Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup J

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.

Investigation of chicken housekeeping genes using next-generation sequencing data

Accurate normalization of the gene expression assays, using housekeeping genes (HKGs), is critically necessary. To do so, selection of a proper set of HKGs for a specific experiment is of great importance. Despite many studies, there is no consensus about the suitable set of HKGs for implementing in the quantitative real-time PCR analyses of chicken tissues. A limited number of HKGs have been widely used. However, wide utilization of a little number of HKGs for all tissues is challenging. The emergence of high-throughput gene expression RNA-seq data has enabled the simultaneous comparison of the stability of multiple HKGs. Therefore, employing the average coefficient of variations of at least three datasets per tissue, we sorted all reliably expressed genes (REGs; with FPKM ≥ 1 in at least one sample) and introduced the top 10 most suitable and stable reference genes for each of the 16 chicken tissues. We evaluated the consistency of the results of five tissues using the same methodology on other datasets. Furthermore, we assessed 96 previously widely used HKGs (WU-HKGs) in order to challenge the accuracy of the previous studies. The New Tuxedo software suite was used for the main analyses. The results revealed novel, different sets of reference genes for each of the tissues with 17 common genes among the top 10 genes lists of 16 tissues. The results did disprove the suitability of WU-HKGs such as Actb, Ldha, Scd, B2m, and Hprt1 for any of the tissues examined. On the contrary, a total of 6, 13, 14, 23, and 32 validated housekeeping genes (V-HKGs) were discovered as the most stable and suitable reference genes for muscle, spleen, liver, heart, and kidney tissues, respectively. Although we identified a few new HKGs usable for multiple tissues, the selection of suitable HKGs is required to be tissue specific. The newly introduced reference genes from the present study, despite lacking experimental validation, will be able to contribute to the more accurate normalization for future expression analysis of chicken genes.

Hypothalamus-pituitary axis transcriptomic modification dependent on growth rate in geese (Anser anser domesticus)

The hypothalamus-pituitary axis is involved in digest processing, stress response, energy storage and many other processes. In birds, this control differs from in mammals, such as regulation of appetite and satiety centre. The transcriptomics analyses of both brain structures can explain and identify the molecular processes related to body growth and development and nutritional status. Many reports describe chicken transcriptome in literature, but gene expression studies in the other poultry species are extremely rare. Therefore, the present research undertook the attempt to explain hypothalamus-pituitary processes in domestic geese-Polish White Kołuda®, main Polish line. After 16 weeks of fattening, significant differences in geese weight were observed. Therefore, transcriptome of pituitary and hypothalamus profiles could be compared between low and high growth rate geese groups. Due to the lack of domestic geese genome assembly in the public databases, we used three mapping approaches: de novo analysis, mapping to two other pink-footed and swan geese genomes. The functional examination showed that the most enriched biological process in the geese hypothalamus covered the immune response. Moreover, in the hypothalamus, proteins typical for the pituitary such as PRL and GH were differentially expressed (DE). Our study recommends one gene as a candidate for growth rate in geese-the FOS gene, which encodes Fos proto-oncogene-DE in both analysed tissues. The FOS gene is involved in regulating feeding behaviour, immune regulation, stimulating cellular proliferation and controlling growth hormone synthesis. Moreover, the present investigation indicates DE genes involved in gene expression regulation. The study delivers new information about the changes in the pituitary-hypothalamic axis in geese dependent on growth rate differences.

Hulless barley and β-glucanase affect ileal digesta soluble beta-glucan molecular weight and digestive tract characteristics of coccidiosis-vaccinated broilers

Exogenous β-glucanase (BGase) in barley-based feed has been shown to reduce digesta viscosity in chickens, and thereby improve performance. Less well studied is the potential for BGase to convert barley β-glucan into low molecular weight carbohydrates, which might influence digestive tract function and enteric disease. Coccidiosis-vaccinated broiler chickens were fed graded levels of hulless barley (HB) and BGase to determine their effects on β-glucan depolymerization and digestive tract characteristics. Broilers were fed high β-glucan HB (0%, 30% and 60% replacing wheat) and BGase (0%, 0.01% and 0.1%) in a 3 × 3 factorial arrangement. A total of 5,346 broilers were raised in litter floor pens and vaccinated for coccidiosis on d 5. Each treatment was assigned to 1 pen in each of 9 rooms. The significance level was set at P ≤ 0.05. At both 11 and 33 d of broiler ages, peak molecular weight of β-glucan in ileal digesta decreased with increasing BGase for 30% and 60% HB. The maximum molecular weight for the smallest 10% β-glucan molecules (MW-10%) decreased with BGase at both ages for 30% and 60% HB; for birds fed 0% HB, only 0.1% BGase decreased MW-10%. The 0.1% BGase increased caecal short chain fatty acids (SCFA) compared to the 0.01% BGase at d 11 only for the 60% HB. Ileal pH increased with increasing HB and BGase at d 11 and 33. Caecal pH was lower for 0.1% BGase than 0% BGase for 60% HB at d 11. Relative mRNA expression of interleukin 6 (IL-6) and IL-8 in the ileum increased with 0.1% BGase at d 11 and 33, respectively, whereas expression of ileal mucin 2 (MUC2) decreased with 0.1% BGase at d 33. In the caeca, interactions between HB and BGase were significant for monocarboxylate transporter 1 (MCT1) and mucin 5AC (MUC5 AC) on d 11, but no treatment effects were found at d 33. In conclusion, BGase depolymerized high molecular weight β-glucan in HB in a dose-dependent manner. Hulless barley and BGase did not increase SCFA concentrations (except for 60% HB with 0.1% BGase at d 11) and caused minor effects on digestive tract histomorphological measurements and relative mRNA gene expression.

Multi-carbohydrase enzymes improve feed energy in broiler diets containing standard or low crude protein

This study evaluated the effect of multi-carbohydrase (MC) on energy and nitrogen (N) balance and gene expression in broilers fed diets with different crude protein (CP) contents. The study employed a 2 × 2 factorial arrangement of treatments. The factors were presence or absence of MC, and standard (SCP) or low (LCP) dietary CP concentration. A 3-phase feeding program was used, including starter (0 to 7 d), grower (8 to 17 d) and finisher (18 to 28 d) phases. The study was undertaken in closed calorimetry chambers. Each of the 4 dietary treatments was replicated 8 times in total across 2 runs, with 2 birds per replicate (n = 64). Data for energy partitioning and N balance were collected from d 25 to 28. On d 28, birds were euthanized to collect muscle and intestinal tissue samples for gene expression. The results showed that the MC increased apparent metabolizable energy (AME, P < 0.01) and net energy (NE, P < 0.05), and reduced the feed conversion ratio (FCR, P < 0.01) in all diets. The proportion of energy retained as fat per total energy retention (REf/RE) was positively correlated with feed AME and NE (r = 0.541, P < 0.01 and r = 0.665, P < 0.001, respectively), suggesting that feed energy augmented with increased fat gain. Muscle ATP synthase subunit alpha (ATP5A1W) gene expression had a positive correlation with REf/RE and feed NE (r = 0.587, P < 0.001 and r = 0.430, P < 0.05, respectively). Similarly, muscle peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1A) expression was negatively correlated with weight gain and positively correlated with FCR (r = −0.451, P < 0.05 and r = 0.359, P < 0.05, respectively). These correlations show that over-expressions of muscle genes related to energy production reduce bird performance. This study demonstrated that MC increase dietary energy utilization, regardless of dietary CP concentration. However, the energy released by the enzymes increases feed energy-to-CP ratio, meaning there is excess energy that is then deposited as body fat. This suggests that supplemental MC in broiler feeds is beneficial if diets are formulated to contain marginal energy levels.

Monoglyceride Blend Reduces Mortality, Improves Nutrient Digestibility, and Intestinal Health in Broilers Subjected to Clinical Necrotic Enteritis Challenge

This study evaluated the potential of monoglyceride blend (MG) and buffered formic acid (FA) as alternatives to antibiotics in the performance and intestinal health of broilers under clinical necrotic enteritis (NE) challenge. A total of 544 as-hatched Ross 308 broiler chicks were randomly distributed to 32-floor pens housing 17 birds per pen. The four treatments were: NC-non-additive control; ZBS-antibiotic group supplemented with zinc bacitracin and salinomycin; MG-additive MG supplementation in the starter phase only; and MGFA-additive MG in starter phase and FA in grower and finisher phases. All birds were challenged with Eimeria spp. and Clostridium perfringens. Results showed that the NC group had lower BWG and higher FCR than the ZBS group in the grower and overall period (p < 0.05). The NC group had higher NE-caused mortality (days 14 to 17) than the ZBS group (p < 0.05). Birds fed MG had lower NE-caused mortality than the NC group (p < 0.05). Birds fed MG had upregulated jejunal tight junction protein1 (TJP1) and immunoglobulin (IgG) on day 16 and improved gross energy digestibility on day 24 than the NC group (p < 0.05). These findings suggest that supplementation of MG may improve intestinal health and protect birds from clinical NE occurrence.

Screening of Reference Genes for RT-qPCR in Chicken Adipose Tissue and Adipocytes

Reverse transcription quantitative real-time PCR is the most commonly used method to detect gene expression levels. In experiments, it is often necessary to correct and standardize the expression level of target genes with reference genes. Therefore, it is very important to select stable reference genes to obtain accurate quantitative results. Although application examples of reference genes in mammals have been reported, no studies have investigated the use of reference genes in studying the growth and development of adipose tissue and the proliferation and differentiation of preadipocytes in chickens. In this study, GeNorm, a reference gene stability statistical algorithm, was used to analyze the expression stability of 14 candidate reference genes in the abdominal adipose tissue of broilers at 1, 4, and 7 weeks of age, the proliferation and differentiation of primary preadipocytes, as well as directly isolated preadipocytes and mature adipocytes. The results showed that the expression of the TATA box binding protein (TBP) and hydroxymethylbilane synthase (HMBS) genes was most stable during the growth and development of abdominal adipose tissue of broilers, the expression of the peptidylprolyl isomerase A (PPIA) and HMBS genes was most stable during the proliferation of primary preadipocytes, the expression of the TBP and RPL13 genes was most stable during the differentiation of primary preadipocytes, and the expression of the TBP and HMBS genes was most stable in directly isolated preadipocytes and mature adipocytes. These results provide reference bases for accurately detecting the mRNA expression of functional genes in adipose tissue and adipocytes of chickens.

Efficacy of supplemental multi-carbohydrases in broiler diets depends on soluble arabinoxylan-to-total arabinoxylan content

1. The objective of this study was to investigate the effect of multi-carbohydrase enzymes (MC) on net energy (NE), performance and gene expression in Cobb 500 broilers fed diets containing different levels of soluble and total arabinoxylan (sAX/tAX) ratios.2. The study employed a 2 × 3 factorial arrangement of treatments, with factors including with or without MC and three ratios of sAX/tAX: high (HS, 27.3%), intermediate (IS, 21.3%) and low (LS, 15.7%).3. Six dietary treatments were formulated, with each diet replicated five times in the calorimetric study (Experiment 1) and eight times for a floor pen feeding trial (Experiment 2).4. Experiment 1 showed significant (P < 0.01) MC × sAX/tAX interactions for apparent metabolisable energy (AME) and NE. These interactions indicated that the supplemental MC increased AME only in the HS diet, and NE in the HS and LS diets.5. Experiment 2 results showed MC × sAX/tAX interactions for feed conversion ratio (FCR, P < 0.01) and ileal digesta viscosity (P < 0.05), demonstrating that MC lowered FCR only in the LS-fed birds, and reduced digesta viscosity only in the HS-fed birds. Apparent ileal digestible crude protein (AID CP) was negatively correlated with ileal digesta viscosity (r = -0.735, P < 0.001), which suggested that increasing ileal digesta viscosity reduced AID CP.6. A significant (P < 0.05) MC × sAX/tAX interaction was observed for duodenal COX III mRNA gene expression, which indicated that this gene was upregulated in the IS-fed birds relative to the HS-fed birds, but only when MC was added. This gene was downregulated (P < 0.05) in the muscle in the presence of MC application in all diets.7. The results from this study showed that supplemental MC can improve NE and FCR in birds fed diets containing the low sAX/tAX ratios.

Probiotic Bacillus subtilis 29,784 improved weight gain and enhanced gut health status of broilers under necrotic enteritis condition

The study investigated the benefit of a Bacillus subtilis probiotic (Bs 29,784) in necrotic enteritis (NE)-challenged broilers. Four treatments were performed with 312 male day-old Ross 308 reared in floor pens from day 0 to day 35: 2 groups fed control diet without or with NE challenge (CtrlNC and CtrlNE); 2 groups fed probiotic and antibiotic supplements in the control diet with NE challenge (ProNE and AntNE). Necrotic enteritis challenge procedures commenced with inoculation of Eimeria spp 1 mL/bird per os at day 9 and Clostridium perfringens EHE-NE18 (approximately 10⁸ cfu/mL) 1 mL/bird per os at day 14 and day 15. Performance parameters were measured on day 16 and day 35. Lesion, cecal microbiota, and jejunal gene expression were analyzed on day 16. Necrotic enteritis challenge significantly suppressed the performance parameters compared with CtrlNC: 27% weight gain reduction, 11 points feed conversion ratio (FCR) increase at day 16, and 12% weight gain reduction, 5-point FCR increase at day 35. By day 35, ProNE and AntNE treatments enabled significantly higher weight gain (4 and 9%, respectively) than CtrlNE. Compared with CtlrNE and contrary to AntNE, ProNE treatment exhibited upregulation of genes coding for tight junctions proteins (CLDN1, JAM2, TJP1), cytokines (IL12, interferon gamma, TGFβ), and Toll-like receptors (TLR5, TLR21) suggesting enhanced immunity and intestinal integrity. 16S NGS analysis of cecal microbiota at day 16 showed a decreased alpha diversity in challenged groups. Principal component analysis of operational taxonomic unit (OTU) abundance revealed that ProNE and AntNE grouped closely while both distantly from CtrlNC and CtrlNE, which were separately grouped, indicating the similar effects of ProNE and AntNE on the OTU diversity that were however different from both CtrlNC and CtrlNE. Microbiota analysis revealed an increase of genera Faecalibacterium, Oscillospira, and Butyricicoccus; and a decrease of genera Ruminococcus, Lactobacillus, and Bacteroides; and an increase of the Firmicutes-to-Bacteroidetes ratio in ProNE and AntNE groups compared with the CtlrNE group. It is concluded that Bs 29,784 may enable improved health of broiler chickens under NE conditions thus performance implications.

Over-processed meat and bone meal and phytase effects on broilers challenged with subclinical necrotic enteritis: Part 2. Inositol phosphate esters hydrolysis, intestinal permeability, hematology, jejunal gene expression and intestinal morphology

This study investigated the hypothesis that feeding broilers over-processed meat and bone meal (MBM) would impair gut health in the absence of phytase and in turn, affect inositol phosphate (inositol x-phosphate, IPx: IP3, IP4, IP5 and IP6) ester hydrolysis, intestinal permeability, hematology, jejunal gene expression and intestinal morphology during necrotic enteritis (NE). Ross 308 male broilers (n = 768) were assigned to one of 8 dietary treatments in a 2 × 2 × 2 factorial arrangement, with 6 replicate pens per diet and 16 birds per pen in a completely randomized design. Factors were: NE challenge (no or yes), phytase level (500 or 5,000 FTU/kg) and MBM processing (as-received or over-processed). For the NE challenge, half of the birds were challenged with field strains of Eimeria spp. on d 9 and 10⁸ CFU/mL of Clostridium perfringens strain EHE-NE18 on d 14 and 15. A 3-way challenge, phytase and MBM processing interaction was detected for IP5 (P < 0.05) and IP6 (P < 0.05) levels in the ileum. Birds fed low phytase had increased IP5 and IP6 in unchallenged birds only when diets contained over-processed MBM. Challenge with NE increased intestinal permeability as measured by serum fluorescein isothiocyanate dextran (FITC-d; P < 0.001), increased white blood cells (WBC; P < 0.001), decreased mean corpuscular volume (MCV; P < 0.001) and mean corpuscular hemoglobin (MCH; P < 0.05), and decreased crypt-to-villi ratio (P < 0.05). The over-processed MBM reduced the villi-to-crypt ratio (P < 0.05). A 3-way challenge × phytase × MBM processing interaction was detected for mucin 2 (MUC-2) expression (P < 0.05) where only in unchallenged birds fed over-processed MBM did high phytase reduce MUC-2 expression. A lower expression of aminopeptidase N (APN; P < 0.001) and vitamin D receptor (VDR; P < 0.001) were recorded in NE challenged birds. In conclusion, NE has a negative impact on the gut and hematology of broilers, but its effect on phytate hydrolysis is minimal.

Interactive effect of dietary calcium and phytase on broilers challenged with subclinical necrotic enteritis: part 2. Gut permeability, phytate ester concentrations, jejunal gene expression, and intestinal morphology

Calcium has the capacity to interact with phytate-P to form Ca-phytate complexes and decrease the ability of exogenous phytase to degrade phytic acid. This study investigated the hypothesis that high dietary Ca would impair gut permeability, phytate esters (inositol x-phosphate, IPx: IP3, IP4, IP5, and IP6) degradation, jejunal gene expression, and intestinal morphology. Ross 308 day-old male broilers (n = 768) were distributed into 48-floor pens each housing 16 birds in a factorial arrangement. Factors were NE challenge-no or yes; phytase level of 500 or 1,500 FTU/kg, and Ca level 0.6 or 1.0% starter, 0.5 or 0.9% grower, 0.4 or 0.8% finisher with available P in each phase. Challenged birds were gavaged with 3 field strains of Eimeria on day 9 and 108 CFU per mL of Clostridium perfringens Strain EHE-NE18 on day 14 and day 15. A phytase × Ca interaction was observed in the ileum for IP3 (P < 0.01), IP4 (P < 0.05), and IP6 (P < 0.01). The IP3 and IP4 concentrations were similar for both doses of phytase in the presence of low Ca, but with high Ca, both increased significantly but to a greater extent when the high dose of phytase was used. While IP6 concentrations were low and similar between both doses of phytase at low Ca levels, increasing dietary Ca levels increased IP6 concentrations regardless of phytase dose, but the effect was greater in the low phytase diet. A phytase × Ca interaction was detected for vitamin D receptor (VDR) (P < 0.05) expression where bird fed low phytase and low Ca recorded the highest expression of VDR, all other treatments being equivalent. The challenge decreased crypt depth to villus height ratio (P < 0.001). Challenge birds had higher fluorescein isothiocyanate dextran (P < 0.05) in blood compared with unchallenged birds. Thus, high Ca and high phytase, while not the best for IP6 destruction, did not lead to huge reductions in indicators of gut health.

Identification of Reference Genes in Chicken Intraepithelial Lymphocyte Natural Killer Cells Infected with Very-virulent Infectious Bursal Disease Virus

Due to the limitations in the range of antibodies recognising avian viruses, quantitative real-time PCR (RT-qPCR) is still the most widely used method to evaluate the expression of immunologically related genes in avian viruses. The objective of this study was to identify suitable reference genes for mRNA expression analysis in chicken intraepithelial lymphocyte natural killer (IEL-NK) cells after infection with very-virulent infectious bursal disease virus (vvIBDV). Fifteen potential reference genes were selected based on the references available. The coefficient of variation percentage (CV%) and average count of these 15 genes were determined by NanoString technology for control and infected samples. The M and V values for shortlisted reference genes (ACTB, GAPDH, HMBS, HPRT1, SDHA, TUBB1 and YWHAZ) were calculated using geNorm and NormFinder. GAPDH, YWHAZ and HMBS were the most stably expressed genes. The expression levels of three innate immune response related target genes, CASP8, IL22 and TLR3, agreed in the NanoString and RNA sequencing (RNA-Seq) results using one or two reference genes for normalisation (not HMBS). In conclusion, GAPDH and YWHAZ could be used as reference genes for the normalisation of chicken IEL-NK cell gene responses to infection with vvIBDV.

Influence of meat and bone meal, phytase, and antibiotics on broiler chickens challenged with subclinical necrotic enteritis: 2. intestinal permeability, organ weights, hematology, intestinal morphology, and jejunal gene expression

Undigested proteins entering the hindgut may favor the proliferation of Clostridium perfringens. Using phytase to eliminate the need for meat and bone meal (MBM) as a P source may reduce potential infection with C. perfringens. A study was conducted to determine the impact of MBM, phytase, and antibiotics (AB) on intestinal permeability and morphology, organ weights, and jejunal gene expression in Ross 308 chickens challenged with subclinical necrotic enteritis (NE). Male Ross 308-day-old chicks (672 each) were randomly allocated to 8 treatments with 6 replicate pens each housing 14 birds. A 2 × 2 × 2 factorial arrangement of treatments was used: MBM (no or yes); AB (no or yes-Zn bacitracin 100 in S and 50 ppm in G/F and salinomycin Na 60 ppm in all phases); phytase (500 or 1,500 FTU/kg, both using 500 FTU matrix values) using wheat-SBM-canola meal diets. Birds were challenged with Eimeria spp on day 9, and C. perfringens strain EHE-NE18 on day 14 and 15. An AB × MBM interaction (P < 0.05) was detected for relative gizzard weight (with contents) being lower in birds fed MBM and AB compared to those fed MBM and no AB. A MBM × AB interaction (P > 0.01) was detected for lymphocyte counts being lower with MBM and AB compared to MBM without AB. A phytase × AB interaction (P < 0.05) was observed for villi length being increased with high phytase and no AB compared to with AB. Inclusion of MBM increased (P < 0.05) blood FICT-d concentration, whereas AB decreased it (P < 0.05). Antibiotics increased RBC (P < 0.05), Hgb (P < 0.05), and PCV (P < 0.05) and expression of Ca-binding protein, CALB1 (P > 0.05). Inclusion of MBM decreased expression of MUC2 (P < 0.05). Results indicate that dietary MBM has a detrimental effect on gut health of broilers but this may be counteracted using AB.

Validation of the Reference Genes for the Gene Expression Studies in Chicken DT40 Cell Line

The selection of a suitable reference gene assures a reliable gene expression analysis when using the qPCR method. Normalization of the reaction is based on the basic metabolism genes. These genes show a constant, unregulated expression in all cells and function throughout their lifetime. In the current study, seven reference gene candidates were screened using RT-qPCR, to determine the best-matched pair of reference genes in the chicken DT40 cell line. The DT40 was derived from bursal lymphoma cells that were subjected to RAV-1 bird retroviral infection. It is a simplified in vitro model that allows tracking the direct interaction of stimulants on the lymphoid population and profiling of the hepatocellular B cell transcriptome. The reference gene analysis was carried out using statistical tools integrating four independent methods—geNorm, Best Keeper, NormFinder, delta Ct and RefFinder. Based on the selected reference genes, the relative gene expression analysis was done using the ddCt method. Complete relative gene expression study on a panel of the target genes revealed that proper selection of reference genes depending on the tissue eliminate decreases in data quality. The SDHA and RPL4 genes constitute stable internal controls as reference genes when analyzing gene expression in the DT40 cell line.

Ginseng Extract Ameliorates the Negative Physiological Effects of Heat Stress by Supporting Heat Shock Response and Improving Intestinal Barrier Integrity: Evidence from Studies with Heat-Stressed Caco-2 Cells, C. elegans and Growing Broilers

Climatic changes and heat stress have become a great challenge in the livestock industry, negatively affecting, in particular, poultry feed intake and intestinal barrier malfunction. Recently, phytogenic feed additives were applied to reduce heat stress effects on animal farming. Here, we investigated the effects of ginseng extract using various in vitro and in vivo experiments. Quantitative real-time PCR, transepithelial electrical resistance measurements and survival assays under heat stress conditions were carried out in various model systems, including Caco-2 cells, Caenorhabditis elegans and jejunum samples of broilers. Under heat stress conditions, ginseng treatment lowered the expression of HSPA1A (Caco-2) and the heat shock protein genes hsp-1 and hsp-16.2 (both in C. elegans), while all three of the tested genes encoding tight junction proteins, CLDN3, OCLN and CLDN1 (Caco-2), were upregulated. In addition, we observed prolonged survival under heat stress in Caenorhabditis elegans, and a better performance of growing ginseng-fed broilers by the increased gene expression of selected heat shock and tight junction proteins. The presence of ginseng extract resulted in a reduced decrease in transepithelial resistance under heat shock conditions. Finally, LC-MS analysis was performed to quantitate the most prominent ginsenosides in the extract used for this study, being Re, Rg1, Rc, Rb2 and Rd. In conclusion, ginseng extract was found to be a suitable feed additive in animal nutrition to reduce the negative physiological effects caused by heat stress.

Stable reference genes for expression studies in breast muscle of normal and white striping-affected chickens

The normalization with proper reference genes is a crucial step to obtain accurate mRNA expression levels in quantitative PCR (qPCR) studies. Therefore, in this study, 10 reference candidate genes were evaluated to determine their stability in normal pectoralis major muscle of broilers and those counterparts affected with White Striping (WS) myopathy at 42 days age. Four different tools were used for ranking the most stable genes: GeNorm, NormFinder, BestKeeper and Comparative Ct (ΔCt), and a general ranking was performed using the RankAggreg tool to select the best reference genes among all tools. From the 10 genes evaluated in the breast muscle of broilers, 8 were amplified. Most of the algorithms/tools indicated the same two genes, RPL30 and RPL5, as the most stable in the broilers breast muscle. In addition, there was agreement among the tools for the least stable genes: MRPS27, GAPDH and RPLP1 in the broilers breast muscle. Therefore, it is interesting to note that even with different tools for evaluating gene expression, there was consensus on the most and least stable genes. These results indicate that the Ribosomal protein L30 (RPL30) and Ribosomal protein L5 (RPL5) can be recommended for accurate normalization in qPCR studies with chicken pectoralis major muscle affected with White Striping and other myopathies.

Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection

Identification of suitable candidate reference genes is an important prerequisite for validating the gene expression data obtained from downstream analysis of RNA sequencing using quantitative real time PCR (qRT-PCR). Though existence of a universal reference gene is myth, commonly used reference genes can be assessed for expression stability to confer their suitability to be used as candidate reference genes in gene expression studies. In this study, we evaluated the expression stability of ten most commonly used reference genes (GAPDH, ACTB, HSP90, HMBS, 18S rRNA, B2M, POLR2A, HPRT1, ACAC, YWHAZ) in fourteen different Peste des petits ruminants virus (PPRV) infected tissues of goats and sheep. RefFinder and RankAggreg software were used to deduce comprehensive ranking of reference genes. Our results suggested HMBS and B2M in goats and HMBS and HPRT1 in sheep can be used as suitable endogenous controls in gene expression studies of PPRV infection irrespective of tissues and condition as a whole, thus eliminating the use of tissue specific/ condition specific endogenous controls. We report for the first time suitable reference genes for gene expression studies in PPRV infected tissues. The reference genes determined here can be useful for future studies on gene expression in sheep and goat infected with PPRV, thus saving extra efforts and time of repeating the reference gene determination and validation.

Co-expulsion of Ascaridia galli and Heterakis gallinarum by chickens

Worm expulsion is known to occur in mammalian hosts exposed to mono-species helminth infections, whilst this phenomenon is poorly described in avian hosts. Mono-species infections, however, are rather rare under natural circumstances. Therefore, we quantified the extent and duration of worm expulsion by chickens experimentally infected with both Ascaridia galli and Heterakis gallinarum, and investigated the accompanying humoral and cell-mediated host immune responses in association with population dynamics of the worms. Results demonstrated the strong co-expulsion of the two ascarid species in three phases. The expulsion patterns were characterized by non-linear alterations separated by species-specific time thresholds. Ascaridia galli burden decreased at a daily expulsion rate (e) of 4.3 worms up to a threshold of 30.5 days p.i., followed by a much lower second expulsion rate (e = 0.46), which resulted in almost, but not entirely, complete expulsion. Heterakis gallinarum was able to induce reinfection within the experimental period (9 weeks). First generation H. gallinarum worms were expelled at a daily rate of e = 0.8 worms until 36.4 days p.i., and thereafter almost no expulsion occurred. Data on both humoral and tissue-specific cellular immune responses collectively indicated that antibody production in chickens with multispecies ascarid infections is triggered by Th2 polarisation. Local Th2 immune responses and mucin-regulating genes are associated with the regulation of worm expulsion. In conclusion, the chicken host is able to eliminate the vast majority of both A. galli and H. gallinarum in three distinct phases. Worm expulsion was strongly associated with the developmental stages of the worms, where the elimination of juvenile stages was specifically targeted. A very small percentage of worms was nevertheless able to survive, reach maturity and induce reinfection if given sufficient time to complete their life cycle. Both humoral and local immune responses were associated with worm expulsion.

Upregulation of genes encoding digestive enzymes and nutrient transporters in the digestive system of broiler chickens by dietary supplementation of fiber and inclusion of coarse particle size corn

BACKGROUND

Measures to improve bird performance have been sought due to the imminent phase out of in-feed antibiotics in poultry and continued demand for higher poultry feeding efficiency. Increasing grain particle size and dietary fibre may improve gizzard function, digestive efficiency and nutrient absorption. This study was conducted to evaluate the effect increased particle size of corn and inclusion of sugarcane bagasse (SB) on mRNA expression of genes encoding digestive enzymes and nutrient transporters in broilers.

RESULTS

A total of 336 day-old Ross 308 males were assigned in a 2 × 2 factorial arrangement of treatments with corn particle size - coarse 3576 μm or fine 1113 μm geometric mean diameter, and SB - 0 or 2% inclusion. Feed conversion ratio (FCR), weight gain and feed intake were measured from d 0-10 and d 10-24. The relative gizzard weight and mRNA expression of genes encoding digestive enzymes and intestinal nutrient transporters were measured on d 24. During d 10-24, a particle size × SB interaction was observed for FCR (P < 0.01), where birds fed coarsely ground corn (CC) with 2% SB had lower FCR than those fed CC without SB. A particle size × SB interaction was observed for both expression of pepsinogen A and C (P < 0.01) which were negatively correlated with FCR on d 24. Addition of 2% SB upregulated pepsinogen A and C only in CC fed birds. Further, 2% SB also upregulated pancreatic amylase (AMY2A) and intestinal cationic amino acid transporter-1 (CAT1). Inclusion of dietary CC upregulated duodenal amino peptidase N (APN), jejunal alanine, serine, cysteine and threonine transporter-1 (ASCT1), and ileal peptide transporter-2 (PepT2).

CONCLUSION

These results suggest that both SB and coarse particle size modulate expression of genes encoding important digestive enzymes and nutrient transporters and thus are directly related to bird performance. These findings provide insights into the combination effects of dietary fiber and particle size in the future management of broiler feeding.

Selection of reference genes for quantitative real-time PCR analysis in chicken ovary following silver nanoparticle treatment

Reliable results of quantitative real time PCR (qPCR) analysis require normalization of target gene expression level using reference genes (RGs). However housekeeping genes expression may vary under experimental conditions, so selection of the proper RGs is a crucial step in a qPCR analysis. Several algorithms have been developed to address this problem: geNorm, NormFinder and BestKeeper. In this study, we have used these three tools to evaluate the stability of RGs in the ovarian tissues of hens treated with silver nanoparticles. Eight genes were selected for the validation: HPRT, HMBS, VIM, SDHA, TBP, RPL13, GAPDH and 18S rRNA. According to geNorm the best combination of reference genes is SDHA and TPP. NormFinder also selected SDHA as the most suitable gene, but in combination with RPL13. Analysis in BestKeeper showed that SDHA, RPL13 might be the best choice in gene expression studies using the chicken ovary. In conclusion, the results obtained depend on the algorithm used and it arises from the diverse calculation strategies used in these programs. The outcome from the NormFinder is considered to be the most trustworthy and used in further qPCR analysis.

Reference gene selection for gene expression study in shell gland and spleen of laying hens challenged with infectious bronchitis virus

Ten reference genes were investigated for normalisation of candidate target gene expression data in the shell gland and spleen of laying hens challenged with two strains of infectious bronchitis virus (IBV). Data were analysed with geNorm, NormFinder and BestKeeper, and a comprehensive ranking (geomean) was calculated. In the combined data set of IBV challenged shell gland samples, the comprehensive ranking showed TATA-box binding protein (TBP) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ) as the two most stable, and succinate dehydrogenase complex flavoprotein subunit A (SDHA) and albumin (ALB) as the two least stable reference genes. In the spleen, and in the combined data set of the shell gland and spleen, the two most stable and the two least stable reference genes were TBP and YWHAZ, and ribosomal protein L4 (RPL4) and ALB, respectively. Different ranking has been due to different algorithms. Validation studies showed that the use of the two most stable reference genes produced accurate and more robust gene expression data. The two most and least stable reference genes obtained in the study, were further used for candidate target gene expression data normalisation of the shell gland and spleen under an IBV infection model.

Downregulation of ALAS1 by nicarbazin treatment underlies the reduced synthesis of protoporphyrin IX in shell gland of laying hens

Shell colour is an important trait for eggs and an understanding of pigment deposition will assist potential management of egg shell colour loss. We demonstrated that nicarbazin feeding down-regulated ALAS1 and reduced protoporphyrin IX (PP IX) in both shell gland and eggshell, indicating the role of nicarbazin in inhibiting the synthesis of PP IX. Additionally, the expression levels of the genes did not show sequential upregulation in the same order of diurnal time-points (TP) during egg formation. The gene SLC25A38, responsible for transporting glycine from cytoplasm to mitochondria, and the gene ALAS1, encoding rate-limiting enzyme (delta-aminolevulinic acid synthase 1), had higher expression at 15 hr, as compared with 2, 5 and 23.5 hrs postoviposition. Interestingly, ABCB6, a gene encoding an enzyme responsible for transporting coproporphyrinogen III, showed higher expression level at 2 and 5 hrs. However, the expression of CPOX that converts coproporphyrinogen III to protoporphyrinogen III, and ABCG2 that transports PP IX out from mitochondria did not alter. Nevertheless, mitochondrial count per cell did not show consistent change in response to time-points postoviposition and nicarbazin feeding. The information obtained in the study sheds light on how nicarbazin disrupts the synthesis of PP IX.

Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin

Ten reference genes were investigated for normalization of gene expression data in the shell gland of laying hens. Analyses performed with geNorm revealed that hypoxanthine phosphoribosyltransferase 1 (HPRT1) and hydroxymethylbilane synthase (HMBS) were the two most stable reference genes in response to post-oviposition time alone (POT) or with nicarbazin treatment (POT+N) of laying hens. NormFinder analyses showed that the two most stable reference genes in response to POT and POT+N were 18S ribosomal RNA (18S rRNA), ribosomal protein L4 (RPL4) and HMBS, RPL4, respectively. BestKeeper analyses showed that 18S rRNA, RPL4 and HPRT1, HMBS were the two most stable reference genes for POT, and POT+N, respectively. Of the ten reference genes, all except B2M showed geNorm M <0.5, suggesting that they were stably expressed in the shell gland tissue. Consensus from these three programs suggested HPRT1 and HMBS could be used as the two most stable reference genes in the present study. Expression analyses of four candidate target genes with the two most and the two least stable genes showed that a combination of stable reference genes leads to more discriminable quantification of expression levels of target genes, while the least stable genes failed to do so. Therefore, HMBS and HPRT1 are recommended as the two most stable reference genes for the normalization of gene expression data at different stages of eggshell formation in brown-egg laying hens. Available statistical programs for reference gene ranking should include more robust analysis capability to analyse the gene expression data generated from factorial design experiments.

Widespread extrahepatic expression of acute-phase proteins in healthy chicken (Gallus gallus) tissues

Acute phase proteins (APP) are plasma proteins that can modify their expression in response to inflammation caused by tissue injury, infections, immunological disorders or stress. Although APP are produced mainly in liver, extrahepatic production has also been described. As a prerequisite to get insight the expression of APP in chicken during diseases, this study investigated the presence of five APP, including alpha1-acid glycoprotein (AGP), Serum Amyloid A (SAA), PIT54, C-Reactive protein (CRP) and Ovotransferrin (OVT) in twenty tissues collected from healthy chicken (Gallus gallus) by quantitative Real Time PCR and immunohistochemistry. As expected, APP gene abundance was higher in liver compared with other tissues. The mRNA coding for CRP, OVT and SAA was detected in all analyzed tissues with a higher expression in gastrointestinal tract, respiratory and lymphatic samples. SAA expression was particularly high in cecal tonsil, lung, spleen and Meckel's diverticulum, whereas OVT in lung, bursa of Fabricius and pancreas. AGP and PIT54 mRNA expression were detected in all tissues but at negligible levels. Immunohistochemical expression of AGP and OVT was variably detected in different organs, being identified in endothelium of every tissue. Positive cells were present in the epithelium of the mucosal layer of gastrointestinal tract and kidney. Lung and central nervous system stained for both proteins. No positive staining was detected in lymphoid tissues and muscle. These results suggest that most tissues can express different amount of APP even in healthy conditions and are therefore capable to mount a local acute phase reaction.

Selection of reference genes for gene expression analysis by real-time qPCR in avian cells infected with infectious bronchitis virus

Infectious bronchitis virus (IBV) causes infectious bronchitis in poultry, a respiratory disease that is a source of major economic loss to the poultry industry. Detection and the study of the molecular pathogenesis of the virus often involve the use of real-time quantitative PCR assays (qPCR). To account for error within the experiments, the levels of target gene transcription are normalized to that of suitable reference genes. Despite publication of the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines in 2009, single un-tested reference genes are often used for normalization of qPCR assays in avian research studies. Here, we use the geNorm algorithm to identify suitable reference genes in different avian cell types during infection with apathogenic and pathogenic strains of IBV. We discuss the importance of selecting an appropriate experimental sample subset for geNorm analysis, and show the effect that this selection can have on resultant reference gene selection. The effects of inappropriate normalization on the transcription pattern of a cellular signalling gene, AKT1, and the interferon-inducible, MX1, were studied. We identify the possibility of the misinterpretation of qPCR data when an inappropriate normalization strategy is employed. This is most notable when measuring the transcription of AKT1, where changes are minimal during infection.

The 60S ribosomal protein L13 is the most preferable reference gene to investigate gene expression in selected organs from turkeys and chickens, in context of different infection models

Evaluation of reference genes for expression studies in chickens and turkeys is very much limited and unavailable for various infectious models. In this study, eight candidate reference genes HMBS, HPRT1, TBP, VIM, TFRC, RPLP0, RPL13 and RPS7 were evaluated by five different algorithms (GeNorm, NormFinder, BestKeeper©, delta CT, RefFinder) to assess their stability. In order to analyze a broad variation of tissues, spleen, liver, caecum and caecal tonsil of different aged specific pathogen free (SPF) layer chickens and commercial turkeys, uninfected or infected with the extracellular pathogen Histomonas meleagridis, were included. For tissue samples from SPF chickens RPL13 and TBP were found to be the most stable reference genes. Further testing of RPL13 and TBP in the same organs of uninfected and infected SPF broiler chickens with the intracellular pathogen fowl aviadenovirus confirmed this finding. In tissue samples from turkeys, a stable expression of RPL13 and TFRC genes was noticed. Overall, the determined reference genes should be considered whenever gene expression studies in spleen, liver, caecum and caecal tonsil of chickens and turkeys are performed.

Avian Leukosis Virus Activation of an Antisense RNA Upstream of TERT in B-Cell Lymphomas

Avian leukosis virus (ALV) induces tumors by integrating its proviral DNA into the chicken genome and altering the expression of nearby genes via strong promoter and enhancer elements. Viral integration sites that contribute to oncogenesis are selected in tumor cells. Deep-sequencing analysis of B-cell lymphoma DNA confirmed that the telomerase reverse transcriptase (TERT) gene promoter is a common ALV integration target. Twenty-six unique proviral integration sites were mapped between 46 and 3,552 nucleotides (nt) upstream of the TERT transcription start site, predominantly in the opposite transcriptional orientation to TERT Transcriptome-sequencing (RNA-seq) analysis of normal bursa revealed a transcribed region upstream of TERT in the opposite orientation, suggesting the TERT promoter is bidirectional. This transcript appears to be an uncharacterized antisense RNA. We have previously shown that TERT expression is upregulated in tumors with integrations in the TERT promoter region. We now report that the viral promoter drives the expression of a chimeric transcript containing viral sequences spliced to exons 4 through 7 of this antisense RNA. Clonal expansion of cells with ALV integrations driving overexpression of the TERT antisense RNA suggest it may have a role in tumorigenesis.

IMPORTANCE

The data suggest that ALV integrations in the TERT promoter region drive the overexpression of a novel antisense RNA and contribute to the development of lymphomas.

Associations between organohalogen concentrations and transcription of thyroid-related genes in a highly contaminated gull population

A number of studies have reported altered circulating thyroid hormone levels in birds exposed either in controlled settings or in their natural habitat to ubiquitous organohalogen compounds including organochlorines (OCs) and polybrominated diphenyl ether (PBDE) flame retardants. However, limited attention has been paid to underlying homeostatic mechanisms in wild birds such as changes in the expression of genes in the hypothalamic-pituitary-thyroid (HPT) axis. The objective of the present study was to investigate the relationships between hepatic concentrations of major organohalogens (PBDEs and OCs), and circulating thyroid hormone (free and total thyroxine (T4) and triiodothyronine (T3)) levels and transcription of 14 thyroid-related genes in three tissues (thyroid, brain, and liver) of an urban-adapted bird exposed to high organohalogen concentrations in the Montreal area (QC, Canada), the ring-billed gull (Larus delawarensis). Positive correlations were found between liver concentrations of several polychlorinated biphenyls (PCBs), PBDEs as well as chlordanes and total plasma T4 levels. Hepatic concentrations of several PBDEs were negatively correlated with mRNA levels of deiodinase type 3, thyroid peroxidase, and thyroid hormone receptor β (TRβ) in the thyroid gland. Liver PCB (deca-CB) correlated positively with mRNA levels of sodium-iodide symporter and TRα. In brain, concentrations of most PBDEs were positively correlated with mRNA levels of organic anion transporter protein 1C1 and transthyretin, while PCBs positively correlated with expression of TRα and TRβ as well as deiodinase type 2. These multiple correlative linkages suggest that organohalogens operate through several mechanisms (direct or compensatory) involving gene transcription, thus potentially perturbing the HPT axis of this highly organohalogen-contaminated ring-billed gull population.

A Panel of Stably Expressed Reference Genes for Real-Time qPCR Gene Expression Studies of Mallards (Anas platyrhynchos)

Determining which reference genes have the highest stability, and are therefore appropriate for normalising data, is a crucial step in the design of real-time quantitative PCR (qPCR) gene expression studies. This is particularly warranted in non-model and ecologically important species for which appropriate reference genes are lacking, such as the mallard--a key reservoir of many diseases with relevance for human and livestock health. Previous studies assessing gene expression changes as a consequence of infection in mallards have nearly universally used β-actin and/or GAPDH as reference genes without confirming their suitability as normalisers. The use of reference genes at random, without regard for stability of expression across treatment groups, can result in erroneous interpretation of data. Here, eleven putative reference genes for use in gene expression studies of the mallard were evaluated, across six different tissues, using a low pathogenic avian influenza A virus infection model. Tissue type influenced the selection of reference genes, whereby different genes were stable in blood, spleen, lung, gastrointestinal tract and colon. β-actin and GAPDH generally displayed low stability and are therefore inappropriate reference genes in many cases. The use of different algorithms (GeNorm and NormFinder) affected stability rankings, but for both algorithms it was possible to find a combination of two stable reference genes with which to normalise qPCR data in mallards. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies in ducks. The fact that nearly all previous studies of the influence of pathogen infection on mallard gene expression have used a single, non-validated reference gene is problematic. The toolkit of putative reference genes provided here offers a solid foundation for future studies of gene expression in mallards and other waterfowl.

Identification of stable reference genes for quantitative PCR in cells derived from chicken lymphoid organs

Quantitative polymerase chain reaction (qPCR) is a powerful technique for quantification of gene expression, especially genes involved in immune responses. Although qPCR is a very efficient and sensitive tool, variations in the enzymatic efficiency, quality of RNA and the presence of inhibitors can lead to errors. Therefore, qPCR needs to be normalised to obtain reliable results and allow comparison. The most common approach is to use reference genes as internal controls in qPCR analyses. In this study, expression of seven genes, including β-actin (ACTB), β-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-glucuronidase (GUSB), TATA box binding protein (TBP), α-tubulin (TUBAT) and 28S ribosomal RNA (r28S), was determined in cells isolated from chicken lymphoid tissues and stimulated with three different mitogens. The stability of the genes was measured using geNorm, NormFinder and BestKeeper software. The results from both geNorm and NormFinder were that the three most stably expressed genes in this panel were TBP, GAPDH and r28S. BestKeeper did not generate clear answers because of the highly heterogeneous sample set. Based on these data we will include TBP in future qPCR normalisation. The study shows the importance of appropriate reference gene normalisation in other tissues before qPCR analysis.

The effect of transport stress on turkey (Meleagris gallopavo) liver acute phase proteins gene expression

The aim of this study was to investigate the effects of transport-related stress on the liver gene expression of four acute phase proteins (APP), namely α1-acid glycoprotein (AGP), C-Reactive Protein (CRP), Serum Amyloid A (SAA) and PIT54, in turkeys (Meleagris gallopavo). A group of seven BUT BIG 6 commercial hens was subjected to a two-hour long road transportation and the quantitative gene expression of APP in the liver was compared to that of a non transported control group. The expression of AGP and CRP mRNA was found to be increased in animals slaughtered after road transport. The presence of AGP protein was also confirmed by immunohistochemistry and Western blotting. The results of this study showed that road-transport may induce the mRNA expression of immune related proteins. The finding that AGP and CRP can be upregulated during transport could suggest their use as for the assessment of turkey welfare during transport.

Identification of Suitable Reference Genes for Real Time Quantitative Polymerase Chain Reaction Assays on Pectoralis major Muscle in Chicken (Gallus gallus )

Thirteen reference genes were investigated to determine their stability to be used as a housekeeping in gene expression studies in skeletal muscle of chickens. Five different algorithms were used for ranking of reference genes and results suggested that individual rankings of the genes differed among them. The stability of the expression of reference genes were validated using samples obtained from the Pectoralis major muscle in chicken. Samples were obtained from chickens in different development periods post hatch and under different nutritional diets. For gene expression calculation the ΔΔCt approach was applied to compare relative expression of pairs of genes within each of 52 samples when normalized to mitochondrially encoded cytochrome c oxidase II (MT-CO2) target gene. Our findings showed that hydroxymethylbilane synthase (HMBS) and hypoxanthine phosphoribosyl transferase 1 (HPRT1) are the most stable reference genes while transferrin receptor (TFRC) and beta-2-microglobulin (B2M) ranked as the least stable genes in the Pectoralis major muscle of chickens. Moreover, our results revealed that HMBS and HPRT1 gene expression did not change due to dietary variations and thus it is recommended for accurate normalization of RT-qPCR data in chicken Pectoralis major muscle.

Investigating reference genes for quantitative real-time PCR analysis across four chicken tissues

Accurate normalization of data is required to correct for different efficiencies and errors during the processing of samples in reverse transcription PCR analysis. The chicken is one of the main livestock species and its genome was one of the first reported and used in large scale transcriptomic analysis. Despite this, the chicken has not been investigated regarding the identification of reference genes suitable for the quantitative PCR analysis of growth and fattening genes. In this study, five candidate reference genes (B2M, RPL32, SDHA, TBP and YWHAZ) were evaluated to determine the most stable internal reference for quantitative PCR normalization in the two main commercial muscles (pectoralis major (breast) and biceps femoris (thigh)), liver and abdominal fat. Four statistical methods (geNorm, NormFinder, CV and BestKeeper) were used in the evaluation of the most suitable combination of reference genes. Additionally, a comprehensive ranking was established with the RefFinder tool. This analysis identified YWHAZ and TBP as the recommended combination for the analysis of biceps femoris and liver, YWHAZ and RPL32 for pectoralis major and RPL32 and B2M for abdominal fat and across-tissue studies. The final ranking for each tool changed slightly but overall the results, and most particularly the ability to discard the least robust candidates, were consistent between tools. The selection and number of reference genes were validated using SCD, a target gene related to fat metabolism. Overall, the results can be directly used to quantitate target gene expression in different tissues or in validation studies from larger transcriptomic experiments.