Hyperspectral Reflectance-Based High Throughput Phenotyping to Assess Water-Use Efficiency in Cotton

Abstract

Cotton is a pivotal global commodity underscored by its economic value and widespread use. In the face of climate change, breeding resilient cultivars for variable environmental conditions becomes increasingly essential. However, the process of phenotyping, crucial to breeding programs, is often viewed as a bottleneck due to the inefficiency of traditional, low-throughput methods. To address this limitation, this study utilizes hyperspectral remote sensing, a promising tool for assessing crucial crop traits across forty cotton varieties. The results from this study demonstrated the effectiveness of four vegetation indices (VIs) in evaluating these varieties for water-use efficiency (WUE). The prediction accuracy for WUE through VIs such as the simple ratio water index (SRWI) and normalized difference water index (NDWI) was higher (up to R2 = 0.66), enabling better detection of phenotypic variations (p < 0.05) among the varieties compared to physiological-related traits (from R2 = 0.21 to R2 = 0.42), with high repeatability and a low RMSE. These VIs also showed high Pearson correlations with WUE (up to r = 0.81) and yield-related traits (up to r = 0.63). We also selected high-performing varieties based on the VIs, WUE, and fiber quality traits. This study demonstrated that the hyperspectral-based proximal sensing approach helps rapidly assess the in-season performance of varieties for imperative traits and aids in precise breeding decisions.

Code and data availability

The paper's hyperspectral reflectance and physiological WUE measurements are not publicly deposited: the Data Availability Statement says 'Data are available upon request from the corresponding authors.' The only supplement (Table S1) is a list of cultivar names, not phenotype data, images, or analysis code. No author-

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