First European Farm Animal Functional Genomics Conference
18-20 September 2005
Edinburgh, UK

Organiser:

Dave Burt, Roslin Institute, Edinburgh, Scotland

Draft Report

Summary

The First European Farm Animal Functional Genomics Conference was held at Heriot Watt University in Edinburgh Scotland in September 2005. The conference focused on genomics resources and tools and their application in research - with a major theme of gene function with agricultural and biomedical importance

The three day conference incorporated sessions on genetics and quantitative traits (QTL), genome analysis, disease resistance, innate immunity and functional genomics in physiology. Broader participation was encouraged with poster and open talk sessions, which were supported with a bursary scheme to encourage participation of PhD students and young post-docs.

Built upon the successful series of annual workshops organised by ARK-Genomics, (www.ark-genomics.org) the conference provided an excellent opportunity for networking between laboratories from Europe and around the world. It was attended by 180 delegates from 15 European countries as well as the USA, Canada, Australia, India, South Korea, Kenya and Australia. Industrial interactions were encouraged by a commercial exhibition for sponsors and a "Farm animals in industry" session supported by Genesis Faraday (www.genesis-faraday.org/) a non-profit organisation funded aimed at technology transfer between basic research and the livestock industry.

The support of the main conference sponsor, European Science Foundation, allowed the development of a conference with a major impact on Farm animal Genomics. Feedback gathered from delegates (via questionnaires) after the conference showed that delegates found the conference informative and provided excellent opportunities for networking. The funding of a bursary scheme with reduced registration fees enabling greater participation of students and young post docs was very successful. Other sponsors supporting the meeting were ARK-Genomics, Genesis Faraday, Operon, Affymetrix, Roche, Aviagen, Schott and Illumina.

The feedback also indicates a strong interest and demand for the continuation of the conference series. ARK-Genomics is planning a continuation of the "European Farm Animal Functional Genomics" conference series and is contemplating a venue within continental Europe for the next event.

The event took stock of the current European position in "Farm Animal Functional Genomics" and it also provided a unique networking opportunity (not only through the presence of members of the Genesis Faraday and the EADGENE (www.eadgene.org) networks). Plenty of opportunities were given to discuss future funding opportunities in Europe and also to exchange information with fellow researchers.

Scientific Content & Discussion

An international panel of speakers was invited by the scientific committee. The scientific committee was comprised of international and local members, for each of the main sessions: Luc Janss and DJ DeKoning (Genetics and QTLs); Chris Warkup (Farm animal genomics in industry); Ewan Birney and Andy Law (Genome Analysis); Francois Hatey and Claire Wathes (Functional Genomics meets Physiology); Marie-Hélène Pinard-van der Laan and Steve Bishop (Disease Resistance); Pete Kaiser and David Haig (Innate Immunity); Dave Burt (Open Session) and Alan Archibald (Funding Opportunities).

The scientific sessions were opened with a keynote speech from Professor Daniel Pomp from Iowa State University integrating the data from QTL studies and microarray gene expression studies to gain an overall hypothetical map of the relationships between the Fat and growth biology in Pigs. Daniel is a well known scientist in both basic and applied areas of livestock research, and always at the cutting edge of his science - this talk was no exception. QTL studies in livestock have gone from strength to strength with many whole genome mapping studies in all the major species. In recent years, high throughput gene expression studies (through ARK-Genomics and other efforts) have added new tools to understand QTL and hopefully identify the genes that control these traits. Daniel's talk was about the integration of these two tools to map genes and loci that control gene expression - eQTL in the model mouse. Daniel was able to explain the new ideas and answered many questions. It was also clear that many delegates were starting or will think about new research in this area, but in livestock species.

The session on "Genetics and QTL's" explored several aspects in the use of QTL's as research tools. Professor Dan Nettleton (U.S.A.) uses QTL's in selective transcriptional profiling which uses the estimated QTL position, trait values, and marker genotypes of the individuals used to map the QTL, to select a subset of individuals for measurement with microarrays. The goal is to choose the best subset of individuals for finding genes whose expression is associated with the QTL and/or directly associated with the quantitative trait. Such genes potentially act in the molecular genetic pathways responsible for establishing levels of the quantitative trait. This talk was an excellent companion talk to Daniel Pomp's talk on eQTL - in particular on the cost of such experiments and how to minimise them. The uses and application of advance intercross lines in the dissection of complex QTLS was highlighted by Professor Lief Anderson (Sweden). Dr Micha Ron (Israel) discussed the identification of the causative SNP in a previously localized quantitative trait locus (QTL) on chromosome 6 affecting milk fat and protein concentrations. Using Haplotype mapping and sequencing of the resulting segregating genes a single nucleotide change capable of encoding a substitution of tyrosine-581 to serine (Y581S) in the ABCG2 transporter was the only polymorphism corresponding to the segregation status for the QTL.

Bioinformatics tools were highlighted in the session on "Genomes Analysis". Narcisse is a tool dedicated to the comparison of completely sequenced genomes, developed by Dr. Thomas Feraut and colleagues (INRA, France). The software is designed to explore the conserved synteny that exists between species. The latest developments in gene orthology/paralogy prediction based on gene tree and species tree reconciliation being used at ENSEMBL (www.ensembl.org) were described by Dr. Abel Ureta-Vidal (U.K.). Using the new chicken Genome Sequence Dr. Laura Elnitski (U.S.A.) discussed higher alignment specificity in functional regions between human and chicken genomes than in human-mouse or human-fugu comparisons. Using these alignments better insights are being gained in the collections of functional promoters and regulators of gene expression. In the "Open session" a talk form the Gene Ontology Consortium (www.geneontology.org) highlighted the benefits of GO annotation for the unification of studies from diverse groups and made a call for GO annotation groups to be set up for each major farm animal species. It is hoped that such groups can be set up through such activities as AvianNet (www.chicken-genome.org) and PigNet (www.toulouse.inra.fr/pignet/). Since the workshop a Farm Animal GO List has been formed (www.geneontology.org/GO.list.farmanimals.shtml) and further initiatives are coming together to join the GO Consortium.

"Functional Genomics meets Physiology" focussed more on gene expression in different physiological models. Dr. Marinus te Pas (Netherlands) demonstrated the expression profiles of the developing muscles in pigs building a pattern of the pathways that are adjusted during the prenatal period. Microarrays were used by Dr. Matt Lucy (U.S.A.) to examine the extensive gene expression profiles that occur in the ovary of cattle and pigs. Comparison between the expression profiles for these species indicated many similarities as would be expected but it is the differences in expression of some genes that may shed light on the different levels of prolificacy in the two species. These differences were supported by work from Dr. Alex Evans (Ireland) looking at the transcriptional patterns during cattle follicular development using in vivo and in vitro models. These studies show a deficiency in the machinery of transcription and translation in in vitro embryos compared to those in vivo. Using a different approach Dr. Phillippe Monget (France) used in silico tools to create a virtual subtractive library of mouse genes expressed in the ovary finding over 100 new oocyte genes. Searches are now being used to identify the orthologues of these genes in farm animals.

The session on "Disease resistance" highlighted different approaches to discovering the factors involved. Dr. Hans Cheng (U.S.A.) discussed the QTL analysis of Mareks Disease resistance in chickens which has produced 15 QTL's and a number of candidate genes. These results are being put together with a range of characterised chicken lines, the chicken genome sequence and immunological assay to take a multidisciplinary approach to identifying the factors and their relationships. Dr. Claire Rogel-Gaillard (France) described the structure and activities of the Major Histocompatability Complex in pigs where many of the genes are intimately involved in innate and adaptive immune responses. The new tools and approaches to dissecting the functional relationships and interactions were presented.

Further immune topics were discussed in the "Innate Immunity" session. Dr. Aisling Dunne (Ireland) gave an excellent overview of Toll-Like receptors highlighting the differences between species and exploring these differences for a further understanding of the TLR's and their signalling mechanisms. Dr. Dirk Werling (U.K.) presented work on pathogen recognition receptors in cattle looking particularly at the TLR4 receptor. In chickens there is clear evidence for this genes involvement in disease resistance whereas in cattle it has not yet been associated with resistance to any disease.

The last session of the conference was aimed at highlighting funding mechanisms in the UK and Europe. These provided delegates with a clear overview of funding possibilities, in particular, those that may fund those embryonic projects discussed during the networking opportunities at this First European Farm Animal Functional Genomics Conference.