as the top enriched pathways. For the 7 week broilers, 1,195 transcripts were identified (FDR < 0.05) with regulation of actin cytoskeleton, mitogen-activated protein kinase (MAPK) signaling, protein processing in endoplasmic reticulum and FA signaling highlighted as the enriched affected pathways. Absolute transcript levels of eight genes (actinin-1 - ACTN1, integrin-linked kinase - ILK, integrin subunit alpha 8 - ITGA8, integrin subunit beta 5 - ITGB5, protein tyrosine kinase 2 - PTK2, paxillin - PXN, talin 1 - TLN1, and vinculin - VCL) of FA signaling pathway were further elucidated using a droplet digital polymerase chain reaction. The results indicated that, in 6 week broilers, ITGA8 abundance in WB was greater than that of non-WB samples (p < 0.05). Concerning 7 week broilers, greater absolute levels of ACTN1, ILK, ITGA8, and TLN1, accompanied with a reduced ITGB5 were found in WB compared with non-WB (p < 0.05). Transcriptional modification of FA signaling underlined the potential of disrupted cell-cell communication that may incite aberrant molecular events in association with development of WB myopathy.

SEaCorAl: Identifying and contrasting the regulation-correlation bias in RNA-Seq paired expression data of patient groups

The Cancer Genome Atlas database offers the possibility of analyzing genome-wide expression RNA-Seq cancer data using paired counts, that is, studies where expression data are collected in pairs of normal and cancer cells, by taking samples from the same individual. Correlation of gene expression profiles is the most common analysis to study co-expression groups, which is used to find biological interpretation of -omics big data. The aim of the paper is threefold: firstly we show for the first time, the presence of a "regulation-correlation bias" in RNA-Seq paired expression data, that is an artifactual link between the expression status (up- or down-regulation) of a gene pair and the sign of the corresponding correlation coefficient. Secondly, we provide a statistical model able to theoretically explain the reasons for the presence of such a bias. Thirdly, we present a bias-removal algorithm, called SEaCorAl, able to effectively reduce bias effects and improve the biological significance of correlation analysis. Validation of the SEaCorAl algorithm is performed by showing a significant increase in the ability to detect biologically meaningful associations of positive correlations and a significant increase of the modularity of the resulting unbiased correlation network.

A critical review of the mechanisms involved in the occurrence of growth-related abnormalities affecting broiler chicken breast muscles

In the past decade, the poultry industry has faced the occurrence of growth-related muscular abnormalities that mainly affect, with a high incidence rate, the Pectoralis major of the fast-growing genotypes selected for their production performances (high growth rate and breast yield). These myopathies are termed as White Striping, Wooden Breast, and Spaghetti Meat and exhibit distinctive phenotypes. A spatiotemporal distribution has been demonstrated for these disorders as in the early stage they primarily affect the superficial area in the cranial portion of the muscle and, as the birds grow older, involve the entire tissue. Aside from their distinctive phenotypes, these myopathies share common histological features. Thus, it might be speculated that common causative mechanisms might be responsible for the physiological and structural perturbations in the muscle associated with these conditions and might underpin their occurrence. The present review paper aims to represent a critical survey of the outcomes of all the histologic and ultrastructural observations carried out on White Striping, Wooden Breast, and Spaghetti Meat affected muscles. Our analysis has been performed by combining these outcomes with the findings of the genetic studies, trying to identify possible initial causative mechanisms triggering the onset and the time-series of the events ultimately resulting in the development and progression of the growth-related myopathies currently affecting broilers Pectoralis major muscles. Several evidences support the hypothesis that sarcoplasmic reticulum stress, primarily induced an accumulation of misfolded proteins (but also driven by other factors including altered calcium homeostasis and accumulation of fatty acids), may be responsible for the onset of these growth-related myopathies in broilers. At the same time, the development of hypoxic conditions, as a direct consequence of an inadequate vascularization, triggers a time-series sequence of events (i.e., phlebitis, oxidative stress, etc.) resulting in the activation of response mechanisms (i.e., modifications in the energetic metabolism, inflammation, degeneration, and regeneration) which are all strictly related to the progression of these myopathic disorders.

Dissecting the Gene Expression Networks Associated with Variations in the Major Components of the Fatty Acid Semimembranosus Muscle Profile in Large White Heavy Pigs

Simple Summary

The amount and fatty acid composition of intramuscular fat are important features for the qualitative characteristics of processed and fresh meat products, but the knowledge of the key molecular drivers controlling these traits is still scant. To this aim, the present study investigated the co-expression networks of genes related to variations in the major fatty acids deposited in pig Semimembranosus muscle. Palmitic and palmitoleic acid contents were associated with a downregulation of genes involved in autophagy, mitochondrial fusion, and mitochondrial activity, suggesting that the deposition of these fatty acids may be enhanced in muscles with a reduced mitochondrial function. A higher proportion of oleic acid and a reduction in the percentages of n-6 and n-3 polyunsaturated fatty acids were related to changes in the mRNA levels of genes involved in Mitogen-Activated Protein Kinase (MAPK) signaling. The obtained results indicated gene expression networks and new candidate genes associated with the studied traits. Further studies are needed to confirm our results and identify in the discussed genes molecular markers for future selection schemes aimed at improving pork nutritional and technological quality. Furthermore, as pigs are considered reliable animal models for several human conditions, the obtained results may also be of interest for improving the knowledge of the molecular pathways associated with obesity and diabetes.

Abstract

To date, high-throughput technology such as RNA-sequencing has been successfully applied in livestock sciences to investigate molecular networks involved in complex traits, such as meat quality. Pork quality depends on several organoleptic, technological, and nutritional characteristics, and it is also influenced by the fatty acid (FA) composition of intramuscular fat (IMF). To explore the molecular networks associated with different IMF FA compositions, the Semimembranosus muscle (SM) from two groups of Italian Large White (ILW) heavy pigs divergent for SM IMF content was investigated using transcriptome analysis. After alignment and normalization, the obtained gene counts were used to perform the Weighted Correlation Network Analysis (WGCNA package in R environment). Palmitic and palmitoleic contents showed association with the same gene modules, comprising genes significantly enriched in autophagy, mitochondrial fusion, and mitochondrial activity. Among the key genes related to these FAs, we found TEAD4, a gene regulating mitochondrial activity that seems to be a promising candidate for further studies. On the other hand, the genes comprised in the modules associated with the IMF contents of oleic, n-6, and n-3 polyunsaturated FAs (PUFAs) were significantly enriched in Mitogen-Activated Protein Kinase (MAPK) signaling, in agreement with previous studies suggesting that several MAPK players may have a primary role in regulating lipid deposition. These results give an insight into the molecular cascade associated with different IMF FA composition in ILW heavy pigs. Further studies are needed to validate the results and confirm whether some of the identified key genes may be effective candidates for pork quality.

Weighted gene co-expression network analysis identifies molecular pathways and hub genes involved in broiler White Striping and Wooden Breast myopathies

In recent years, the poultry industry has experienced an increased incidence of myopathies affecting breasts of fast-growing broilers, such as White Striping (WS) and Wooden Breast (WB) defects. To explore the molecular mechanisms and genes involved in WS and WB onset, we decided to perform a Weighted Gene Co-expression Network Analysis (WGCNA) using the gene expression profile and meat quality parameters of Pectoralis major muscles analysed in our previous study. Among the 212 modules identified by WGCNA, the red, darkred, midnightblue and paleturquoise4 modules were chosen for subsequent analysis. Functional analysis evidenced pathways involved in extracellular matrix (ECM) organization, collagen metabolism, cellular signaling and unfolded protein response. The hub gene analysis showed several genes coding for ECM components as the most interconnected nodes in the gene network (e.g. COL4A1, COL4A2, LAMA2, LAMA4, FBLN5 and FBN1). In this regard, this study suggests that alterations in ECM composition could somehow activate the cascade of biological reactions that result in the growth-related myopathies onset, and the involvement of Collagen IV alterations in activating the endoplasmic reticulum (ER) stress response may be hypothesized. Therefore, our findings provide further and innovative knowledge concerning the molecular mechanisms related to the breast abnormalities occurrence in modern broilers.

Enhanced cytokine expression and upregulation of inflammatory signaling pathways in broiler chickens affected by wooden breast myopathy

BACKGROUND

Wooden breast (WB) myopathy in broiler chickens is a growing challenge for the poultry industry. Previous multi-omic data have implied that the pathogenesis of WB is associated with the activation of immune system and inflammatory response. However, the intricate mechanisms are not fully understood. This study was therefore conducted to systematically investigate the morphology, expression of cytokines as well as the underlying signaling pathways regulating the inflammatory response in pectoralis major (PM) muscle of WB myopathic broilers.

RESULTS

wHistopathological changes, increased plasma creatine kinase and lactate dehydrogenase activities, elevated myeloperoxidase activity and overproduction of nitric oxide in muscle indicated the enhancement of muscle damage and inflammation in WB broilers. The messenger RNA (mRNA) expressions of inflammatory cytokines were dysregulated in PM muscle and contents of interleukin (IL)-1β, IL-8 and tumor necrosis factor-α were increased in serum of WB myopathic broilers, indicating this myopathy was associated with immune disorder and systemic inflammation response. Additionally, toll-like receptor (TLR) levels were upregulated, the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathway was activated and the mRNA expression levels of downstream inflammatory mediators were enhanced in PM muscle of WB myopathy affected birds.

CONCLUSION

The results indicated an immune disorder and a systemic inflammation response in WB myopathic broilers, which might be related to a synergetic effect of TLRs and NF-κB pathway. © 2020 Society of Chemical Industry.

Evidence of vascular endothelial dysfunction in Wooden Breast disorder in chickens: Insights through gene expression analysis, ultra-structural evaluation and supervised machine learning methods

Several gene expression studies have been previously conducted to characterize molecular basis of Wooden Breast myopathy in commercial broiler chickens. These studies have generally used a limited sample size and relied on a binary disease outcome (unaffected or affected by Wooden Breast), which are appropriate for an initial investigation. However, to identify biomarkers of disease severity and development, it is necessary to use a large number of samples with a varying degree of disease severity. Therefore, in this study, we assayed a relatively large number of samples (n = 96) harvested from the pectoralis major muscle of unaffected (U), partially affected (P) and markedly affected (A) chickens. Gene expression analysis was conducted using the nCounter MAX Analysis System and data were analyzed using four different supervised machine-learning methods, including support vector machines (SVM), random forests (RF), elastic net logistic regression (ENET) and Lasso logistic regression (LASSO). The SVM method achieved the highest prediction accuracy for both three-class (U, P and A) and two-class (U and P+A) classifications with 94% prediction accuracy for two-class classification and 85% for three-class classification. The results also identified biomarkers of Wooden Breast severity and development. Additionally, gene expression analysis and ultrastructural evaluations provided evidence of vascular endothelial cell dysfunction in the early pathogenesis of Wooden Breast.

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.

Molecular Phenotyping of White Striping and Wooden Breast Myopathies in Chicken

The White Striping (WS) and Wooden Breast (WB) defects are two myopathic syndromes whose occurrence has recently increased in modern fast-growing broilers. The impact of these defects on the quality of breast meat is very important, as they greatly affect its visual aspect, nutritional value, and processing yields. The research conducted to date has improved our knowledge of the biological processes involved in their occurrence, but no solution has been identified so far to significantly reduce their incidence without affecting growing performance of broilers. This study aims to follow the evolution of molecular phenotypes in relation to both fast-growing rate and the occurrence of defects in order to identify potential biomarkers for diagnostic purposes, but also to improve our understanding of physiological dysregulation involved in the occurrence of WS and WB. This has been achieved through enzymatic, histological, and transcriptional approaches by considering breast muscles from a slow- and a fast-growing line, affected or not by WS and WB. Fast-growing muscles produced more reactive oxygen species (ROS) than slow-growing ones, independently of WS and WB occurrence. Within fast-growing muscles, despite higher mitochondria density, muscles affected by WS or WB defects did not show higher cytochrome oxidase activity (COX) activity, suggesting altered mitochondrial function. Among the markers related to muscle remodeling and regeneration, immunohistochemical staining of FN1, NCAM, and MYH15 was higher in fast- compared to slow-growing muscles, and their amount also increased linearly with the presence and severity of WS and WB defects, making them potential biomarkers to assess accurately their presence and severity. Thanks to an innovative histological technique based on fluorescence intensity measurement, they can be rapidly quantified to estimate the injuries induced in case of WS and WB. The muscular expression of several other genes correlates also positively to the presence and severity of the defects like TGFB1 and CTGF, both involved in the development of connective tissue, or Twist1, known as an inhibitor of myogenesis. Finally, our results suggested that a balance between TGFB1 and PPARG would be essential for fibrosis or adiposis induction and therefore for determining WS and WB phenotypes.

Transcriptional Profiles of Skeletal Muscle Associated With Increasing Severity of White Striping in Commercial Broilers

Development of the white striping (WS) abnormality adversely impacts overall quality of broiler breast meat. Its etiology remains unclear. This study aimed at exploring transcriptional profiles of broiler skeletal muscles exhibiting different WS severity to elucidate molecular mechanisms underlying the development and progression of WS. Total RNA was isolated from pectoralis major of male 7-week-old Ross 308 broilers. The samples were classified as mild (n = 6), moderate (n = 6), or severe (n = 4), based on number and thickness of the white striations on the meat surface. The transcriptome was profiled using a chicken gene expression microarray with one-color hybridization technique. Gene expression patterns of each WS severity level were compared against each other; hence, there were three comparisons: moderate vs. mild (C1), severe vs. moderate (C2), and severe vs. mild (C3). Differentially expressed genes (DEGs) were identified using the combined criteria of false discovery rate ≤ 0.05 and absolute fold change ≥1.2. Differential expression of 91, 136, and 294 transcripts were identified in C1, C2, and C3, respectively. There were no DEGs in common among the three comparisons. Based on pathway analysis, the enriched pathways of C1 were related with impaired homeostasis of macronutrients and small biochemical molecules with disrupted Ca²⁺-related pathways. Decreased abundance of the period circadian regulator suggested the shifted circadian phase when moderate WS developed. The enriched pathways uniquely obtained in C2 were RNA degradation, Ras signaling, cellular senescence, axon guidance, and salivary secretion. The DEGs identified in those pathways might play crucial roles in regulating cellular ion balances and cell-cycle arrest. In C3, the pathways responsible for phosphatidylinositol 3-kinase-Akt signaling, p53 activation, apoptosis, and hypoxia-induced processes were modified. Additionally, pathways associated with a variety of diseases with the DEGs involved in regulation of [Ca²⁺], collagen formation, microtubule-based motor, and immune response were identified. Eight pathways were common to all three comparisons (i.e., calcium signaling, Ras-associated protein 1 signaling, ubiquitin-mediated proteolysis, vascular smooth muscle contraction, oxytocin signaling, and pathway in cancer). The current findings support the role of intracellular ion imbalance, particularly Ca²⁺, oxidative stress, and impaired programmed cell death on WS progression.