Beyond the reference genome: A grapevine pangenome reveals hidden genetic architecture of agronomic traits

Abstract

Pangenomes capture the genetic diversity included in several genome assemblies. We can then use these pangenomes as a new reference for genomic studies. In this work, we sequenced and assembled nine cultivated grapevine genomes. We completed this dataset with six publicly available genomes and the PN40024 T2T, which resulted in 16 high quality assemblies of Vitis vinifera subsp. vinifera distributed within the genomic diversity of the species as defined previously.

From these genomes, we built a 1.1 Gb pangenome graph including 600 Mb of sequence absent from the reference genome and used it to genotype SNPs and structural variants in a diversity panel of 277 grapevine cultivars. As a proof of concept, we demonstrated that using this pangenome increases GWAS power for traits related to phenology, berry development and berry composition.

Acknowledgements

This work was funded by “PlastiVigne”, a Vinid’Occ flagship project from the Occitanie region coordinated by University of Montpellier, the “AgroDIV” PEPR project, and a financial support of INRAe and Institut Agro Montpellier, in France.