Abstract
Leaf morphology in tea plants (Camellia sinensis L.) profoundly influences tea quality and agronomic value, yet its genetic basis remains elusive due to labor-intensive phenotyping, foliage architecture, and ecological sensitivity of traits. Moreover, traditional methods forfeit quantitative color gradients and population-level morphological complexity. To address this challenge, we developed coleaf, an open-source image recognition-based software that demonstrated 97.6% accuracy over conventional ImageJ measurements, while offering higher efficiency and color hues quantification. We then estimated 7 key morphological traits focusing on leaves from a collection of ~ 4,200 mature leaves and ~ 5,000 bud-leaf samples across 167 genetically diverse tea accessions by coleaf. While classical understanding suggests leaf shape differentiation between two varieties in genus sinensis assamica (CSA) and sinensis (CSS), our phenotypic clustering revealed incomplete congruence with phylogenetic relationships, suggesting the presence of additional genetic or environmental modulators beyond population divergence. Furthermore, we integrated phenotypic data with whole-genome resequencing for multi-model genome-wide association studies (GWAS). Candidate genes associated with leaf architecture were involved in plant development (e.g., CsFAS2), cell division and elongation (e.g., CsFIP1), and cellular morphogenesis (e.g., CsRLK), whereas those associated with leaf color, regulated pigment accumulation (e.g., ABC transporters, CsMYB113). In conclusion, this study establishes a standardized computational framework validating automated image recognition for plant leaf phenomics. The end-to-end framework from high-throughput phenotyping to gene discovery provides critical genetic targets for tea breeding, demonstrating transformative potential in accelerating the genetic improvement of tea plants. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13007-026-01518-5.