Sewing the future of cotton: An integrated omics study combining nanomechanics, transcriptomics, and phenotypic traits

Cellulose microfibrils in plant cell walls are essential for mechanical strength and overall quality of cotton fibers. This study quantified and compared the nano-omics : nanoscale structural, and mechanical properties of cellulose microfibrils such as microfibril dimensions, crossover count and angles, roughness, and Young’s modulus for two popular cotton species: Gossypium hirsutum (Gh) and Gossypium barbadense (Gb) fibers across four stages of growth (8, 12, 18, and 22 days post-anthesis) using atomic force microscopy (AFM). Our results revealed that Gb fibers exhibited better alignment, finer surface, and higher stiffness compared to Gh fibers at the nanoscale, resulting in smoother fiber surfaces and improved quality at the macroscale. We have also developed an integrative machine learning (ML) framework combining nanoscale AFM-derived features with gene expression data to model variation in key fiber traits. This framework was used to compare feature modalities and assess their relative contributions across developmental stages. To further characterize feature importance, we applied Shapley Additive exPlanations (SHAP), which highlighted nanoscale and transcriptomic variables associated with model behavior at different growth stages. Overall, this study demonstrates that nanoscale mechanical properties provide complementary information to transcriptomics and establishes a framework for integrating nanoscale and molecular features to generate mechanistic hypotheses linking gene expression to cotton fiber structure and quality.