Abstract
Chardonnay is the basis of some of the world’s most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propagation. However, the genetic variation that underlies these differences remains largely unknown. To address this knowledge gap, a high-quality, diploid-phased Chardonnay genome assembly was produced from single-molecule real time sequencing, and combined with re-sequencing data from 15 different Chardonnay clones. There were 1620 markers identified that distinguish the 15 clones. These markers were reliably used for clonal identification of independently sourced genomic material, as well as in identifying a potential genetic basis for some clonal phenotypic differences. The predicted parentage of the Chardonnay haplomes was elucidated by mapping sequence data from the predicted parents of Chardonnay (Gouais blanc and Pinot noir) against the Chardonnay reference genome. This enabled the detection of instances of heterosis, with differentially-expanded gene families being inherited from the parents of Chardonnay. Most surprisingly however, the patterns of nucleotide variation present in the Chardonnay genome indicate that Pinot noir and Gouais blanc share an extremely high degree of kinship that has resulted in the Chardonnay genome displaying characteristics that are indicative of inbreeding.
Highlights
Phenotypic variation within a grapevine cultivar arises from an accumulation of mutations from serial vegetative propagation
Funding was obtained from Genome British Columbia and the Wine Research Centre at The University of British Columbia
The marker detection framework we describe for authenticity testing would be applicable to other grapevine cultivars or even other agriculturally important woody-plant crops that are vegetatively propagated such as fruit orchards
Summary
Chardonnay is known for the production of some of the world’s most iconic wines and is predicted to be the result of a cross between the Vitis vinifera cultivars Pinot noir and Gouais blanc [1, 2]. High genetic variability existed between individual plants within a single vineyard and this heterogeneity often lead to inconsistent fruit quality, production levels, and in some wine-producing regions, poor vine health [4]. Clonal selection arose as a technique to combat these shortcomings, preserving the genetic profile of superior plants, while amplifying favourable characteristics and purging viral contamination, leading to improved yields [4, 5]. The availability of virus-free clonal material of I10V1 helped cement productivity gains in the viticultural sector and I10V1 quickly dominated the majority of the Australian Chardonnay plantings [4, 5]
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