ARK-Genomics - UK centre for farm animal functional genomics

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The primary aim of ARK-Genomics is to support the research needs of the Farm Animal Genomics Community. Genomics is a research field in which scientists study the function and role of genes at the whole genome (the collection of genes in a living organism) level. This is particularly timely with the release of the genome sequences of many organisms, including the chicken and soon the cow. The UK Centre for Farm Animal Genomics, ARK-Genomics (http://www.ark-genomics.org), was established with funds from the BBSRC Investigating Gene Function initiative. ARK-Genomics works together with scientists, mostly from research institutes and universities, on research problems. Currently, 55 applications have been successful and 28 are still awaiting a decision from funding bodies. These projects cover a wide range of needs, including the association of genes with physical characteristics (genetic linkage) in specific populations of farm animals and the function of genes, for example, in response to infectious diseases. Genetic linkage studies require the tracking of genes within families, a process known as genotyping. ARK-Genomics has established methods that can track 100s of DNA variants in 1000s of animals. However with the release of the genome sequences of farm animals, millions of DNA variants are being recognised. These differences in DNA sequences between individual or single nucleotide polymorphisms (SNPs) have spawned new technologies for rapid and cheap genotyping of large numbers of SNPs on 1000s of animals. ARK-Genomics provides access to these technologies. Working together with our collaborators we have characterised thousands of genes from chickens, pigs and cattle. These have been used to create DNA chips (DNA specific for each gene spotted onto glass slides) that can be used to detect the expression of genes in any tissue. These arrays will be developed further increasing the representation of genes on the arrays whilst decreasing the costs of their production and use. With the reduction in oligonucleotide (synthetic DNA sequences) prices new arrays based on 20,000 oligonucleotides will be produced. These will reduce the cost of the standard gene arrays by 50 percent. Initially a chicken 20K gene array will be produced in collaboration with a consortium of scientists with interests in development, disease and behaviour. Later similar arrays will be made for cattle, pigs and other farm animals. The details of each array will be matched to the genome databases being created by the ENSEMBL team in Cambridge, the UK home for the human genome sequence. The recent development of methods to manipulate the expression of genes through the application of inhibitory RNAs (siRNA molecules) in cell lines and whole organisms provides a powerful tool to examine the role of genes and their function in the cell. In collaboration with the University of Sheffield ARK-Genomics will provide siRNA specific to over 1000 chicken genes. We expect these will be of immense value to developmental biologists wishing to understand the function of key genes in the development of the chick embryo. These studies will also be aided by the full length copies of the genes (cDNA) available for almost 50 percent of the 18,000 chicken genes. The original development of this genomics facility has created a core of expertise for farm animal genomics and in this application these will be extended. New technologies and resources will be developed, including genomic arrays to compare the genomes of related organisms and the mapping of control regions, sites that determine when and where genes work. This application is for funds to maintain and develop the genomic facilities and resources provided by ARK-Genomics for the needs of the farm animal research community in the most cost effective and timely manner. The establishment of ARK-Genomics has enable d the UK to be at the leading edge of farm animal science, these funds are needed to remain there.