Jessica A. Vervalle, Laura Costantini, Silvia Lorenzi, Massimo Pindo, Riccardo Mora, Giada Bolognesi, Martina Marini, Justin G. Lashbrooke, Ken R. Tobutt, Melané A. Vivier, Rouvay Roodt-Wilding, Maria Stella Grando & Diana Bellin

Theoretical and Applied Genetics December 2022; vol. 135: 4371–4390

Key message

We present a high-density integrated map for grapevine, allowing refinement and improved understanding of the grapevine genome, while demonstrating the applicability of the Vitis18K SNP chip for linkage mapping.

Abstract

The improvement of grapevine through biotechnology requires identification of the molecular bases of target traits by studying marker-trait associations. The Vitis18K SNP chip provides a useful genotyping tool for genome-wide marker analysis. Most linkage maps are based on single mapping populations, but an integrated map can increase marker density and show order conservation. Here we present an integrated map based on three mapping populations. The parents consist of the well-known wine cultivars ‘Cabernet Sauvignon’, ‘Corvina’ and ‘Rhine Riesling’, the lesser-known wine variety ‘Deckrot’, and a table grape selection, G1-7720. Three high-density population maps with an average inter-locus gap ranging from 0.74 to 0.99 cM were developed. These maps show high correlations (0.9965–0.9971) with the reference assembly, containing only 93 markers with large order discrepancies compared to expected physical positions, of which a third is consistent across multiple populations. Moreover, the genetic data aid the further refinement of the grapevine genome assembly, by anchoring 104 yet unanchored scaffolds. From these population maps, an integrated map was constructed which includes 6697 molecular markers and reduces the inter-locus gap distance to 0.60 cM, resulting in the densest integrated map for grapevine thus far. A small number of discrepancies, mainly of short distance, involve 88 markers that remain conflictual across maps. The integrated map shows similar collinearity to the reference assembly (0.9974) as the single maps. This high-density map increases our understanding of the grapevine genome and provides a useful tool for its further characterization and the dissection of complex traits.

See https://link.springer.com/article/10.1007/s00122-022-04225-6

Figure 4: Grapevine integrated map based on three mapping populations (CSxC: ‘Cabernet Sauvignon’ × ‘Corvina’, DRxG1: ‘Deckrot’ × G1-7720 and RRxCS: ‘Rhine Riesling’ × ‘Cabernet Sauvignon’). Marker regions that are in conflict with the ‘PN40024 12X.v2’ assembly are indicated in blue (dark blue if supported by more than one population map, with exception of those introduced by forcing orders during the between maps conflict solving step), whereas marker regions in conflict between population maps are indicated in red. List of these markers are given in Tables S11 and S10 respectively. Marker positions are indicated with horizontal lines. Abbreviation: chr = chromosome