Time-Related Mapping of Quantitative Trait Loci Controlling Developmental and Physiological Traits in Cotton.

The long-term sustainability of the U.S. Southwest cotton industry is at risk from global climate change and heightened competition for scarce water resources. The development of high-throughput tools to phenotype developmental and physiological traits that dynamically vary over time under field conditions creates the possibility to more efficiently breed superior cotton cultivars that are resilient to environmental stress. In this light, we developed and evaluated a novel, tractor-based phenotyping system that deployed sets of sensors to simultaneously measure canopy height, reflectance, and temperature on a cotton recombinant inbred mapping population. The population was evaluated under managed well-watered and water-limited conditions in a replicated field trial in a hot, arid environment. Measurements were taken at different times on multiple days to monitor the extent to which these traits changed throughout plant development and prolonged exposure to environmental stress. Canopy height, normalized difference vegetation index, and temperature were found to be moderately to highly heritable and showed expected interactions of genotype with water regime and time of day. Through a quantitative trait loci (QTL) analysis of these traits on a time axis, identified QTL were shown to have an expression pattern that varied by water regime, developmental stage, and time of day. Taken together, these results indicate that the phenotyping system enables the repeated, heritable measurement of multiple traits throughout the growing season, facilitating the identification of differentially expressed QTL for stress-responsive traits.