Research uncovers interesting findings in Chardonnay’s family tree

Until now, it has been impossible to definitively identify particular clones of any given grapevine cultivar.

However, new work by researchers at the Australian Wine Research Institute (AWRI) characterising clonal genetics for a single cultivar now makes that a possibility.

‘This is exciting, because it opens the door on a new set of tools for grapevine germplasm management that provides not only a means for identifying specific clones, but also permits an assessment of diversity within a cultivar’.

– Simon Schmidt, AWRI Research Manager.

Chardonnay is a particularly rich example of a cultivar with many commercially available clones. Many of these clones exhibit differences in key viticultural and oenological traits – the result of centuries of asexual propagation.

However, the genetic variation that underlies these differences was largely unknown.

To address this knowledge gap, a multi-centre research team – including Anthony Borneman and Michael Roach from the AWRI – set out to characterise the differences between the many clones of Chardonnay. To do that, they used the latest long-read genome sequencing technologies, high-performance computing and customised bioinformatics tools – and combined it with re-sequencing data from 15 different Chardonnay clones.

‘We specifically looked for single base differences (SNPs)^[1] between clones, rather than copy number differences of repeat elements (transposons and microsatellites) that have been used for the identification of varieties in the past’, explained Simon.

The team identified 1620 base pair changes that were different among the 15 Chardonnay clones that they examined in this study. They found individual clones ranged in their diversity, having as many as 221 (Mendoza) or as few as 27 (Clone 118) unique SNPs.

A key finding was that very few of the clones in the study shared these SNPs, indicating that few clones shared a common clonal heritage.

‘We would expect to see shared SNPs if multiple clones had, at some point in the past, been derived from the same plant but had diverged during subsequent propagation. This type of divergence was apparent when we examined two samples of the same clone, one obtained in Australia and one obtained from Canada. For example, both samples of clone 95 shared 109 marker SNPs, with the Canadian sample having 11 unique marker SNPs and the Australian sample having 15 unique marker SNPs. This example shows how plant material continues to evolve despite our best efforts to capture and maintain a particular lineage’, Simon said.

One finding in particular surprised the team.

‘It is well known that Chardonnay is the product of a cross between Pinot Noir and Gouais Blanc; therefore, the Chardonnay genome should be made up of half from each parent. But our initial assessment of the Chardonnay genome showed that large parts appeared to be derived only from Pinot Noir. We were lucky to have access to Gouais Blanc at the SARDI Research station at Nuriootpa, and sequencing of that material showed that Gouais Blanc is also closely related to Pinot Noir. As a result of this work the wine grape family tree just got a bit more interesting’, the team said.