Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Michael J Roach; Daniel L Johnson; Joerg Bohlmann; Hennie J J van Vuuren; Steven J M Jones; Isak S Pretorius; Simon A Schmidt; Anthony R Borneman

doi:10.1371/journal.pgen.1007807

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

PLoS Genet. 2018 Nov 20;14(11):e1007807. doi: 10.1371/journal.pgen.1007807. eCollection 2018 Nov.

Authors

Michael J Roach¹, Daniel L Johnson¹, Joerg Bohlmann^{2

3}, Hennie J J van Vuuren^{2

3}, Steven J M Jones⁴, Isak S Pretorius⁵, Simon A Schmidt¹, Anthony R Borneman^{1

6}

Affiliations

¹ The Australian Wine Research Institute, Glen Osmond, South Australia, Australia.
² Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada.
³ Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada.
⁴ Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
⁵ Chancellery, Macquarie University, Sydney, New South Wales, Australia.
⁶ Department of Genetics and Evolution, University of Adelaide, South Australia, Australia.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosome Mapping
DNA, Plant / genetics
Genetic Markers
Genetic Variation
Genome, Plant
Genomics
INDEL Mutation
Inbreeding
Mutation
Phenotype
Phylogeny
Plant Breeding
Polymorphism, Single Nucleotide
Vitis / classification
Vitis / genetics*
Wine

Substances

DNA, Plant
Genetic Markers

Grants and funding

This project is supported by Australia’s grapegrowers and winemakers through their investment body Wine Australia, with matching funds from the Australian Government. Grapevine genomics work at the AWRI is also supported by Bioplatforms Australia as part of the National Collaborative Research Infrastructure Strategy, an initiative of the Australian Government. Funding was also obtained from Genome British Columbia and the Wine Research Centre at The University of British Columbia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.