Identification of novel candidate genes for regulation of follicle selection in the avian ovary

Selective breeding of chickens for high growth rate and other production traits has led to the modern commercial broiler, a bird that has the genetic potential for reaching an average body weight of 2.7kg within 6 weeks of hatch. However, the breeding stock for modern broilers has to be feed controlled in order to lay large numbers of viable hatching eggs. Broiler breeders, when fed ad libitum, have a propensity to produce internal ovulations, double-yolked, misshapen or shell-less eggs. This is due to the release of multiple ova at ovulation, which results in a significant loss of production. Feed control has been shown to mitigate this effect but welfare concerns have been raised as to the side-effects for the birds. The main objective of this research was to determine the genetic basis for the regulation of ovarian follicle selection and its dysfunction in ad libitum-fed broiler breeders, and how this might be addressed by genetic selection to limit the impact on the management and welfare of future broiler breeders. A multi-layered statistical, expression profiling and cluster analysis of ovarian gene expression data from a microarray study was carried out to identify candidate genes for further study.Key stages of development were investigated for feed restricted and ad libitum-fed broiler breeders. Several gene candidate genes were validated by qPCR in a comparison of different ovarian tissues in layer type hens for subsequent analysis in broiler breeders. Sequencing of the founders of an Advanced Intercross Line (AIL) of commercial broiler breeders and White Leghorn layers was performed covering 3 regions of each of the primary candidate genes in order to identify genetic variation that could account for differences in follicle number between broilers and layers. Expression data from a microarray study highlighted a number of potential candidate genes for regulation of follicle development. One of these genes, Platelet Derived Growth Factor Receptor Like (PDGFRL), shares significant sequence homology with the active domains of Platelet Derived Growth Factor Receptor β. Expression profiling in layers showed peak PDGFRL expression in 5-6 mm follicles and the F2 follicle (P <0.001). PDGFRL was also up-regulated in response to ad libitum feeding in broiler breeders in 6-8 mm follicles (P<0.016), the point at which follicle selection and recruitment is considered to occur. In addition to this, while PDGFRL expression remains relatively constant between tissues under ad libitum conditions, it shows a clear reduction in expression (P <0.001) in prehierarchical follicles relative to the stroma and the F1 follicle under feed restriction. This observation is consistent with results from the original microarray study. Sequencing of the AIL Founders highlighted several SNPs in the broiler that have the potential to be used as markers for incorporation into commercial selection programs. EST alignment in preparation for targeted sequencing of PDGFRL also highlighted three potential forms of the protein, each with a different 5’ starting sequence. Initial investigation has shown all three to be expressed in ovarian follicles. QPCR in a panel of 13 tissues shows marked differences between the 3 variants, implying different and perhaps specialised roles for each. The PDGFR family has a potential role in steroidogenesis, and the expression profiling, combined with the clear effect on expression from ad libitum feeding in broiler breeders, suggest that PDGFRL is a strong candidate for involvement in the regulation of follicle development GDF9, shown to be associated with multiple ovulation in sheep, and FSH receptor, a mediator of neuroendocrine signalling to the ovary, were also investigated. They behaved as expected in layer type birds but both showed significant differential expression (P = 0.005 and 0.018 respectively) as a result of ad libitum feeding in broiler breeders. Though these two genes have been extensively investigated, these are previously unobserved effects. SNPs have also been identified in these genes which have the potential to be used as markers for incorporation into commercial selection programs. To fully exploit these results, additional investigation is recommended to confirm these results in commercial populations and to determine how they can be employed to best effect

Identification of novel candidate genes for follicle selection in the broiler breeder ovary

BACKGROUND: Broiler breeders fed ad libitum are characterised by multiple ovulation, which leads to poor shell quality and egg production. Multiple ovulation is controlled by food restriction in commercial flocks. However, the level of food restriction raises welfare concerns, including that of severe hunger. Reducing the rate of multiple ovulation by genetic selection would facilitate progress towards developing a growth profile for optimum animal welfare. RESULTS: The study utilised 3 models of ovarian follicle development; laying hens fed ad libitum (experiment 2) and broiler breeders fed ad libitum or a restricted diet (experiments 1 & 3). This allowed us to investigate gene candidates for follicular development by comparing normal, abnormal and “controlled” follicle hierarchies at different stages of development. Several candidate genes for multiple ovulation were identified by combining microarray analysis of restricted vs. ad libitum feeding, literature searches and QPCR expression profiling throughout follicle development. Three candidate genes were confirmed by QPCR as showing significant differential expression between restricted and ad libitum feeding: FSHR, GDF9 and PDGFRL. PDGFRL, a candidate for steroidogenesis, showed significantly up-regulated expression in 6–8 mm follicles of ad libitum fed broiler breeders (P = 0.016), the period at which follicle recruitment occurs. CONCLUSIONS: Gene candidates have been identified and evidence provided to support a possible role in regulation of ovarian function and follicle number. Further characterisation of these genes will be required to assess their potential for inclusion into breeding programmes to improve the regulation of follicle selection and reduce the need for feed restriction

Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

<p>Abstract</p> <p>Background</p> <p>In an effort to better understand the molecular networks that underpin macrophage activation we have been assembling a map of relevant pathways. Manual curation of the published literature was carried out in order to define the components of these pathways and the interactions between them. This information has been assembled into a large integrated directional network and represented graphically using the modified Edinburgh Pathway Notation (mEPN) scheme.</p> <p>Results</p> <p>The diagram includes detailed views of the toll-like receptor (TLR) pathways, other pathogen recognition systems, NF-kappa-B, apoptosis, interferon signalling, MAP-kinase cascades, MHC antigen presentation and proteasome assembly, as well as selected views of the transcriptional networks they regulate. The integrated pathway includes a total of 496 unique proteins, the complexes formed between them and the processes in which they are involved. This produces a network of 2,170 nodes connected by 2,553 edges.</p> <p>Conclusions</p> <p>The pathway diagram is a navigable visual aid for displaying a consensus view of the pathway information available for these systems. It is also a valuable resource for computational modelling and aid in the interpretation of functional genomics data. We envisage that this work will be of value to those interested in macrophage biology and also contribute to the ongoing Systems Biology community effort to develop a standard notation scheme for the graphical representation of biological pathways.</p