A Vitis vinifera L. core collection suitable for association studies of fruit quality and resilience traits

Abstract

The wide genetic and phenotypic diversity of Vitis vinifera L. varieties represents a valuable resource for improving grapevine fruit quality traits and crop resilience to biotic and abiotic stresses. The development of well-structured core collections that capture the maximum diversity of the species while maintaining a manageable number of varieties is therefore a key step toward efficient genetic mapping studies. Starting from the V. vinifera accessions preserved in the ICVV germplasm collection, we designed a core collection of 150 varieties suitable for association studies. Using available genotypic data from 240 SNP markers, we first investigated the genetic structure of the entire collection, which revealed three major genetic groups consistent with current knowledge of grape usage and geographic origin: wine grapes from the Iberian Peninsula, wine grapes from Central Europe, and table grapes of diverse origins. Within each genetic group, individuals showing low levels of admixture were retained, generating three datasets that were subsequently used to construct independent core collections of 50 varieties each. After their assembly, the final core collection comprises 150 varieties with limited genetic relatedness, and represents the three genetic backgrounds in a balanced manner. To evaluate its suitability for association studies, we assessed the extent of phenotypic variation for different traits of interest. The use of a high-throughput berry image acquisition platform coupled with an automated image-processing pipeline revealed substantial diversity for berry size and shape traits in the collection, with berries varying between 3.1 and 0.7 cm in length and 2.1 and 0.7 cm in width. An image-based approach to quantify sunburn-like damage in whole clusters subjected to a standardized heat stress treatment under controlled conditions further highlighted wide phenotypic variation, identifying varieties that were nearly unaffected and others with massive necrotic damage. In addition, controlled inoculation of individual berries with Botrytis cinerea revealed marked differences in susceptibility, with varieties ranging from low to extensive mycelial growth under identical experimental conditions.

Altogether, this V. vinifera core collection and the established phenotyping methods provide a robust and efficient resource for association studies aimed at dissecting the genetic basis of fruit quality and resilience traits, for adaptation of grapevine cultivation to current viticultural challenges.

Acknowledgements

This work is part of the research project PID2023-152513OB-I00 funded by MICIU/AEI/10.13039/501100011033 and by ERDF/EU. JT was supported by the Ramón y Cajal Programme (RYC2022-037758-I) funded by MCIU/AEI/10.13039/501100011033 and by ERDF/EU. Authors acknowledge the support of the Chinese Academy of Sciences President’s International Fellowship Initiative (2025PG0014).