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

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.

Somatic Variation and Cultivar Innovation in Grapevine

“…More recently, long-read sequencing technologies such as PacBio are facilitating the release of haplotype-resolved assemblies, which are already available for the heterozygous grapevine cultivars Cabernet Sauvignon and Chardonnay [23,24]. By the time being, the availability of reference genomes combined with the development of next-generation sequencing (NGS) technologies enable genome-wide analysis of the grapevine germplasm at affordable costs, which is extremely useful in genetic diversity studies as well as to search for mutations causing phenotypic variation [15,[24][25][26]. Although the use of these approaches to characterize somatic variation in grapevine is still scarce, an increasing number of publications are shedding light on the magnitude and type of variation that accumulates at the genome level within given cultivars.…”

“…However, these numbers might be over-estimated considering that the validation success was 61% for a quality-trimmed sub-selection of SNV [28]. More recently, the re-sequencing of 15 clones of Chardonnay compared to a de novo genome draft assembly for this cultivar identified a much more reduced number of SNV using a stringent k-merbased calling strategy variation [24]. The sum of SNV + INDEL ranged between 221 and 2 polymorphisms per clone (0.004-0.455 per Mb of genome), which corresponds to at least three orders of magnitude of lower rates than in the Nebbiolo study, despite that Chardonnay accessions corresponded to diverse geographical origins and phenotypes including seedlessness and berry color variation [24].…”

“…More recently, the re-sequencing of 15 clones of Chardonnay compared to a de novo genome draft assembly for this cultivar identified a much more reduced number of SNV using a stringent k-merbased calling strategy variation [24]. The sum of SNV + INDEL ranged between 221 and 2 polymorphisms per clone (0.004-0.455 per Mb of genome), which corresponds to at least three orders of magnitude of lower rates than in the Nebbiolo study, despite that Chardonnay accessions corresponded to diverse geographical origins and phenotypes including seedlessness and berry color variation [24]. Concerning the putative impact of these polymorphisms, a total of 21 (0.07%) and 55 (3.4%) clone-specific variants were predicted as potentially altering protein function in Nebbiolo and Chardonnay, respectively, including one nonsynonymous substitution in the VviDXS gene as the possible origin of the Muscat flavor of one Chardonnay clone [24,28].…”

Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity

“…The grapevine genome has an estimated size of~500 Mb. It is arranged in 19 chromosomes and includes over 33,500 protein-coding genes [33]. The availability of this resource favors the re-sequencing of many individuals to delineate inter-and intra-species genetic variations across the Vitaceae family [34].…”

A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping

“…The first de novo assembly of domesticated grapevine using PacBio sequencing was from V. vinifera cv. 'Cabernet Sauvignon' (Chin et al, 2016) followed recently by the diploid assembly of the cultivar 'Chardonnay' (Roach et al, 2018;Zhou et al, 2019). The first and only wild Vitis genome sequence so far comes from the rootstock Vitis riparia 'Gloire de Montpellier' and reached considerable continuity by incorporating PacBio and 10X Chromium (Girollet et al, 2019).…”