Feature: In vino veritas

Science and wine seem natural companions. Now the relationship will be taken to the next level with the initiation of a landmark genome study of the ubiquitous Chardonnay grape, that paragon white wine variety with such enduring popularity here and abroad.

Not only is it hoped the project will reveal insights into the links between genome and phenome but, perhaps best of all, it seeks to arm winemakers with the information they need to make even better wine.

Chardonnay is a particularly fruitful candidate for genomic probing. It is the second most widely grown variety in Australia, with it accounting for nearly 20 per cent of the 1.5 million tonnes of wine grapes produced in 2009-2010, according to the Australian Bureau of Agricultural and Resource Economics and Sciences.

It is second only to the recent up-and-comer Shiraz, which now takes the number one position, with 26 per cent of production. However, Chardonnay is still the grape of choice in warmer regions, accounting for 46 per cent of production in those areas.

“In the Australian context Chardonnay is critically important,” says Dr Simon Schmidt, Research Scientist at the Australian Wine Research Institute (AWRI), who is part of the team working on the Chardonnay genome. “For the Australian wine industry, Chardonnay wine making has to continue to develop in order for it to remain competitive.

“While there are a lot of other up-and-coming varieties, Chardonnay is one of those bedrock varieties that the Australian industry has not only invested in heavily, but is also used to make some of the world’s great wines,” he says.

“From an agricultural perspective we’re also at an interesting junction with Chardonnay. There are quite a few new Chardonnay clones becoming available that aren’t used yet in Australia.

“Many of the Chardonnay vineyards that are currently in use were planted in the 1980s using predominantly one clone type. But if you were to plant a Chardonnay vineyard now, you’d have much greater choice of clones to choose form. However, it’s not exactly clear how these clones will express themselves in the Australian environment.”

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Varieties and variations

Thus one of the key goals of the Chardonnay genome project is to gain a deeper understanding of how the genetic variations between these clones affect the way they grow, develop, ferment and ultimately translate into the finished product in your wine glass.

Yet there’s a lot we currently don’t know about how genetic variation corresponds to phenotypic variation in clonal varieties. To date, only colour formation is well understood genetically, leaving other crucial traits like fruit composition, flavour and aroma profile, ripening time, flower and bunch morphology and yield largely a mystery.

Chardonnay’s interesting genetic heritage also makes it a good candidate to explore how genetic variation affects these traits. Chardonnay was originally spawned as a cross between Pinot noir and Gouais blanc, enacted by pioneering French winemakers (probably somewhere near Chardonnay, Saône-et-Loire, funnily enough) centuries ago.

Interestingly, while Pinot noir is still in wide use, Gouais blanc is considered an inferior wine grape, and has largely been abandoned in modern winemaking. Yet the pairing of the two produced one of the most iconic wine grapes in use today.

Since its inception, Chardonnay has been cloned repeatedly, and has acquired many minor genetic variations along the way. It is precisely this relatively solid genetic foundation and subsequent mutation and selection that has produced the genetic and phenotypic diversity we see today, making it an ideal candidate for genome sequencing.

The study is a collaboration between the AWRI with the University of British Columbia in Canada, the Yalumba Wine Company and the South Australian Research and Development Institute, and is supported by BioPlatforms Australia and Genome British Columbia. It will ultimately examine 15 clonal varieties of Chardonnay. The reference genome will be based on i10v1, one of the more popular varieties planted in Australia.

The plan is to sequence i10v1 using a hybrid strategy, starting with a 454 run at 10x coverage of insert libraries ranging from 3 kb to 20 kb in length, then a high-depth Illumina sequence with around 100 kb inserts. “That will give us both in-depth sequence and structural variation for the reference genome,” says Schmidt.

The remaining 14 clones will be sequenced with only the Illumina technology using a short insert library of around 500 bp at 30x coverage. “Illumina is one of the most reliable deep sequencing strategies available,” says Schmidt. “Illumina sequencing will be the workhorse technology for this project.”

That said, Schmidt is keeping a close eye on new sequencing technologies that could potentially handle longer sequence reads, thus speeding up the assembly process, which inevitably gobbles up a lot of time and resources. “If they come online in the timeframe of the project, they could accelerate what we’re trying to do here,” he says. “But the current strategy will deliver us what we need, but a massive effort in assembly will be required.”

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It’s anticipated that the clones will all have very similar genomes, but the Illumina runs should highlight any nucleotide polymorphisms and structural variations that have accumulated over the generations. “We don’t anticipate any large genome rearrangements, but I do anticipate SNPs [single nucleotide polymorphisms] and potentially deletions – the kinds of things that can arise via somatic mutation,” says Schmidt.

“This is because in the propagation of a single variety like Chardonnay, there’s no out-crossing at all. Since the original selection of that variety, the whole world’s Chardonnay has been derived from cuttings. But over hundreds of years of somatic mutation, there’s going to be some build up of genetic diversity.”

Drinking science

However, the study doesn’t stop at probing nucleotides. Each of the 15 clonal varieties of Chardonnay will be made into wine at the Hickinbotham Roseworthy Wine Science Laboratory at Urrbrae from fruit picked at Yalumba’s Oxford Landing Estates in South Australia.

From here the researchers will bring the AWRI’s extensive resources for chemical and sensory assessment to bear to see how the fruit and wine varies in a real world context and to provide concrete phenotypes to attach to the genetic variations.

The first batches of wine have been made, and are being bottled right now. “I’m quite keen to see how they taste,” says Schmidt. “I expect for the most part for there to be subtle variation between the clones. But in some cases it’ll be marked. For example, there’s one clone with increased linalool production, and the winemaker could tell straight away just by tasting the grapes.

“It wasn’t a subtle thing, and she couldn’t stop eating the grapes, saying ‘I love these muscat grapes – I’m not sure it’s even Chardonnay’. They’re all Chardonnay, but some have less subtle differences.”

The project is knee deep in sequencing at the moment and will shift to assembly as the sequences are completed. Schmidt expects to be in the assembly stage by the end of the year and to have the full data some time in 2013. From there, it’ll be a matter of piecing together the picture of how the genetic variation relates to the phenotypic variation, and how that translates to wine in the glass.

This understanding will ultimately help winemakers choose the best variety for their climate and soil, and to better produce the wine they want to make, whether that’s white, sparkling or a blend. The improved description of Chardonnay will also enable vignerons to better identify the variety planted at a particular lot, such as if they were about to purchase a new vineyard with grapes already present.

And the fact that Schmidt has the opportunity to drink wine in the name of science in the process is part of the appeal of working for the AWRI. “It’s definitely expanded my wine appreciation. Working on flax seeds as I used to do was not quite the same...”