Characterising genomic diversity in Australia’s grapevine germplasm
The identification of grapevine varieties is complex due to the legacy of many centuries of cultivation in many countries, and the significant movement of material between regions and countries. Using microsatellite and SNP DNA markers, a reliable identification of grapevine varieties can be achieved. However, high quality reference genomes are required to understand and to map the genomic variation in the grapevine, which is responsible for phenotypical and functional differences between varieties and clones.
The enabling technology for reference genome construction in the grapevine is in rapid development, and this project will build on know-how and tools developed as part of previous AWRI projects with Australian and international partners. Briefly, for any particular grapevine variety or species lacking an existing reference sequence, sequencing would be performed using long-read technology, and be de novo assembled to form reference-quality assemblies. Sequencing of RNA may also be used to annotate genomes where appropriate. For varieties/species with a known reference genome, re-sequencing would be performed to map genetic diversity. Rapid genetic tests would be developed based upon diversity identified during the de novo and re-sequencing phase of the project.
In cases where genetic data are required by other AWRI or Wine Australia projects, there are opportunities to build on the fundamental knowledge that will be gained through assembly of a whole genome of Chardonnay clones, and from short-read sequencing approaches of Shiraz clones.
This knowledge could be harnessed to establish the genetic diversity that exists:
- in the form of clonal variation in other widely planted varieties such as Shiraz
- in the small numbers of clones (even single canes) that comprise the total Australian genetic repository of many ‘alternative’ varieties
- within the array of rootstocks that are being actively bred from various species of Vitis.
Important long-term applications of these genetic resources could include:
- knowledge about the relationships between genetic diversity and phenotypic characteristics.
- detailed molecular tests for identifying grapevine clones/varieties/rootstocks by DNA certification, without the use or need of established methods such as ampelography.
Understanding genetic variation in Chardonnay and Shiraz
A high-quality, diploid-phased Chardonnay genome assembly has been completed and, combined with re-sequencing data from 15 different commercial Chardonnay clones, was used to assess grapevine clonal diversity. It was possible to detect instances of differential inheritance from the Pinot Noir and Gouais Blanc parents of Chardonnay. Expanded gene families involved in wax biosynthesis were identified showing how gene expansion has enriched the Chardonnay genome for both redundancy and functionality. Mapping of clonal genetic variation revealed the breadth of nucleotide variation that has accumulated during the long-term asexual propagation of this woody plant species. However, most surprisingly, the patterns of nucleotide variation present in the Chardonnay genome were consistent with high levels of inbreeding and revealed that the two parents of Chardonnay, Gouais Blanc and Pinot Noir, share an extremely high degree of kinship that is not inconsistent with a direct parent-offspring relationship.
Evaluation of Shiraz clonal genetic diversity was the specific aim of the AWRI’s contribution to a collaborative project Clones for climate change, led by SARDI. To this end, seven Australian-selected clones and three imported clones were compared using a whole genome sequencing approach. In the absence of a pre-existing reference genome for Shiraz, one was created, and inter-clonal genetic variation was determined through comparison to this reference. This analysis showed that the Australian-selected clonal material was genetically distinct from more recently imported Shiraz clones, forming a distinct group, but that genetic diversity within the group of Australian-isolated Shiraz was low.
Anthony Borneman, Simon Schmidt