There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits; however, the genetic variation that underlies these differences remains largely unknown. To address this knowledge gap, a Chardonnay reference genome was produced and used to compare sequence data from 15 different Chardonnay clones. A total of 1620 markers were identified that distinguish the 15 clones. The parentage of Chardonnay was explored by mapping sequence data from its parents (Gouais Blanc and Pinot Noir) against the Chardonnay reference genome. The analysis of genome sequence data indicates that Pinot Noir and Gouais Blanc share an extremely high degree of kinship.
Two pre-existing data sets, a high-quality reference genome for Chardonnay I10V1 and high-coverage whole-genome sequence data for 15 Chardonnay clones, were used to identify 1620 high-quality inter-clone nucleotide variants. There were limited shared somatic mutations among the Chardonnay clones, especially outside the highly related I10V1 group. Markers were reliably detected at coverages as low as 9.8-fold. Most of the identified clone-specific markers were also recovered from independently sourced clonal material.
Access to a diploid reference genome for Chardonnay also provided the means to unravel the detailed genetic ancestry of this cultivar and its parents, Pinot Noir and Gouais Blanc. Chardonnay matches both haplotypes of Pinot Noir across approximately one-fifth of its genome and these areas include large tracks of both homozygous and heterozygous variation. Mapping of the Gouais Blanc genome that was also generated through this project to the Chardonnay genome revealed an overlap between regions that mapped to Pinot Noir and regions that mapped to Gouais Blanc. This confirms that Gouais Blanc does indeed have a very close kinship relationship with Pinot Noir.