Table 1.
Quast-based assembly statistics for the Chardonnay clone I10V1 genome.
Fig 1.
The Vitis vinifera cultivar Chardonnay reference genome.
(A) A circos plot showing chromosome-ordered primary contigs (i), haplotig alignments (ii), read-depth of RS II subreads mapped to diploid assembly (read-depth colour scale: yellow, low; blue, high; red, double) (iii), and heterozygous variant density (SNP density colour scale: red, low; blue, high) (iv). (B) An expanded view of Chardonnay Chromosome 2 showing heterozygous variant density (top track), log2 read-depth (middle track), and alignment with Pinot noir Chromosome 2 (bottom track).
Fig 2.
Parental architecture of the Chardonnay genome.
(A) An ideogram of the Chardonnay reference assembly with the positions of both primary contig and haplotig phase-blocks indicated and juxtaposed with a SNP density track (for the primary contigs). Gaps in phase-blocks are indicated in white. (B) An enlargement of a region of Vitis vinifera Chromosome 7 (red box) in Fig 2A.
Fig 3.
A FAR2-like expanded gene family in Chardonnay.
(A) An unrooted tree of FAR2-like genes. (B) A schematic of the predicted genomic arrangement of the FAR2-like genes in Chardonnay. Both Pinot noir-derived (purple) and Gouais blanc-derived genes (green) are shown.
Fig 4.
Genetic diversity in Chardonnay clones.
An unrooted tree of Chardonnay clones based upon bi-allelic SNPs. Sequencing batches are designated by coloured terminal nodes (orange, sequencing batch #1; purple, sequencing batch #2).
Table 2.
A summary of Chardonnay clonal marker variants.
Fig 5.
Validation of clonal markers for Chardonnay.
Results of marker detection pipeline run on four WGS sequencing datasets. The percentage breakdown of clonal markers is shown as either markers identified in the datasets (marker hits), missing from the datasets (missing markers), or missing with low coverage at marker loci (insufficient coverage). (A) Moderate coverage sequencing replicates of marker discovery clonal material. (B) High-coverage sequencing of independently-sourced clonal material. (C) Coverage subsampling of independently-sourced clonal material (clone 95 from Fig 5B). (D) Low-coverage sequencing of DNA derived from several independently-sourced clones (‘ENT’ denotes ENTAV-INRA source material).
Fig 6.
A schematic model for the complex pedigree of Chardonnay, Gouais blanc and Pinot noir.
Two crossing events (akin to a standard genetic backcross) with Pinot noir would result in the homozygous and heterozygous Pinot noir regions present in Chardonnay.