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

Research output: Contribution to journalArticleResearchpeer-review

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.

LanguageEnglish
Article numbere1007807
Pages1-24
Number of pages24
JournalPLoS Genetics
Volume14
Issue number11
DOIs
Publication statusPublished - 20 Nov 2018

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Inbreeding
inbreeding
cultivar
genome
Genome
clones
clone
Clone Cells
cultivars
Population
genome assembly
somatic mutation
kinship
vegetative propagation
parentage
Hybrid Vigor
heterosis
wines
diploidy
Wine

Bibliographical note

Copyright the Author(s) 2018. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Cite this

Roach, M. J., Johnson, D. L., Bohlmann, J., van Vuuren, H. J. J., Jones, S. J. M., Pretorius, I. S., ... Borneman, A. R. (2018). Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PLoS Genetics, 14(11), 1-24. [e1007807]. https://doi.org/10.1371/journal.pgen.1007807
Roach, Michael J. ; Johnson, Daniel L. ; Bohlmann, Joerg ; van Vuuren, Hennie J. J. ; Jones, Steven J. M. ; Pretorius, Isak S. ; Schmidt, Simon A. ; Borneman, Anthony R. / Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. In: PLoS Genetics. 2018 ; Vol. 14, No. 11. pp. 1-24.
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Roach, MJ, Johnson, DL, Bohlmann, J, van Vuuren, HJJ, Jones, SJM, Pretorius, IS, Schmidt, SA & Borneman, AR 2018, 'Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay' PLoS Genetics, vol. 14, no. 11, e1007807, pp. 1-24. https://doi.org/10.1371/journal.pgen.1007807

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. / Roach, Michael J.; Johnson, Daniel L.; Bohlmann, Joerg; van Vuuren, Hennie J. J.; Jones, Steven J. M.; Pretorius, Isak S.; Schmidt, Simon A.; Borneman, Anthony R.

In: PLoS Genetics, Vol. 14, No. 11, e1007807, 20.11.2018, p. 1-24.

Research output: Contribution to journalArticleResearchpeer-review

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