Deciphering the genetic determinants associated with key phenological stages of berry development in table grapes

Abstract

Grapevine (Vitis vinifera L.) is one of the most economically important fruit crops at worldwide level, and its development is highlydependent on environmental conditions. Characterizing the genetic basis of key phenological stages could support the development of new selection tools for table grape breeding aiding adaptation to climate change. In this study, a diverse collection of 116 genotypes wasevaluated across three seasons to identify the genetic determinants of major vegetative and reproductive stages, from woolly-bud to harvest. Vigor-related traits such as effective leaf area index, photosynthetic efficiency, and internode number related were also gauged.

Genotyping-by-sequencing (GBS) identified 116,751 high-quality biallelic SNPs, which were used for genome-wide association studies(GWAS). Multiple genomic regions, or hotspots, associated with vegetative and reproductive phenological stages were identified, withsignificant SNPs clustering on specific chromosomes (chr.), notably chr. 2, 4, 5, 13, 16, and 18. This finding suggests that certain genomic regions act as regulatory hotspots controlling key transitions on budbreak, flowering, and veraison. Significant SNPs associatedwith hormonal signaling and stress responses highlight the interplay between developmental regulation and environmentaladaptability, related to phenology progression.

Significant SNPs associated to reproductive stages revealed a strong over-representation of transmembrane transport, receptor-like kinase activity, ATP-binding, and nucleic acid–binding functions categories, highlighting the importance of membrane-associated perception and gene regulatory control during the reproductive development. Overall, this study reveals the polygenic architecture of grapevine phenology and provides a foundation for marker-assisted selection strategies to optimize phenological timing and quality traits under climate change scenarios.

Acknowledgements

Financed by ANID Chile grants 11190936 and FONDEF TA25I10087.