New genetic test for vine varieties-21 September
September 22, 2015 0 Comments
A new type of genetic test being performed by a liquid-handling robot at Lincoln University is taking DNA testing to the next level with its ability to deliver five times the standard amount of data used to identify grapevine varieties.
Developed by Dr Darrell Lizamore at Lincoln University and delivered by Zebra Biotech, the new transposon marker test is a unique DNA testing process not available anywhere else in the world, offering an alternative to and improvement on existing methods.
While ampelographers have traditionally identified and classified varieties by their leaf shape, DNA testing is now the preferred technique, with short repeat marker tests the most popular form of identification. Sample genetic profiles are screened against an extensive profile database, allowing comparison with over 1000 varieties. Analysing specific genetic markers provides information on variety and species, giving nurseries confidence that they are selling the right varieties, and preventing grape growers from planting the wrong vines.
However, short repeat marker tests only analyse between 10 and 20 markers, and on occasion produce ambiguous results due to changes within this limited set. The transposon marker test analyses between 50 and 100 markers per sample, and focuses on the most variable parts of the plant’s DNA, so is able to resolve unusual results from standard testing.
“Only a limited number of laboratories worldwide offer the short repeat marker tests, and Zebra Biotech is the only accredited provider in New Zealand” says Dr Lizamore. “However, these tests only check a few genetic markers. The transposon test provides results that can be treated with a lot more confidence, so if you need definite or more specific results it’s very useful.” Lincoln University’s collection of over 100 locally-grown varieties is often used as a source of reference material for comparison as there is no public database for the transposon test.
Zebra Biotech’s genetic testing doesn’t stop when vines are dormant. “We offer both tests year round, using fresh leaves in summer and woody material in winter. As far as we know, no-one else is offering this service. The local service is particularly beneficial to growers in New Zealand because of restrictions around the import and export of live tissue. It’s cheaper and faster and they get personal service.”
Dr Lizamore’s experience in DNA testing goes back to his student days at Stellenbosch University in South Africa where he worked on the development of genetic profile tests for abalone to assist police in tracking caches of the smuggled seafood, which has a high market value.“The short repeat DNA tests we carry out on vines are similar to those used for paternity testing, crime scenes and so on. The main difference is how we extract the DNA,” says Dr Lizamore.
It was his PhD research, supervised by Dr Chris Winefield at Lincoln University, which led to the development of the new type of test. They studied the activity of transposons: regions of the genetic code in most species that respond during times of environmental stress, such as drought. These elements shuffle the genetic information of an organism, resulting in new mutations. Dr Lizamore’s work identified which transposon types are active in modern cultivated vines, along with conditions that trigger the grapevine’s DNA to change.
Together Dr Winefield and Dr Lizamore are now using their new understanding of the natural role transposons play in altering vine DNA to create new vines with specific qualities such as disease resistance. This offers an alternative to current breeding programmes as a way to improve the crops planted in New Zealand. With the support of New Zealand Wine, they have already created about 200 new plants which will be of interest to local nurseries and growers.