Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay.
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...
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Series: | PLoS Genetics |
Online Access: | https://doi.org/10.1371/journal.pgen.1007807 |
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doaj-f7227cae27934eaaac27347fd554f12e2021-04-21T13:49:45ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042018-11-011411e100780710.1371/journal.pgen.1007807Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay.Michael J RoachDaniel L JohnsonJoerg BohlmannHennie J J van VuurenSteven J M JonesIsak S PretoriusSimon A SchmidtAnthony R BornemanChardonnay 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.https://doi.org/10.1371/journal.pgen.1007807 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 |
spellingShingle |
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 Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PLoS Genetics |
author_facet |
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 |
author_sort |
Michael J Roach |
title |
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. |
title_short |
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. |
title_full |
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. |
title_fullStr |
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. |
title_full_unstemmed |
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. |
title_sort |
population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar chardonnay. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Genetics |
issn |
1553-7390 1553-7404 |
publishDate |
2018-11-01 |
description |
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. |
url |
https://doi.org/10.1371/journal.pgen.1007807 |
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