High‐throughput phenotyping for the prediction and quantification of flower‐related traits in sugarcane

Abstract Sugarcane ( Saccharum spp.), a C4 plant, is a vital renewable biofuel and sugar source for industries worldwide. However, synchronizing flowering between parental lines often poses challenges for breeders, hindering effective crossbreeding efforts. This study aimed to develop a high‐throughput phenotyping (HTP) strategy to evaluate flowering‐related traits using vegetation indices (VIs) and other metrics alongside artificial intelligence (AI)‐based prediction methods. A total of 154 genotypes were planted in an augmented block design at the IAC sugarcane breeding station in Serra Grande‐BA, Brazil. Raw RGB (Red, Green, Blue) images were captured using a DJI Mavic 3 Enterprise drone during the plant cane (PC) and first ratoon (FR) crop seasons. These images were processed to create orthomosaics and compute metrics/vegetation index; subsequently, machine learning (ML) and deep learning pipelines for systematic analysis were developed. A convolutional neural network (CNN) model achieved promising results, with an accuracy rate of up to 84% in the flowering detection task. Additionally, flower counts from the CNN model showed a moderate correlation with field data, evidenced by an R 2 value of 0.72 at the onset and an R 2 value of 0.29 at the conclusion of the flowering season for the PC. This resulted in an overall average regression R 2 of 0.46 with a root mean square error (RMSE) of 13.80. Furthermore, an artificial neural network classification model reached a notable accuracy of 0.87 in differentiating genotypes based on their flowering response (early‐flowering vs. late‐flowering), utilizing VIs and digital model‐based metrics as input parameters. The ML regression model demonstrated performance levels of R 2 = 0.51 and RMSE = 8.06 for days to flag leaf emergence in PC and R 2 = 0.52 and RMSE = 7.93 for days to flowering in FR. These results highlight the potential of HTP strategies, utilizing orthomosaics and AI, to accelerate data collection and analysis, offering significant insights for breeding programs in sugarcane.