ShinyFruit: interactive fruit phenotyping software and its application in blackberry

Horticultural plant breeding programs often demand large volumes of phenotypic data to capture visual variation in quality of harvested products. Increasing the throughput potential of phenomic pipelines enables breeders to consider data-hungry molecular breeding strategies such as genome-wide association studies and genomic selection.

We present an R-based web application called ShinyFruit for image-based phenotyping of size, shape, and color-related qualities in fruits and vegetables. Here, we have demonstrated one potential application for ShinyFruit by comparing its estimates of fruit length, width, and red drupelet reversion (RDR) with ImageJ and analogous manual phenotyping techniques in a population of blackberry cultivars and breeding selections from the University of Arkansas System Division of Agriculture Fruit Breeding Program.

ShinyFruit results shared a strong positive correlation with manual measurements for blackberry length (r = 0.96) and ImageJ estimates of RDR (r = 0.96) and significant, albeit weaker, correlations with manual RDR estimation methods (r = 0.62 - 0.70). Neither phenotyping method detected genotypic differences in blackberry fruit width, suggesting that this trait is unlikely to be heritable in the population observed.

It is likely that implementing a treatment to promote RDR expression in future studies might strengthen the documented correlation between phenotyping methods by maximizing genotypic variance. Even so, our analysis has suggested that ShinyFruit provides a viable, open-source solution to efficient phenotyping of size and color in blackberry fruit. The ability for users to adjust analysis settings should also extend its utility to a wide range of fruits and vegetables.