Genetic basis of reproductive and plumage polymorphism in the ruff

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The objectives will be achieved by collaboration among three research groups. David Lank (Simon Fraser University) has studied the reproductive behaviour of ruffs in a captive population for 18 generations, and will provide tissue samples to Terry Burke and Jon Slate (University of Sheffield) to enable completion of the ruff pedigree and study of gene expression. Mark Blaxter and colleagues (University of Edinburgh) will support the work by providing new-generation sequencing and associated bioinformatic expertise. Specifically, we will use high-density RAD sequencing to search for genetic markers associated with the three genetically determined reproductive strategies and with plumage patterning. We will use low-density RAD screening of the entire available pedigree to map each trait. The ruff genome will be sequenced and assembled so that we can locate the RAD markers. In combination, we expect to identify the causative loci for both reproductive and plumage traits. We will investigate the expression of the identified loci in the brain and feather follicles. We will investigate the mechanism that maintains the association between behaviour and morphology, and also use standard population genetic tools to test for evidence of selection at the identified loci.

RAD sequencing as a genome discovery tool

The new approach of RAD sequencing is just beginning to get established as an efficient and cost-effective gene discovery tool, and we anticipate that this project will be one of the first to demonstrate the use of RAD to discover the genetic basis of multiple Mendelian genes. MB and colleagues have promoted RAD to the academic community through annual workshops. We now propose to share the knowledge we have gained, and particularly the experience that we will gain in the proposed study, with the wider non-academic user community. The most obvious potential users belong to the plant and animal breeding community.

Mendelian traits are of particular significance in agriculture and horticulture, but relatively few such traits have as yet been identified at the molecular level or even mapped in the genome. This project will demonstrate the power of using RAD to identify the molecular basis of such traits. This may be particularly important in the commercial protection of new traits and for understanding the epistatic physiological effects of mutants. Additionally, breeders have increasingly used molecular approaches such as gene mapping and marker assisted selection to assist the development of new breeds and strains. The efficiency of mapping can be improved through the use of RAD sequencing, and gene identification potentially allows direct selection as an improvement over the marker-assisted approach.

We therefore anticipate significant potential interest from the plant and animal breeding community and will host a workshop aimed at their needs, plus offer additional direct specific advice to interested potential end users in the form of one-to-one tutorial or surgery sessions. The workshop will include speakers from overseas and we anticipate that Floragenix, the US company that owns the patent to the RAD technology, would be one of the contributors.

Outreach

The ruff's impressively visual reproductive biology and morphology lends itself beautifully to public communication. We believe that the results from this proposed work would provide an unusually accessible opportunity to showcase the link between genomic and organismal biology. We therefore propose to produce a high quality free-standing display stand that would include large LED video of displaying ruffs and other aspects of the work, accompanied by ruff specimens and feathers. This stand would be offered to appropriate scientific events and exhibitions and otherwise housed in one of the University's public exhibition spaces. These are being actively developed as part of the University's increasing outreach activities.

Budget

We have budgeted £7000 to cover the costs of hosting the workshop (£4000) and the travel costs to enable interactions with interested companies (either direct visits to companies or participation in breeding industry meetings, £1000), in producing a display stand (£2000) and one additional month of PDRA time to cover the cost of organizing the workshop, participating in meetings, and in outreach activities.