UAV-based time series phenotyping reveals the genetic basis of plant height in upland cotton.

Plant height (PH) is an important agronomic trait affecting crop architecture, biomass, resistance to lodging and mechanical harvesting. Elucidation of the genetic control of plant height is crucial due to the global demand for high crop yields. However, PH largely varies daily during rapid growth period of plants, which makes it difficult to accurately phenotype the trait by hand on large scale. In this study, an unmanned aerial vehicle (UAV)-based remote sensing phenotyping platform was applied to obtain time series PHs of 320 upland cotton accessions in three different field trials. The results showed the extracted PH based on UAV images were significantly correlated with that of the ground-based manual measurement at three trials (R 2 = 0.96, 0.95 and 0.96). Two genetic loci on chromosomes A01 and A11 associated with PH were identified by genome-wide association studies (GWAS). GhUBP15 and GhCUL1 were identified to regulate PH by further analysis. We obtained the time series of PH values in three field conditions based on UAV. The key genes identified in this study are of great value for the breeding of ideal plant architecture in cotton.