Development of transgenic chickens expressing enhanced green fluorescent protein

Sequential verification of exogenous protein production in OVA gene-targeted chicken bioreactors

The chicken has potential as an efficient bioreactor system because of its outstanding protein production capacity and low cost. The CRISPR/Cas9-mediated gene-editing system enables production of highly marketable exogenous proteins in transgenic chicken bioreactors. However, because it takes approximately 18 mo to evaluate the recombinant protein productivity of the bioreactor due to the generation interval from G0 founders to G1 egg-laying hens, to verification of the exogenous protein at the early stage is difficult. Here we propose a system for sequential validation of exogenous protein production in chicken bioreactors as in hatching female chicks as well as in egg-laying hens. We generated chicken OVALBUMIN (OVA) EGFP knock-in (KI) chicken (OVA EGFP KI) by CRISPR/Cas9-mediated nonhomologous end joining at the chicken OVA gene locus. Subsequently, the estrogen analog, diethylstilbestrol (DES), was subcutaneously implanted in the abdominal region of 1-wk-old OVA EGFP KI female chicks to artificially increase OVALBUMIN expression. The oviducts of DES-treated OVA EGFP KI female chicks expressed OVA and EGFP at the 3-wk-old stage (10 d after DES treatment). We evaluated the expression of EGFP protein in the oviduct, along with the physical properties of eggs and egg white from OVA EGFP KI hens. The rapid identification and isolation of exogenous protein can be confirmed at a very early stage and high-yield production is possible by targeting the chicken oviduct.

Genetically engineered birds; pre-CRISPR and CRISPR era

Generating biopharmaceuticals in genetically engineered bioreactors continues to reign supreme. Hence, genetically engineered birds have attracted considerable attention from the biopharmaceutical industry. Fairly recent genome engineering methods have made genome manipulation an easy and affordable task. In this review, we first provide a broad overview of the approaches and main impediments ahead of generating efficient and reliable genetically engineered birds, and various factors that affect the fate of a transgene. This section provides an essential background for the rest of the review, in which we discuss and compare different genome manipulation methods in the pre-CRISPR and CRISPR era in the field of avian genome engineering.

Applications of Gene Editing in Chickens: A New Era Is on the Horizon

The chicken represents a valuable model for research in the area of immunology, infectious diseases as well as developmental biology. Although it was the first livestock species to have its genome sequenced, there was no reverse genetic technology available to help understanding specific gene functions. Recently, homologous recombination was used to knockout the chicken immunoglobulin genes. Subsequent studies using immunoglobulin knockout birds helped to understand different aspects related to B cell development and antibody production. Furthermore, the latest advances in the field of genome editing including the CRISPR/Cas9 system allowed the introduction of site specific gene modifications in various animal species. Thus, it may provide a powerful tool for the generation of genetically modified chickens carrying resistance for certain pathogens. This was previously demonstrated by targeting the Trp38 region which was shown to be effective in the control of avian leukosis virus in chicken DF-1 cells. Herein we review the current and future prospects of gene editing and how it possibly contributes to the development of resistant chickens against infectious diseases.

Expression of recombinant human lysozyme in transgenic chicken promotes the growth of Bifidobacterium in the intestine and improves postnatal growth of chicken

Lysozyme is one kind of antimicrobial proteins and often used as feed additive which can defend against pathogenic bacteria and enhance immune function of animals. In this study, we have injected the lentiviral vector expressing recombinant human lysozyme (rhLZ) gene into the blastoderm of chicken embryo to investigate the effect of recombinant human lysozyme on postnatal intestinal microbiota distribution and growth performance of chicken. Successfully, we generated 194 transgenic chickens identified by Southern blot with a positive transgenic rate of 24%. The average concentration of rhLZ was 29.90 ± 6.50 μg/mL in the egg white. Lysozyme in egg white of transgenic chickens had a significantly higher antibacterial activity than those of non-transgenic chickens by lysoplate assay (P < 0.05). The feces of transgenic and non-transgenic chickens were collected and five types of bacteria (Lactobacillus, Salmonella, Bifidobacterium, Staphylococcus aureus and Escherichia coli) were isolated and cultured to detect the impact of rhLZ on gut microbiota. Among the five bacteria, the number of Bifidobacterium in the intestine of those transgenic was significantly increased (P < 0.05). Moreover, the growth traits of the transgenic and non-transgenic chickens were analyzed. It was found that the 6-week shank length, 6-week weight and 18-week weight of transgenic chickens were significantly increased than that of non-transgenic chickens. The results demonstrated that rhLZ-transgenic chicken could promote the growth of Bifidobacterium in the intestine and improve the postnatal growth of chicken.

Human extracellular superoxide dismutase (EC-SOD) expression in transgenic chicken

Extracellular superoxide dismutase (EC-SOD) is a metalloprotein and functions as an antioxidant enzyme. In this study, we used lentiviral vectors to generate transgenic chickens that express the human EC-SOD gene. The recombinant lentiviruses were injected into the subgerminal cavity of freshly laid eggs. Subsequently, the embryos were incubated to hatch using phases II and III of the surrogate shell ex vivo culture system. Of 158 injected embryos, 16 chicks (G0) hatched and were screened for the hEC-SOD by PCR. Only 1 chick was identified as a transgenic bird containing the transgene in its germline. This founder (G0) bird was mated with wild-type hens to produce transgenic progeny, and 2 transgenic chicks (G1) were produced. In the generated transgenic hens (G2), the hEC-SOD protein was expressed in the egg white and showed antioxidant activity. These results highlight the potential of the chicken for production of biologically active proteins in egg white. [BMB Reports 2013; 46(8): 404-409]

Transgenic quail production by microinjection of lentiviral vector into the early embryo blood vessels

Several strategies have been used to generate transgenic birds. The most successful method so far has been the injection of lentiviral vectors into the subgerminal cavity of a newly laid egg. We report here a new, easy and effective way to produce transgenic quails through direct injection of a lentiviral vector, containing an enhanced-green fluorescent protein (eGFP) transgene, into the blood vessels of quail embryos at Hamburger-Hamilton stage 13-15 (HH13-15). A total of 80 embryos were injected and 48 G0 chimeras (60%) were hatched. Most injected embryo organs and tissues of hatched quails were positive for eGFP. In five out of 21 mature G0 male quails, the semen was eGFP-positive, as detected by polymerase chain reaction (PCR), indicating transgenic germ line chimeras. Testcross and genetic analyses revealed that the G0 quail produced transgenic G1 offspring; of 46 G1 hatchlings, 6 were transgenic (6/46, 13.0%). We also compared this new method with the conventional transgenesis using stage X subgerminal cavity injection. Total 240 quail embryos were injected by subgerminal cavity injection, of which 34 (14.1%) were hatched, significantly lower than the new method. From these hatched quails semen samples were collected from 19 sexually matured males and tested for the transgene by PCR. The transgene was present in three G0 male quails and only 4/236 G1 offspring (1.7%) were transgenic. In conclusion, we developed a novel bird transgenic method by injection of lentiviral vector into embryonic blood vessel at HH 13-15 stage, which result in significant higher transgenic efficiency than the conventional subgerminal cavity injection.

Different gene transfer methods at the very early, early, late and whole embryonic stages in chicken

New technologies in gene transfer combined with experimental embryology make the chicken embryo an excellent model system for gene function studies. The techniques of in ovo electroporation, in vitro culture for ex ovo electroporation and retrovirus-mediated gene transfer have already been fully developed in chicken. Yet to our knowledge, there are no definite descriptions on the features and application scopes of these techniques. The survival rates of different in vitro culture methods were compared and the EGFP expression areas of different gene transfer techniques were explored. It was that the optimal timings of removing embryo for EC culture and Petri dish system was at E1.5 and E2.5, respectively; and optimal timing of injecting retrovirus is at E0. Results indicated that the EC culture, in ovo electroporation, the Petri dish system and retrovirus-mediated method are, respectively, suitable for the very early, early, late and whole embryonic stages in chicken. Comparison of different gene transfer methods and establishment of optimal timings are expected to provide a better choice of the efficient method for a particular experiment.

Gelatin nanoparticles as gene carriers for transgenic chicken applications

To develop a safe and effective nonviral gene delivery system for transgenic chicken manipulation, we developed gelatin nanocarriers using a reporter plasmid (pEGFP-C1; enhanced green fluorescence protein, EGFP) that expressed EGFP. pEGFP-C1-containing gelatin nanoparticles (GP/pEGFP) were prepared using a water-ethanol solvent displacement method and characterized by size, surface charge, DNA loading, and DNA protection ability. For gene delivery, pEGFP-C1 was stably and efficiently encapsulated in GPs that were approximately 300 nm in diameter with a slight negative surface charge, which was prepared from gelatin solution at pH 8.0. Approximately, 85% of the plasmid DNA was encapsulated in the GPs. Electrophoresis results showed that the GPs provided protection against DNase I digestion. We used the GP/pEGFP as a vector to transfect cells and chicken embryos. The vector was nontoxic to cells, and GFP expression was effectively expressed 24 h after HeLa cell transfection. Direct injection was adapted for vector transport to the chicken embryo; injection in the area opaca (Ao) of the egg resulted in the highest hatching rate without affecting embryo development. GFP gene expression in embryo sections was observed 4 days after injection. The results of this study demonstrate that GPs are a suitable nonviral vector for delivering exogenous genes for transgenic chicken manipulation.

Bone marrow cell-mediated production of transgenic chickens

The transplantation of adult stem cells into recipients is a method used widely in mammals to determine the fate of transferred cells, and for the production of progenies. This study is the first report, to our knowledge, to demonstrate the successful production of chickens using cells transdifferentiated from adult chicken bone marrow cells (BMCs) transplanted into the testes. BMCs from the enhanced green fluorescent protein (eGFP) transgenic (Tg) chickens were induced via in vitro transdifferentiation to male germ cells and injected into the testes of normal recipients. The multipotency of BMC was found with RT-PCR, immunocytochemistry, and FACS using specific markers, such as OCT4 and SSEA-1, -3, and -4. Localization and in vivo transdifferentiation of injected cells in the seminiferous tubules of recipients were traced for up to 40 days' post-injection by GFP expression and immunocytochemical analyses. The integration of the eGFP and the neo(R) genes in sperm gDNAs of recipient was confirmed via PCR analysis. A subsequent testcross of the recipient roosters with non-Tg hens resulted in the production of eGFP Tg progenies, demonstrating the successful transdifferentiation of the adult BMC to the germ cells in the testis. Therefore, we suggest that the use of adult BMCs is a new and promising approach to the production of Tg poultry, and may prove helpful in the study of avian developmental biology.

Genetically-defined lineage tracing of Nkx2.2-expressing cells in chick spinal cord

In the spinal cord, generation of oligodendrocytes (OLs) is totally dependent on the presence of Olig2, a basic helix-loop-helix transcription factor. However, it also requires Nkx2.2 for its generation, whose expression follows the expression of Olig2. Although it is believed that oligodendrocytes originate from the pMN domain, Nkx2.2 is present in the p3 domain located ventral to the pMN domain. According to recent reports, it is possible that oligodendrocytes are directly derived from the p3 domain in addition to the pMN domain in the chick spinal cord. We examined this hypothesis in this paper. To analyze OL development in the spinal cord, chick embryos are widely used for genetic modification by electroporation or for transplantation experiments, because it is relatively easy to manipulate them compared with mouse embryos. However, genetic modification by electroporation is not appropriate for glial development analyses because glia proliferate vigorously before maturation. In order to overcome these problems, we established a novel method to permanently introduce exogenous gene into a specific cell type. We introduced the CAT1 gene, a murine retroviral receptor, by electroporation followed by injection of murine retrovirus. By using this method, we successfully transduced murine retrovirus into the chick neural tube. We analyzed cell lineage from the p3 domain by restricting CAT1 expression by Nkx2.2-enhancer and found that most of the labeled cells became OLs when the cells were labeled at cE4. Moreover, the labeled OLs were found throughout the white matter in the spinal cord including the most dorsal spinal cord. Thus p3 domain directly generates spinal cord OLs in the chick spinal cord.

Production of transgenic chickens from purified primordial germ cells infected with a lentiviral vector

Replication-defective retroviral or lentiviral vectors have been used for the production of transgenic animals. Chicken primordial germ cells (PGCs) are the precursors for ova and spermatozoa. Here, we describe the production of transgenic chickens via a germline transmission system using PGCs infected with a replication-defective lentiviral vector. PGCs were sorted with a fluorescence-activated cell sorter based on the expression of stage-specific embryonic antigen-1 from 2.5- and 5.5-day embryos. PGCs from both stages of embryo were infected with a lentiviral vector at a similar efficiency in vitro. PGCs were then transferred into the bloodstream of 2.5-day recipient embryos. The efficiency with which the PGCs were delivered and settled in the gonads was lower for PGCs from 5.5-day embryos than those from 2.5-day embryos when a limited number of PGCs was transferred, while the difference was not obvious upon the transfer of increased number of cells. Using a high number of 5.5-day PGCs infected with a lentiviral vector, transgenic chimeras (G(0)) with an acceptable efficiency for germline transmission were obtained. G(0) female chickens produced transgenic progeny (G(1)) with higher efficiency compared to G(0) male chickens. In G(1) transgenic chickens obtained by this method, enhanced green fluorescent protein was effectively expressed under the control of the actin promoter.

Murine retroviruses re-engineered for lineage tracing and expression of toxic genes in the developing chick embryo

We describe two replication incompetent retroviral vectors that co-express green fluorescent protein (GFP) and beta-galactosidase. These vectors incorporate either the avian reticuloendotheliosis (spleen necrosis virus; SNV) promoter or the chick beta-actin promoter, into the backbone of the murine leukemia (MLV) viral vector. The additional promoters drive transgene expression in avian tissue. The remainder of the vector is MLV-like, allowing high titer viral particle production by means of transient transfection. The SNV promoter produces high and early expression of introduced genes, enabling detection of the single copy integrated GFP gene in infected cells and their progeny in vivo. Substitution of the LacZ coding DNA with a relevant gene of interest will enable its co-expression with GFP, thus allowing visualization of the effect of specific and stable changes in gene expression throughout development. As the VSV-G pseudotyped viral vector is replication incompetent, changes in gene expression can be controlled temporally, by altering the timing of introduction.

Development of Transgenic Chickens Expressing Human Parathormone Under the Control of a Ubiquitous Promoter by Using a Retrovirus Vector System

Transgenic chickens, ubiquitously expressing a human protein, could be a very useful model system for studying the role of human proteins in embryonic development as well as for efficiently producing pharmaceutical drugs as bioreactors. Human parathormone (hPTH) secreted from parathyroid glands plays a significant role in calcium homeostasis and is an important therapeutic agent for the treatment of osteoporosis in humans. Here, by using a robust replication-defective Moloney murine leukemia virus-based retrovirus vector encapsidated with vesicular stomatitis virus G glycoprotein, we generated transgenic chickens expressing hPTH under the control of a ubiquitous Rous sarcoma virus promoter. The recombinant retrovirus was injected into the subgerminal cavity of freshly laid eggs at the blastodermal stage. After 21 d of incubation, 42 chicks hatched from 473 retrovirus-injected eggs. All 42 living chicks were found to express the vector-encoded hPTH gene in diverse organs, as revealed by PCR and reverse transcription-PCR analysis by using primer pairs specific for hPTH. Four days after hatching, 6 chicks died and 14 chicks showed phenotypic deformities. At 18 wk of age, only 3 G(0) chickens survived. They also released the hPTH hormone in their blood and transmitted the hPTH gene to G(1) embryos. However, although the embryos were alive at d 18 of incubation, none hatched. An electrochemiluminescence immunoassay further showed that the hPTH expression level was markedly elevated in mammalian cells infected by the retrovirus vector. Thus, we demonstrated that transgenic chickens, expressing a human protein under the control of a ubiquitous promoter, not only could be an efficient bioreactor for the production of pharmaceutical drugs, but also could be useful for studies on the role of human proteins in embryonic development. To our knowledge, this is the first report on the production of a human protein (hPTH) in transgenic chickens under the control of a ubiquitous promoter by using a replication-defective Moloney murine leukemia virus-based retrovirus vector system.

Retrovirus-mediated in vitro gene transfer into chicken male germ line cells

Chicken testicular cells, including spermatogonia, transplanted into the testes of recipient cockerels sterilized by repeated γ-irradiation repopulate the seminiferous epithelium and resume the exogenous spermatogenesis. This procedure could be used to introduce genetic modifications into the male germ line and generate transgenic chickens. In this study, we present a successful retroviral infection of chicken testicular cells and consequent transduction of the retroviral vector into the sperm of recipient cockerels. A vesicular stomatitis virus glycoprotein G-pseudotyped recombinant retroviral vector, carrying the enhanced green fluorescent protein reporter gene was applied to the short-term culture of dispersed testicular cells. The efficiency of infection and the viability of infected cells were analyzed by flow cytometry. No significant CpG methylation was detected in the infected testicular cells, suggesting that epigenetic silencing events do not play a role at this stage of germ line development. After transplantation into sterilized recipient cockerels, these retrovirus-infected testicular cells restored exogenous spermatogenesis within 9 weeks with approximately the same efficiency as non-infected cells. Transduction of the reporter gene encoding the green fluorescent protein was detected in the sperms of recipient cockerels with restored spermatogenesis. Our data demonstrate that, similarly as in mouse and rat, the transplantation of retrovirus-infected spermatogonia provides an efficient system to introduce genes into the chicken male germ line.

Expression of enhanced green fluorescent protein in porcine- and bovine-cloned embryos following interspecies somatic cell nuclear transfer of fibroblasts transfected by retrovirus vector

Interspecies somatic cell nuclear transfer (iSCNT) has emerged as an important tool for studying nucleo-cytoplasmic interactions and cloning of animals whose oocytes are difficult to obtain. This study was designed to explore the feasibility of employing transgenic fibroblasts as donor cells for iSCNT. The study examined the chromatin morphology, in vitro development, and expression of an enhanced green fluorescent protein (EGFP) gene in porcine- and bovine-cloned embryos produced by iSCNT of fetal fibroblast transfected with a pLNbeta-EGFP retroviral vector. Parthenogenetic and transfected or nontransfected intraspecies SCNT embryos were used as controls for comparison. Analysis of data revealed that xenogenic oocyte was able to reprogram somatic cells of different genus and supports their in vitro development to the blastocyst stage. However, the developmental rates of transgenic iSCNT embryos to the blastocyst stage were significantly lower than those of intraspecies SCNT embryos. The reduction in development rates was however, not due to integration of the transgene as the lower (P < 0.05) development rates of the intraspecies SCNT porcine or bovine embryos did not differ between transgenic and nontransgenic groups. Expression of EGFP was observed in 100% of blastocysts and mosaicism was not observed. Furthermore, after iSCNT of porcine or bovine donor nuclei into xenogenic ooplasm, patterns of nuclear remodeling in reconstructed embryos were similar. In conclusion, our data demonstrated the feasibility of producing transgenic iSCNT embryos. To our knowledge, this is the first report of transgenic cloned embryo production by iSCNT approach. In the future, this may provide a powerful research tool for studying developmental events in domestic animals and provide marked cell lines for other genetic manipulations.

Production of germline transgenic chickens expressing enhanced green fluorescent protein using a MoMLV-based retrovirus vector

The Moloney murine leukemia virus (MoMLV) -based retrovirus vector system has been used most often in gene transfer work, but has been known to cause silencing of the imported gene in transgenic animals. In the present study, using a MoMLV-based retrovirus vector, we successfully generated a new transgenic chicken line expressing high levels of enhanced green fluorescent protein (eGFP). The level of eGFP expression was conserved after germline transmission and as much as 100 microg of eGFP could be detected per 1 mg of tissue protein. DNA sequencing showed that the transgene had been integrated at chromosome 26 of the G1 and G2 generation transgenic chickens. Owing to the stable integration of the transgene, it is now feasible to produce G3 generation of homozygous eGFP transgenic chickens that will provide 100% transgenic eggs. These results will help establish a useful transgenic chicken model system for studies of embryonic development and for efficient production of transgenic chickens as bioreactors.

Go with the glow: fluorescent proteins to light transgenic organisms

Once a biological novelty known for their role in bioluminescence, fluorescent proteins (FPs) from marine invertebrates have revolutionized the life sciences. Organisms from all kingdoms have been transformed with the Aequorea victoria green fluorescent protein (GFP), and biotechnology has been advanced by the use of FPs. This article reviews the current uses of FPs in whole transgenic organisms and genomics and looks beyond GFP to the complete color palette and spectral properties afforded by FPs from other marine organisms. Coupled with electronic devices for visualizing and quantifying FPs, recently cloned FP genes might be useful for the ecological monitoring of transgenic organisms in the environment. Therefore, this review also addresses the in vivo labeling of organisms with an emphasis on plants.

Identification of the lacZ insertion site and beta-galactosidase expression in transgenic chickens

The quail:chick chimera system is a classical research model in developmental biology. An improvement over the quail:chick chimera system would be a line of transgenic chickens expressing a reporter gene. Transgenic chickens carrying lacZ and expressing bacterial beta-galactosidase have been generated, but complete characterization of the insertion event and characterization of beta-galactosidase expression have not previously been available. The genomic sequences flanking the retroviral insertion site have now been identified by using inverse polymerase chain reaction (PCR), homozygous individuals have been identified by using PCR-based genotyping, and beta-galactosidase expression has been evaluated by using Western analysis and histochemistry. Based upon the current draft of the chicken genome, the viral insertion carrying the lacZ gene has been located on chromosome 11 within the predicted gene for neurotactin/fractalkine (CX3CL1); neurotactin mRNA expression appears to be missing from the brain of homozygous individuals. When Generation 2 (G2) lacZ-positive individuals were inter-mated, they generated 361 G3 progeny; 82 were homozyous for lacZ (22.7%), 97 were wild-type non-transgenic (26.9%), and 182 (50.4%) were hemizygous for lacZ. Western analysis revealed the highest expression in the muscle and liver. With the identification of homozygous birds, the line of chickens is now designated NCSU-Blue1.

Excision of foreign gene product with cathepsin D in chicken hepatoma cell line

To easily and rapidly recover exogenous gene products from chicken egg yolk, we constructed pVTG-catD (VTG, vitellogenin; catD, cathepsin D), a vector cassette carrying two catD-recognition signal peptides (catD-RSPs) in addition to the cloning site. An enhanced green fluorescence protein (EGFP)-encoding DNA fragment was ligated into the pVTG-catD. When the resultant construct pVTG-EGFP-catD containing histidine- and myc-tags was transfected into the chicken hepatoma cell line LMH, EGFP-expression at 24h post-cultivation was confirmed by fluorescence microscopy. Because a signal peptide (NTVLAEF) encoded in pVTG-EGFP-catD is recognized by catD, the VTG-EGFP fusion protein digested with catD was detectable by Western blotting. Digested exogenous gene product was recovered with nickel resin. These results indicate that catD-recognition sites bearing pVTG-catD and His-tags are functional in chicken LMH cells. Therefore, the system described here may be of use in making excision exogenous gene products in the chicken and in creating homozygous knock-in chickens.

Ubiquitous GFP expression in transgenic chickens using a lentiviral vector

We report the first ubiquitous green fluorescent protein expression in chicks using a lentiviral vector approach, with eGFP under the control of the phosphoglycerol kinase promoter. Several demonstrations of germline transmission in chicks have been reported previously, using markers that produce tissue-specific, but not ubiquitous, expression. Using embryos sired by a heterozygous male, we demonstrate germline transmission in the embryonic tissue that expresses eGFP uniformly, and that can be used in tissue transplants and processed by in situ hybridization and immunocytochemistry. Transgenic tissue is identifiable by both fluorescence microscopy and immunolabeling, resulting in a permanent marker identifying transgenic cells following processing of the tissue. Stable integration of the transgene has allowed breeding of homozygous males and females that will be used to produce transgenic embryos in 100% of eggs laid upon reaching sexual maturity. These results demonstrate that a transgenic approach in the chick model system is viable and useful even though a relatively long generation time is required. The transgenic chick model will benefit studies on embryonic development, as well as providing the pharmaceutical industry with an economical bioreactor.

Chicken functional genomics: an overview

Chickens have undergone intensive selection to produce highly productive strains with excellent growth rates and feed conversion ratios. There does not appear to be any reduction in the rate of strain improvement. The recently completed chicken genome sequencing project and adjunct projects cataloging single nucleotide polymorphisms demonstrate that there is still a high level of genetic variation present in modern breeds. The information provided by genome and transcriptome studies furnishes the chicken biologist with powerful tools for the functional analysis of gene networks. Gene microarrays have been constructed and used to investigate gene expression patterns associated with certain production traits and changes in expression induced by pathogen challenge. Such studies have the potential to identify important genes involved in biological processes influencing animal productivity and health. Fundamental regulatory mechanisms controlled by non-coding RNAs, such as microRNAs, can now be studied following the identification of many potential genes by homology with previously identified genes from other organisms. We demonstrate here that microarrays and northern blotting can be used to detect expression of microRNAs in chicken tissue. Other tools are being used for functional genomic analysis including the production of transgenic birds, still a difficult process, and the use of gene silencing. Gene silencing via RNA interference is having a large impact in many areas of functional genomics and we and others have shown that the mechanisms needed for its action are functional in chickens. The chicken genome sequence has revealed a large number of immune related genes that had not previously been identified in chickens. Functional analysis of these genes is likely to lead to applications aimed at improving chicken health and productivity.