Plant Face: Machine learning decodes genetic, environmental and developmental imprints in leaf appearance

Leaf appearance is a crucial plant phenotype. However, traditional methods for extracting this information are inefficient, limiting its full utilization. Deep learning based on convolutional neural networks (CNNs) enables us to capture previously inaccessible information from images. In this study, we made the surprising discovery that the leaf appearance of each individual plant is unique. Using deep learning, leaves from one plant could be efficiently distinguished from those of another plant of the same species and cultivar. We term this phenomenon the "Plant Face" and suggest the potential to develop a "plant face recognition system," analogous to human facial recognition. We also applied similar methods to study the relationship between leaflet appearance and their position on compound leaves, leaf bilateral symmetry, and differences in leaves from twining stems with different chirality. These results collectively indicate that plant genetic characteristics, growth conditions, and developmental features can be stored within their appearance. With appropriate decoding, leaf appearance is poised to play an increasingly important role in phenomics. SignificanceThe saying "no two leaves in the world are identical" holds philosophical significance, as such variation encompasses considerable contingency and randomness. Here, we assert that no two trees have identical leaves; meaning that even for plants of the same species and cultivar, the leaf morphology of each individual plant is distinct at the population level, even though single leaves may overlap in appearance. Genetic, environmental, and developmental information is recorded in some manner within the phenotypic appearance of leaves. With advancements in computational technologies like artificial intelligence, this information can now be decoded. HighlightsO_LIThe leaves of each individual plant are statistically unique. C_LIO_LIThe relationship between leaflet appearances in compound leaves hints at their developmental patterns. C_LIO_LILeaves are not necessarily bilaterally symmetric in a statistical sense. C_LIO_LILeaves from stems with different chirality (twining direction) exhibit distinct appearances. C_LI