Deer genome showcases technology

Deer genome collaborators, from left Rudi Brauning, John McEwan, Paul Fisher and Jason Archer.

10-02-2010 | Not Specified

The sequencing of a substantial portion of the deer genome in the past few months is a milestone for international genome technology as well as for the deer industry.

The deer genome sequencing project was quick and it was cheap.

Because of this, the project is a showcase for processes and equipment that have been developed by an international biotechnology company, Illumina, and shows what is possible for other plant- and animal-based industries say researchers.

Samples from seven New Zealand farmed deer were sent to Illumina's Hayward California sequencing facility in September. Then Rudi Brauning and his AgResearch bioinformatics team at Invermay produced an assembly of the genome and identified genetic markers.

This required a bank of computers about a month. It was wrapped up in early January, in time for the project team leader Paul Fisher and colleague John McEwan to present the project results at an international conference in the United States.

The result is 59 percent of the deer gene map and around 4.1 million genetic markers identified. About 2 million of these are suitable for developing an analysis tool.

This is plenty to be getting on with, and further parts of the genome will emerge during subsequent projects says Invermay deer genetics specialist Jason Archer.

The mapping cost just $250,000. This compares with about $2 billion for the human genome 10 years ago, $60 million each for the cattle genome five years ago and $5 million for the sheep genome completed two years ago.

This is partly a result of the evolving technology - "If we'd waited longer we could have got it for 5 bucks," quips Geoff Asher from the Invermay venison research programme. It also helped that the researchers were able to refer to the cattle genome as it is similar enough to give some indication of where the gene parts fit.

The project featured several technical refinements, says McEwan, who has been involved in cattle and sheep genome work.

The initial impetus was AgResearch work on hind seasonality. It would be a real advantage for the deer industry to have more hinds fawning earlier than in early November as they currently do, so that lactation would coincide with spring growth in lowland areas from early September to early November.

Asher says the research team suspected there was a specific gene controlling timing of fawning, as there is in some other mammalian species, and they realised that having the genome sequenced would help identify this and genes for a range of other production traits.

AgResearch decided to fund the gene mapping project itself, and received a contribution from multi-farm operator Landcorp, which farms 119,000 deer and is a regular supporter of research work.

The genome provides a platform for all kinds of research and analysis, both in farmed and wild deer management around the world. There's been keen interest from several international counterparts, says Fisher.

For example, the genome will aid work Fisher has been doing, helping Scottish researchers detect increasing hybridisation of Scottish Red deer in their native homeland with encroaching Sika deer which have been released into the wild there.

A consortium has been assembled of interested parties from the United Kingdom, Europe, North America, Asia, South America and New Zealand. It is likely that Chinese researchers will use it as the basis for developing a genome for the Sika subspecies and North American groups will collaborate on further developing the Canadian Elk genome.

Asher expects the genome will be particularly helpful for research into disease resistance traits, which have very difficult and expensive to measure before now.

For more information and other deer developments, see the February/March issue of The Deer Farmer. Call 0800 852580 for a subscription.

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