Gene mapping: a root to the future? - faster tree trait selection

Wood Focus magazine
,
17 Dec 2012

Affordable gene mapping could cut field test costs and make it quicker and easier to spot desirable tree qualities in the lab. 

Tree breeders have been making tentative explorations into the world of genome mapping. Previously expensive technology has been tumbling in price, enabling researchers to place gene markers on trees to single out strong qualities at the seed stage, potentially reducing a 15-year process to a matter of weeks. 

With this in mind, tree breeding organisations across Europe are trying to spread the use of DNA markers to assist the process, as part of the EU’s NovelTree initiative. This follows the United Nations Economic Commission for Europe, which warned that understanding tree genetics is essential if the region’s forests are to cope with challenges such as climate change, and the growing need for raw materials. A Forestry Commission team has used reference genome sequencing to make marker maps of Sitka spruce for the first time. 

Dr Joan Cottrell, the molecular scientist who introduced marker technology to Forest Research, the Forestry Commission’s research agency, has been working together with tree breeder Dr Steve Lee, who heads up the Genetic Improvement Programme at the Centre for Forest Resources and Management (both based in Midlothian, UK), to demonstrate how the method can pinpoint desirable traits such as growth, better strength, straightness, finer branches or high wood quality. 

‘About 10 years ago, Steve and I could see this was coming over the horizon,’ says Cottrell. Sensing the possibilities of the burgeoning field of molecular genetics, Cottrell and Lee started test trials for Sitka spruce, planting 54,000 trees and replicating clones across sites to ensure any good traits were down to a tree’s genes rather than favourable environment. ‘There were very few molecular markers for Sitka spruce so we had to take a leap of faith and establish these huge trials,’ adds Cottrell. 

Watching for signs of good genes is very much a waiting game. ‘We have been breeding Sitka spruce [in the UK] for about 50 years now and it is a slow process,’ says Lee. ‘We have to grow the trees for about 15 years before we can come to a conclusion as to which are the good ones and which are the bad ones. All of that costs a lot of money and takes too long. How can we cut through it and make it quicker? That’s where this DNA technology comes in.’ 

Covering the Sitka spruce genome with restriction site associated DNA (RAD) markers allows the breeders to dentify trees with high wood density and note what it is in their makeup that differs from those with ordinary density. ‘Once you’ve got that DNA marker, you can start removing bits of DNA from the seed and screening it at an early age,’ says Cottrell. 

The inspiration for using the genome scanning technique came after its proven success in dairy cow breeding, with one team member bringing their experience of genetic selection of cattle. However, instead of milk production or body size, the team tried using RAD markers on Sitka spruce to determine height, and met with success. ‘It’s promising, but we are definitely not there yet,’ says Cottrell. 

Though confident that the method can be used to hone in on other qualities, Lee warned of the dangers of focusing on one particular trait. ‘The trouble with Sitka spruce is that it is not a very high density species – there is a negative correlation between growth rate and wood density. If we did not pay close attention to the wood density and just selected from our fastest growing trees, the density would go down. That would be a bad thing because Sitka spruce is already on the border line for making the lower end of the timber construction grades – the C16 end.’ 

Current field trials can take 10 years and cost £10,000 to run. Although in the recent past getting a DNA screening of a single tree could cost as much as US$1,600, the cost is halving each year, says Lee. ‘It’s already broken through US$100 per tree mark, and in two or three years time it could be down to the US$20 per tree mark.’ With the price of the necessary software and hardware also falling, specialist screening equipment could soon be sitting in most laboratory corners. 

The news has excited senior members in both the Forestry Commission and the private sector. ‘They can see it can give them the answers to their questions much quicker,’ says Lee. ‘Once we’ve learned how to use this technology, we can apply it to any particular tree characteristic, for example disease resistance, then start screening thousands of seeds in the lab for resistant genes, rather than planting them out in the forest and waiting for the fungus to hit them. It’s transferable technology.’  

Life’s a birch… 
The genetic code of the dwarf birch tree has been sequenced for the first time. Researchers from Queen Mary University of London, have mapped the 450-million-letter-long genome and hope it will help improve understanding of the genetic root of traits such as disease resistance, growth rate and shape. The research will also help convervation efforts to preserve the dwarf birch tree, a species that although common in northern Europe, has been made scarce in Britain by an American pest – the bronze birch borer beetle Agrilus anxius.