A molecular phenology scale of grape berry development

Abstract

Fruit growth and development consist of a continuous succession of physical,biochemical,and physiological changes driven by a genetic program that dynamically responds to environmental cues. Establishing recognizable stages over the whole fruit lifetime represents a fundamental requirement for research and fruit crop cultivation. This is especially relevant in perennial crops like grapevine (Vitis vinifera L.) to scale the development of its fruit across genotypes and growing conditions. In this work, molecular-based information from several grape berry transcriptomic datasets was exploited to build a molecular phenology scale (MPhS) and to map the ontogenic development of the fruit. The proposed statistical pipeline consisted of an unsupervised learning procedure yielding an innovative combination of semiparametric, smoothing, and dimensionality reduction tools. The transcriptomic distance between fruit samples was precisely quantified by means of the MPhS that also enabled to highlight the complex dynamics of the transcriptional program over berry development through the calculation of the rate of variation of MPhS stages by time. The MPhS allowed the alignment of time-series fruit samples proving to be a complementary method for mapping the progression of grape berry development with higher detail compared to classic time- or phenotype-based approaches.

Acknowledgements

This work is based upon work from COST Action CA17111 INTEGRAPE, supported by COST (European Cooperation in Science and Technology). We would like to express our gratitude to Maurizio Rizzini for his insightful discussions on nonparametric regression, which greatly contributed to the development of this research.

Author contributions

GBT and SZ conceived the research; GBT, MS, PZ and SZ designed the experiments; MS, PZ and MF performed experiments; MS, PZ, MF, GBT and SZ analyzed data; GBT, MS, PZ, SZ, MF interpreted data; MP and AA helped drafting the manuscript; GBT, SZ and MF wrote the manuscript; GBT and MS contributed equally.

Data availability

The expression data used for the creation of MPhS was retrieved from Fasoli et al. [13] (data accession number GSE98923), whereas the berry transcriptomes projected onto the MPhS referred to: Massonnet et al. [26] (data accession number GSE62744 and GSE62745); Fasoli et al. [25] (data accession number GSE36128), Dal Santo et al. [24] (data accession number GSE41633); Dal Santo et al. [30] (data accession number GSE75565); Dal Santo et al. [31] (data accession number GSE97578); Pagliarani et al. [32] (data accession number GSE116238).

Conflict of interest

The authors declare no conflict of interest.

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