Scaling the grape berry developmental stage by molecular phenology: Application details and caveats

Determining the developmental stage of grape berries is essential to understand the effect of environmental and/or cultivation factors. Our work aims to illustrate thoroughly the application of the recently established Molecular Phenology Scale (MPhS) to any custom berry transcriptomic dataset to map the ontogenic development of the fruit with high precision. We detail the code components and instructions to run the MPhS package in R for berry transcriptomic datasets. We describe the output of the application of this tool on berry samples from plants subjected to various cultivation and environmental factors (e.g. cluster thinning, defoliation, water limitation, and varying temperature regimes). We illustrate the procedure for unveiling molecular responses uniquely related to the tested factor by comparing differentially expressed genes upon alignment of fruit samples by MPhS stage. We demonstrated that the MPhS application allows defining the shifts of fruit development driven by various agronomic and environmental factors. Moreover, by performing statistical analysis on grape samples aligned according to the MPhS, we clearly highlighted some modulation of secondary metabolism specifically triggered by crop load manipulation, beyond the anticipation or delay of developmental progression. The application of the MPhS to align time-series samples has proven to be an advanced method to define the developmental stage of grape berries. This is particularly important when the effect of cultivation/environmental factors is studied through gene expression analysis. The method is now fully available to all users for their own research scopes and applications.