Growth hormone-regulated mRNAs and miRNAs in chicken hepatocytes

Comparative study and relationship analysis between purine content, uric acid, superoxide dismutase, and growth traits in purebred and crossbred Thai native chickens

The objective was to compare and analyze the relationship between growth, purine content, uric acid, and superoxide dismutase (SOD) in purebred and crossbred Thai native chickens. A total of 300 Thai native chickens were divided into 3 groups. Group 1 was purebred Thai native chickens (100%TN), Group 2 was 50% Thai native chickens (50%TN), and Group 3 was 25% Thai native chickens (25%TN). Data included the body weight (BW), average daily gain (ADG), and breast circumference (BrC). At 6, 8, and 10 weeks of age, 10 chickens from each group were randomly euthanized to collect breast meat, liver, and blood samples to analyze the purine content consisting of total purine, adenine, guanine, xanthine, and hypoxanthine, and uric acid, in breast meat and liver and SOD in blood. A general linear model, Pearson correlation and principal component analysis were used to analyze the significant differences and relationship between variables. The results showed the 25%TN group had the highest growth traits at every age, while the 100%TN group had the lowest (p < 0.05). Consistent with the analysis results of purine values, purine content and uric acid in breast meat and liver and SOD in blood decreased with age (p < 0.05). The correlations between purine content (total purine, adenine, guanine, xanthine, and hypoxanthine) and growth traits (BW, ADG, and BrC) ranged from moderate negative to moderate positive (-0.542 to 0.253)(p < 0.05). The correlations between uric acid and growth traits (0.348-0.760) and SOD and growth traits (0.132-0.516) were low to moderate positive with significant differences (p < 0.05). The principal component plot, which highlighted three principal components (PC 1, PC 2, and PC 3), explained 86.44 and 86.53% of the total information in breast meat and liver for selecting animals for optimal balance of the variation in the growth traits, purine content, uric acid, and SOD. Although purebred Thai native chickens showed the lowest growth traits, purine content, uric acid, and SOD were also lowest compared to crossbred Thai native chickens. Therefore, the development of genetics in Thai native chickens to produce healthy food could be possible.

Role of microRNA in Endocrine Disruptor-Induced Immunomodulation of Metabolic Health

The prevalence of poor metabolic health is growing exponentially worldwide. This condition is associated with complex comorbidities that lead to a compromised quality of life. One of the contributing factors recently gaining attention is exposure to environmental chemicals, such as endocrine-disrupting chemicals (EDCs). Considerable evidence suggests that EDCs can alter the endocrine system through immunomodulation. More concerning, EDC exposure during the fetal development stage has prominent adverse effects later in life, which may pass on to subsequent generations. Although the mechanism of action for this phenomenon is mostly unexplored, recent reports implicate that non-coding RNAs, such as microRNAs (miRs), may play a vital role in this scenario. MiRs are significant contributors in post-transcriptional regulation of gene expression. Studies demonstrating the immunomodulation of EDCs via miRs in metabolic health or towards the Developmental Origins of Health and Disease (DOHaD) Hypothesis are still deficient. The aim of the current review was to focus on studies that demonstrate the impact of EDCs primarily on innate immunity and the potential role of miRs in metabolic health.

The Diverse Roles of 17β-Estradiol in Non-Gonadal Tissues and Its Consequential Impact on Reproduction in Laying and Broiler Breeder Hens

Estradiol-17β (E2) has long been studied as the primary estrogen involved in sexual maturation of hens. Due to the oviparous nature of avian species, ovarian production of E2 has been indicated as the key steroid responsible for activating the formation of the eggshell and internal egg components in hens. This involves the integration and coordination between ovarian follicular development, liver metabolism and bone physiology to produce the follicle, yolk and albumen, and shell, respectively. However, the ability of E2 to be synthesized by non-gonadal tissues such as the skin, heart, muscle, liver, brain, adipose tissue, pancreas, and adrenal glands demonstrates the capability of this hormone to influence a variety of physiological processes. Thus, in this review, we intend to re-establish the role of E2 within these tissues and identify direct and indirect integration between the control of reproduction, metabolism, and bone physiology. Specifically, the sources of E2 and its activity in these tissues via the estrogen receptors (ERα, ERβ, GPR30) is described. This is followed by an update on the role of E2 during sexual differentiation of the embryo and maturation of the hen. We then also consider the implications of the recent discovery of additional E2 elevations during an extended laying cycle. Next, the specific roles of E2 in yolk formation and skeletal development are outlined. Finally, the consequences of altered E2 production in mature hens and the associated disorders are discussed. While these areas of study have been previously independently considered, this comprehensive review intends to highlight the critical roles played by E2 to alter and coordinate physiological processes in preparation for the laying cycle.

Remodeling of Hepatocyte Mitochondrial Metabolism and De Novo Lipogenesis During the Embryonic-to-Neonatal Transition in Chickens

Embryonic-to-neonatal development in chicken is characterized by high rates of lipid oxidation in the late-term embryonic liver and high rates of de novo lipogenesis in the neonatal liver. This rapid remodeling of hepatic mitochondrial and cytoplasmic networks occurs without symptoms of hepatocellular stress. Our objective was to characterize the metabolic phenotype of the embryonic and neonatal liver and explore whether these metabolic signatures are preserved in primary cultured hepatocytes. Plasma and liver metabolites were profiled using mass spectrometry based metabolomics on embryonic day 18 (ed18) and neonatal day 3 (nd3). Hepatocytes from ed18 and nd3 were isolated and cultured, and treated with insulin, glucagon, growth hormone and corticosterone to define hormonal responsiveness and determine their impacts on mitochondrial metabolism and lipogenesis. Metabolic profiling illustrated the clear transition from the embryonic liver relying on lipid oxidation to the neonatal liver upregulating de novo lipogenesis. This metabolic phenotype was conserved in the isolated hepatocytes from the embryos and the neonates. Cultured hepatocytes from the neonatal liver also maintained a robust response to insulin and glucagon, as evidenced by their contradictory effects on lipid oxidation and lipogenesis. In summary, primary hepatocytes from the embryonic and neonatal chicken could be a valuable tool to investigate mechanisms regulating hepatic mitochondrial metabolism and de novo lipogenesis.

The Role of MicroRNAs in Influencing Body Growth and Development

Body growth and development are regulated among others by genetic and epigenetic factors. MicroRNAs (miRNAs) are epigenetic regulators of gene expression that act at the post-transcriptional level, thereby exerting a strong influence on regulatory gene networks. Increasing studies suggest the importance of miRNAs in the regulation of the growth plate and growth hormone (GH)-insulin-like growth factor (IGF) axis during the life course in a broad spectrum of animal species, contributing to longitudinal growth. This review summarizes the role of miRNAs in regulating growth in different in vitro and in vivo models acting on GH, GH receptor (GHR), IGFs, and IGF1R genes besides current knowledge in humans, and highlights that this regulatory system is of importance for growth.

Molecular Regulation of Lipogenesis, Adipogenesis and Fat Deposition in Chicken

In the poultry industry, excessive fat deposition is considered an undesirable factor, affecting feed efficiency, meat production cost, meat quality, and consumer’s health. Efforts to reduce fat deposition in economically important animals, such as chicken, can be made through different strategies; including genetic selection, feeding strategies, housing, and environmental strategies, as well as hormone supplementation. Recent investigations at the molecular level have revealed the significant role of the transcriptional and post-transcriptional regulatory networks and their interaction on modulating fat metabolism in chickens. At the transcriptional level, different transcription factors are known to regulate the expression of lipogenic and adipogenic genes through various signaling pathways, affecting chicken fat metabolism. Alternatively, at the post-transcriptional level, the regulatory mechanism of microRNAs (miRNAs) on lipid metabolism and deposition has added a promising dimension to understand the structural and functional regulatory mechanism of lipid metabolism in chicken. Therefore, this review focuses on the progress made in unraveling the molecular function of genes, transcription factors, and more notably significant miRNAs responsible for regulating adipogenesis, lipogenesis, and fat deposition in chicken. Moreover, a better understanding of the molecular regulation of lipid metabolism will give researchers novel insights to use functional molecular markers, such as miRNAs, for selection against excessive fat deposition to improve chicken production efficiency and meat quality.

Centennial Review: Metabolic microRNA - shifting gears in the regulation of metabolic pathways in poultry

Over 20 yr ago, a small noncoding class of RNA termed microRNA (miRNA) that was able to recognize sequences in mRNAs and inhibit their translation was discovered in Caenorhabditis elegans. In the intervening years, miRNA have been discovered in most eukaryotes and are now known to regulate the majority of protein-coding genes. It has been discovered that disruption of miRNA function often leads to the development of pathological conditions. One physiological system under extensive miRNA-mediated regulation is metabolism. Metabolism is one of the most dynamic of biological networks within multiple organs, including the liver, muscle, and adipose tissue, working in concert to respond to ever-changing nutritional cues and energy demands. Therefore, it is not surprising that miRNA regulate virtually all aspects of eukaryotic metabolism and have been linked to metabolic disorders, such as obesity, fatty liver diseases, and diabetes, just to name a few. Chickens, and birds in general, face their own unique metabolic challenges, particularly after hatching, when their metabolism must completely transform from using lipid-rich yolk to carbohydrate-rich feed as fuel in a very short period of time. Furthermore, commercial poultry breeds have undergone extensive selection over the last century for more desirable production traits, which has resulted in numerous metabolic consequences. Here, we review the current knowledge of miRNA-mediated regulation of metabolic development and function in chickens.

MicroRNA expression profiling reveals potential roles for microRNA in the liver during pigeon (Columba livia) development

The liver is the central organ for metabolism and influence the growth and development of the animals. To date, little is known about the microRNA (miRNA) in pigeon livers, particularly in different developmental stages. A comprehensive investigation into miRNA transcriptomes in livers across 3 pigeon developmental stages (1, 14, 28 d old) and an adult stage (2 y old) was performed by small RNA sequencing. We identified 312 known miRNA, 433 conserved miRNA, and 192 novel miRNA in pigeon livers. A set of differentially expressed (DE) miRNA in livers were screened out during pigeon development. This set of miRNA might be involved in hepatospecific phenotype and liver development. A Short Time-series Expression Miner analysis indicated significant expression variations in DE miRNA during liver development of pigeons. These DE miRNA with different expression patterns might play essential roles in response to growth factor, cell morphogenesis, and gland development, etc. Protein-protein interaction network and Molecular Complex Detection analysis identified several vital target genes (e.g., TNRC6B, FRS2, PTCH1, etc.) of DE miRNA, which is closely linked in liver development and enriched in PI3K cascade and regulation of growth. Our results expanded the repertoire of pigeon miRNA and may be of help in better understanding the mechanism of squab's rapid development from the perspective of liver development.

Quercetin Improving Lipid Metabolism by Regulating Lipid Metabolism Pathway of Ileum Mucosa in Broilers

This study is aimed at evaluating the regulatory mechanism of quercetin on lipid metabolism in the ileum of broilers to better understand these pathways decreasing abdominal fat. 480 chickens were randomly divided into 4 groups (control, 0.02% quercetin, 0.04% quercetin, and 0.06% quercetin). Breast muscle, thigh muscle, and abdominal fat pad were removed and weighed at 42 d of age. Serum was obtained by centrifuging blood samples from the jugular vein (10 ml) to determine high-density lipoprotein (HDL), total cholesterol (TC), low-density lipoprotein (LDL), triglyceride (TG), leptin, and adiponectin using ELISA. About 5 g of the ileum was harvested and immediately frozen in liquid nitrogen for RNA-seq. Then, the confirmation of RNA-seq results by the Real-Time Quantitative PCR (RT-qPCR) method was evaluated using Pearson's correlation. Compared with control, abdominal fat percentage was significantly decreased with increasing quercetin supplementation, and the best result was obtained at 0.06% dietary quercetin supplementation (P < 0.01). Breast muscle percentage was significantly decreased at 0.02% quercetin (P < 0.01), and thigh muscle percentage tended to increase (P = 0.078). Meanwhile, 0.04% and 0.06% quercetin significantly decreased TG (P < 0.01), TC (P < 0.01), and LDL content (P < 0.05) in serum. Serum leptin and adiponectin contents were significantly increased by 0.04% and 0.06% dietary quercetin supplementation, compared with the control (P < 0.01). Analyses of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to identify differently expressed genes and lipid metabolism pathways. Quercetin decreased abdominal fat percentage through regulating fat digestion and absorption, glycerophospholipid metabolism, AMPK signaling pathway, fatty acid degradation, and cholesterol metabolism.

Long Non-coding RNA and mRNA Profile of Liver Tissue During Four Developmental Stages in the Chicken

The liver is the major organ of lipid biosynthesis in the chicken. In laying hens, the liver synthesizes most of the yolk precursors and transports them to developing follicles to produce eggs. However, a systematic investigation of the long non-coding RNA (lncRNA) and mRNA transcriptome in liver across developmental stages is needed. Here, we constructed 12 RNA libraries from liver tissue during four developmental stages: juvenile (day 60), sexual maturity (day 133), peak laying (day 220), and broodiness (day 400). A total of 16,930 putative lncRNAs and 18,260 mRNAs were identified. More than half (53.70%) of the lncRNAs were intergenic lncRNAs. The temporal expression pattern showed that lncRNAs were more restricted than mRNAs. We identified numerous differentially expressed lncRNAs and mRNAs by pairwise comparison between the four developmental stages and found that VTG2, RBP, and a novel protein-coding gene were differentially expressed in all stages. Time-series analysis showed that the modules with upregulated genes were involved in lipid metabolism processes. Co-expression networks suggested functional relatedness between mRNAs and lncRNAs; the DE-lncRNAs were mainly involved in lipid biosynthesis and metabolism processes. We showed that the liver transcriptome varies across different developmental stages. Our results improve our understanding of the molecular mechanisms underlying liver development in chickens.

Identification of microRNAs controlling hepatic mRNA levels for metabolic genes during the metabolic transition from embryonic to posthatch development in the chicken

Background

The transition from embryonic to posthatch development in the chicken represents a massive metabolic switch from primarily lipolytic to primarily lipogenic metabolism. This metabolic switch is essential for the chick to successfully transition from the metabolism of stored egg yolk to the utilization of carbohydrate-based feed. However, regulation of this metabolic switch is not well understood. We hypothesized that microRNAs (miRNAs) play an important role in the metabolic switch that is essential to efficient growth of chickens. We used high-throughput RNA sequencing to characterize expression profiles of mRNA and miRNA in liver during late embryonic and early posthatch development of the chicken. This extensive data set was used to define the contributions of microRNAs to the metabolic switch during development that is critical to growth and nutrient utilization in chickens.

Results

We found that expression of over 800 mRNAs and 30 miRNAs was altered in the embryonic liver between embryonic day 18 and posthatch day 3, and many of these differentially expressed mRNAs and miRNAs are associated with metabolic processes. We confirmed the regulation of some of these mRNAs by miRNAs expressed in a reciprocal pattern using luciferase reporter assays. Finally, through the use of yeast one-hybrid screens, we identified several proteins that likely regulate expression of one of these important miRNAs.

Conclusions

Integration of the upstream regulatory mechanisms governing miRNA expression along with monitoring the downstream effects of this expression will ultimately allow for the construction of complete miRNA regulatory networks associated with the hepatic metabolic switch in chickens. Our findings support a key role for miRNAs in controlling the metabolic switch that occurs between embryonic and posthatch development in the chicken.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4096-5) contains supplementary material, which is available to authorized users.

RNA-Seq analysis on chicken taste sensory organs: An ideal system to study organogenesis

RNA-Seq is a powerful tool in transcriptomic profiling of cells and tissues. We recently identified many more taste buds than previously appreciated in chickens using molecular markers to stain oral epithelial sheets of the palate, base of oral cavity, and posterior tongue. In this study, RNA-Seq was performed to understand the transcriptomic architecture of chicken gustatory tissues. Interestingly, taste sensation related genes and many more differentially expressed genes (DEGs) were found between the epithelium and mesenchyme in the base of oral cavity as compared to the palate and posterior tongue. Further RNA-Seq using specifically defined tissues of the base of oral cavity demonstrated that DEGs between gustatory (GE) and non-gustatory epithelium (NGE), and between GE and the underlying mesenchyme (GM) were enriched in multiple GO terms and KEGG pathways, including many biological processes. Well-known genes for taste sensation were highly expressed in the GE. Moreover, genes of signaling components important in organogenesis (Wnt, TGFβ/ BMP, FGF, Notch, SHH, Erbb) were differentially expressed between GE and GM. Combined with other features of chicken taste buds, e.g., uniquely patterned array and short turnover cycle, our data suggest that chicken gustatory tissue provides an ideal system for multidisciplinary studies, including organogenesis and regenerative medicine.

Hepatic ELOVL6 mRNA is regulated by the gga-miR-22-3p in egg-laying hen

The elongation of very long chain fatty acids protein 6 (ELOVL6) encodes a fatty acid elongase that is responsible for the final step in endogenous saturated fatty acid synthesis and involves in de novo lipogenesis. Though the regulatory mechanism of ELOVL6 expression has been studied extensively, little is known about the role of miRNA in regulating ELOVL6 gene expression in chicken until now. To investigate the regulatory mechanism of miRNA on the expression of ELOVL6 gene, bioinformatics analysis was employed to predict the potential miRNAs that binding with the 3'untranslated region (3'UTR) of ELOVL6. The putative miRNA was further screened by comparative analysis with previous miRNA-seq results. Gga-miR-22-3p, which could bind with the 3'UTR of ELOVL6 and showed negative expression correlation with ELOVL6 gene in chicken liver, was obtained. Tissue expression profiles showed that gga-miR-22-3p and ELOVL6 are extensively expressed in many tissues, and ELOVL6 with high expression level in kidney and liver tissues, and gga-miR-22-3p with high expression in lung and heart. Dual-luciferase reporter assays results indicated that the expression of luciferase reporter gene linked with part sequence of the 3'UTR of chicken ELOVL6 gene was down-regulated by the overexpression of gga-miR-22-3p in the DF1 cells, and the down-regulation behavior was abolished when the gga-miR-22-3p binding site in 3'UTR of ELOVL6 was mutated (P>0.05). Furthermore, the ELOVL6 expression in chicken hepatocytes was down-regulated when miR-22-3p was over-expressed. Therefore, we concluded that miR-22-3p might involve in controlling the hepatic lipid composition through affecting the expression of ELOVL6 gene, and could serve as a regulator of lipid metabolism in the liver of egg-laying hen.

Prosteatotic and Protective Components in a Unique Model of Fatty Liver: Gut Microbiota and Suppressed Complement System

Goose can develop severe hepatic steatosis without overt injury, thus it may serve as a unique model for uncovering how steatosis-related injury is prevented. To identify the markedly prosteatotic and protective mechanisms, we performed an integrated analysis of liver transcriptomes and gut microbial metagenomes using samples collected from overfed and normally-fed geese at different time points. The results indicated that the fatty liver transcriptome, initially featuring a ‘metabolism’ pathway, was later joined by ‘cell growth and death’ and ‘immune diseases’ pathways. Gut microbiota played a synergistic role in the liver response as microbial and hepatic genes affected by overfeeding shared multiple pathways. Remarkably, the complement system, an inflammatory component, was comprehensively suppressed in fatty liver, which was partially due to increased blood lactic acid from enriched Lactobacillus. Data from in vitro studies suggested that lactic acid suppressed TNFα via the HNF1α/C5 pathway. In conclusion, gut microbes and their hosts respond to excess energy influx as an organic whole, severe steatosis and related tolerance of goose liver may be partially attributable to gut microbiotic products and suppressed complement system, and lactic acid from gut microbiota participates in the suppression of hepatic TNFα/inflammation through the HNF1α/C5 pathway.

Systematic analysis of the regulatory functions of microRNAs in chicken hepatic lipid metabolism

Laying performance is an important economic trait in hens, and this physiological process is largely influenced by the liver function. The livers of hens at 20- and 30-week-old stages were investigated using the next generation sequencing to identify the differences of microRNA expression profiles. Compared with the 20-week-old hens, 67 down- and 13 up-regulated microRNAs were verified to be significant differentially expressed (false discovery rate, FDR ≤ 0.05) (SDE) in the 30-week-old. We also identified 13 down- and 6 up-regulated novel differentially expressed (DE) microRNAs. miR-22-3p and miR-146b-5p, which exhibit critical roles in mammalian lipid metabolism, showed the most abundant expression and the highest fold-change, respectively. A total of 648 potential target genes of the SDE microRNAs were identified through an integrated analysis of microRNAs and the DE genes obtained in previous RNA-sequencing, including FADS1, FADS2, ELOVL6 and ACSL5, which are critical lipid metabolism-related regulators. Bioinformatic analyses revealed that target genes were mainly enriched in lipid-related metabolism processes. This work provides the first study of the expression patterns of hepatic microRNAs between 20- and 30-week old hens. The findings may serve as a fundamental resource for understanding the detailed functions of microRNAs in the molecular regulatory systems of lipid metabolism.

Chicken gga-miR-103-3p Targets CCNE1 and TFDP2 and Inhibits MDCC-MSB1 Cell Migration

Marek’s disease (MD) is a highly contagious viral neoplastic disease caused by Marek’s disease virus (MDV), which can lead to huge economic losses in the poultry industry. Recently, microRNAs (miRNAs) have been found in various cancers and tumors. In recent years, 994 mature miRNAs have been identified through deep sequencing in chickens, but only a few miRNAs have been investigated further in terms of their function. Previously, gga-miR-103-3p was found downregulated in MDV-infected samples by using Solexa deep sequencing. In this study, we further verified the expression of gga-miR-103-3p among MDV-infected spleen, MD lymphoma from liver, noninfected spleen, and noninfected liver, by qPCR. The results showed that the expression of gga-miR-103-3p was decreased in MDV-infected tissues, which was consistent with our previous study. Furthermore, two target genes of gga-miR-103-3p, cyclin E1 (CCNE1) and transcription factor Dp-2 (E2F dimerization partner 2) (TFDP2), were predicted and validated by luciferase reporter assay, qPCR, and western blot analysis. The results suggested that CCNE1 and TFDP2 are direct targets of gga-miR-103-3p in chickens. Subsequent cell proliferation and migration assay showed that gga-miR-103-3p suppressed MDCC-MSB1 migration, but did not obviously modulate MDCC-MSB1 cell proliferation. In conclusion, gga-miR-103-3p targets the CCNE1 and TFDP2 genes, and suppresses cell migration, which indicates that it might play an important role in MD tumor transformation.

Transcriptome profile of liver at different physiological stages reveals potential mode for lipid metabolism in laying hens

Background

Liver is an important metabolic organ that plays a critical role in lipid synthesis, degradation, and transport; however, the molecular regulatory mechanisms of lipid metabolism remain unclear in chicken. In this study, RNA-Seq technology was used to investigate differences in expression profiles of hepatic lipid metabolism-related genes and associated pathways between juvenile and laying hens. The study aimed to broaden the understanding of liver lipid metabolism in chicken, and thereby to help improve laying performance in the poultry industry.

Results

RNA-Seq analysis was carried out on total RNA harvested from the liver of juvenile (n = 3) and laying (n = 3) hens. Compared with juvenile hens, 2567 differentially expressed genes (1082 up-regulated and 1485 down-regulated) with P ≤ 0.05 were obtained in laying hens, and 960 of these genes were significantly differentially expressed (SDE) at a false discovery rate (FDR) of ≤0.05 and fold-change ≥2 or ≤0.5. In addition, most of the 198 SDE novel genes (91 up-regulated and 107 down-regulated) were discovered highly expressed, and 332 SDE isoforms were identified. Gene ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that the SDE genes were most enrichment in steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ≤ 0.05). The top significantly enriched GO terms among the SDE genes included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction, indicating that principal lipogenesis occurred in the liver of laying hens.

Conclusions

This study suggests that the majority of changes at the transcriptome level in laying hen liver were closely related to fat metabolism. Some of the SDE uncharacterized novel genes and alternative splicing isoforms that were detected might also take part in lipid metabolism, although this needs further investigation. This study provides valuable information about the expression profiles of mRNAs from chicken liver, and in-depth functional investigations of these mRNAs could provide new insights into the molecular networks of lipid metabolism in chicken liver.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1943-0) contains supplementary material, which is available to authorized users.

In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq

Since the feed cost is a major determinant of profitability in poultry industry, how to improve feed efficiency through genetic selection is an intriguing subject for breeders and producers. As a more suitable indicator assessing feed efficiency, residual feed intake (RFI) is defined as the difference between observed and expected feed intake based on maintenance and growth. However, the genetic mechanisms responsible for RFI in chickens are still less well appreciated. In this study, we investigated the duodenal transcriptome architecture of extreme RFI phenotypes in the six brown-egg dwarf hens (three per group) using RNA sequencing technology. Among all mapped reads, an average of 75.62% fell into annotated exons, 5.50% were located in introns, and the remaining 18.88% were assigned to intergenic regions. In total, we identified 41 promising candidate genes by differential expression analysis between the low and high RFI groups. Furthermore, qRT-PCR assays were designed for 10 randomly chosen genes, and nine (90.00%) were successfully validated. Functional annotation analyses revealed that these significant genes belong to several specific biological functions related to digestibility, metabolism and biosynthesis processes as well as energy homeostasis. We also predicted 253 intergenic coding transcripts, and these transcripts were mainly involved in fundamental biological regulation and metabolism processes. Our findings provided a pioneering exploration of biological basis underlying divergent RFI using RNA-Seq, which pinpoints promising candidate genes of functional relevance, is helpful to guide future breeding strategies to optimize feed efficiency and assists in improving the current gene annotation in chickens.