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DNA markers: their immediate use in tree breeding

The Gondwana Genomics team (L-R) Robert Southerton, Justine Morgan, Dr Bala Thumma, Dr Saro Thavamanikumar, Dr Tina Liu

The forestry industry has been hearing a lot lately about recent breakthroughs in Marker Assisted Selection using targeted DNA sequencing to identify specific tree traits, such as disease resistance, density, pulp yield and growth. Source: Timberbiz

DTN spoke with the Gondwana Genomics Senior Scientist & Operations Manager, Dr Saro Thavamanikumar to help demystify the immediate application potential of the technology and to discuss its growing place in tree breeding.

Dr Saro Thavamanikuma using a pippette.

What can you do now in marker technology space that you couldn’t have done 10 years ago?

High sample throughput and affordable cost for genotyping. Ten years ago, as part of my PhD I genotyped 96 DNA markers across 400 eucalypt trees. It took me more than a year to do this.

Now with significant technological advancements in DNA sequencing space and the development of an in-house ultra-high throughput genotyping method by Gondwana Genomics, we can genotype ~3000 DNA markers across a couple of thousand trees in a weeks’ time.

The long-term benefits seem apparent, but how can Australian plantation companies immediately benefit from your technology?

There are a number of ways Australian plantation companies can immediately benefit by using our DNA marker technology. For me, first and foremost is to assess their seed orchards from where they collect seeds for advancing their breeding generations or sell it to other clients. Particularly if they have clonal seed orchards, I would encourage them to check if all copies of their clones are actually the correct copies.

The other common error we see is wrong assignment of parents to their offspring. This can easily be checked by DNA testing just 10-15 offspring from each family and all the potential parents available. This is of enormous value for breeders because assigning wrong parents to offspring means the breeding values of those parents are wrong. By doing a DNA test, breeders can quickly reconstruct the pedigree and update the parental breeding values by using the corrected pedigree.

The other important immediate benefit is to have inbreeding rates estimated by DNA test. Crossing two closely related trees will increase the inbreeding rates of the offspring and will affect its growth and other fitness related traits.

Do you see a significant role for DNA marker technology in Australian tree breeding programs?

I certainly do. Recently, a number of Australian plantation companies expressed their interest in testing their key breeding material such as seed orchards. We are actually currently doing these tests for a couple of companies.

This is only a start. I envisage that in due course, DNA marker technology will be heavily used by Australian plantation companies in their breeding programs. They no longer have to wait for ~6 years for a tree to grow before they know the potential of it.

Using our DNA marker technology they can start selecting from young seedlings. This will be a game changer for any tree breeding program.

How is Gondwana Genomics different from other genotyping service providers?

Gondwana Genomics is a one-stop-shop. We are not a typical genotyping service provider. We provide a suite of services to our clients here in Australia and overseas which include DNA extractions, genotyping, fingerprinting analyses, genomic relationship analysis to check and correct pedigree, estimating inbreeding rates and more importantly use DNA markers to predict yet-to-be observed traits in young seedlings.

What do clients need to provide you for a quick DNA test on their trees?

One small leaf, that’s all. In fact, we only need 4-5 small leaf punches to extract DNA from them.

Dr Tina Liu punching a eucalyptus leaf

What is important for you to deliver reliable results to your clients?

Quality control. Errors can creep in at any stage during a breeding program. The last thing I want to do is to introduce further errors during DNA testing.

So I make sure we have all QC steps in place to avoid any mistakes. For example, we use a number of duplicate samples during genotyping to make sure we can replicate the results and to track the leaf plates.

How can someone get in touch to find out more information?

Email [email protected] or call +61 2 61096111