The Animal Functional Genomics Resource

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Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture (animal breeding and animal health), contributing to human and veterinary medicine by providing animal models, and improving animal health and welfare. The chicken also serves as a model for all other avian species, so is important in the fields of embryology and development, neurobiology and behaviour, and the ecology and evolution of natural populations.The genome is the entire DNA content of an organism. For the genome sequence to be useful, the sequence needs to be annotated with the location of genes and their regulatory elements along the DNA sequence. Information on the location of at least coding genes (that is, genes which make proteins) is now available for many economically important farmed and companion animals, and efforts are underway in many parts of the world to increase our knowledge of non-coding regions (i.e. non-coding RNAs and regulatory elements). In addition, the advent of new DNA sequencing technologies now mean that it is possible to sequence many individuals and compare their differences in DNA sequence and gene content and relate this to their physiological differences. It is also possible to generate 'functional' data by sequencing ("assay by sequencing"). Functional sequence data tells us about which genes are active, which genes code for proteins and which genes code for regulatory RNAs. It can also tell us about other features within the DNA sequence that are responsible for genes being switched on or off, for example, in specific tissues or in response to signaling molecules. Functional sequence data is therefore very important in informing us about how differences in the DNA sequence in individuals can affect gene activity and are therefore likely to affect phenotypes, such as production or disease resistance traits. Some DNA databases contain functional data for farmed and companion animals often in its raw form (e.g. sequence reads), however this data is most useful when it has been checked for quality and processed further, for example assigning it to specific genes and transcripts. It would also be preferable if more data were submitted to these databases from the research community around the world.Our proposed research aims to look at the data that is available for these animals in the public DNA databases, and check it for quality. We will also work to ensure that future datasets that are submitted to the databases have as much useful information associated with them as possible, for example, breed, sex and tissue type, etc. We will also define quality standards for such data and improve data discoverability by drawing together datasets from disparate projects into a cohesive collection that is accessible both programmatically and via a website.