Applications of a novel molecular phenology scale to align the stages of grape berry development

Abstract

Context and purpose of the study: Phenology scales widely adopted by viticulturists (i.e., BBCH or modified E-L systems) are classification tools that describe seasonal and precisely recognized stages of fruit growth and development based on specific descriptors such as visual/physical traits or easy-to-measure compositional parameters. Although some stages can be unequivocally described (e.g., fruit set, veraison), defining comparable developmental stages, from berry formation to full ripening, for grapes of the same cultivar when grown in different conditions or for grapes of different cultivars can be challenging. In this work, molecular-based information was accessed to build a Molecular Phenology Scale (MPhS), suitable to map the ontogenic development of the fruit with high precision.

Material and methods: We exploited the transcriptomic data generated from grape berries of different cultivars sampled weekly from vines grown in the same location over consecutive vintages and focused on conserved annual dynamics rather than on the biological significance of the expression program. The statistical pipeline that was applied consisted of an unsupervised learning procedure yielding an innovative combination of semiparametric, smoothing, and dimensionality reduction tools. By interpolating the transcriptomic samples dispersed in a three-dimension Principal Component Analysis (PCA) we built a 30-stage MPhS that was then used to align samples from several grape berry transcriptomic datasets featuring comparisons between different treatments or growing conditions. 

Results: 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 computing the variation rate of the MPhS stages by time. The performance of the scale was assessed projecting both RNA-seq and microarray transcriptomic samples onto the MPhS. The results allowed to align samples on the MPhS and to highlight differences related to variables like the grape variety, the cultivation site, the vintage, or applied treatments e.g., cluster thinning, defoliation, water limitation and temperature regimes.

The MPhS allowed aligning time-series fruit samples and proved to be an advanced method for defining the stage of grape berry development with higher detail compared to classic time- or phenotype-based approaches.