Soybean iron deficiency chlorosis high throughput phenotyping using an unmanned aircraft system

Abstract

Background: Iron deficiency chlorosis (IDC) is an abiotic stress in soybean [Glycine max (L.) Merr.] that causes significant yield reductions. Symptoms of IDC include interveinal chlorosis and stunting of the plant. While there are management practices that can overcome these drastic yield losses, the preferred way to manage IDC is growing tolerant soybean varieties. To develop varieties tolerant to IDC, breeders may easily phenotype up to thousands of candidate soybean lines every year for severity of symptoms related to IDC, a task traditionally done with a 1-5 visual rating scale. The visual rating scale is subjective and, because it is time consuming and laborious, can typically only be accomplished once or twice during a growing season.

Results: The goal of this study was to use an unmanned aircraft system (UAS) to improve field screening for tolerance to soybean IDC. During the summer of 2017, 3386 plots were visually scored for IDC stress on two different dates. In addition, images were captured with a DJI Inspire 1 platform equipped with a modified dual camera system which simultaneously captures digital red, green, blue images as well as red, green, near infrared (NIR) images. A pipeline was created for image capture, orthomosaic generation, processing, and analysis. Plant and soil classification was achieved using unsupervised classification resulting in 95% overall classification accuracy. Within the plant classified canopy, the green, yellow, and brown plant pixels were classified and used as features for random forest and neural network models. Overall, the random forest and neural network models achieved similar misclassification rates and classification accuracy, which ranged from 68 to 77% across rating dates. All 36 trials in the field were analyzed using a linear model for both visual score and UAS predicted values on both dates. In 32 of the 36 tests on date 1 and 33 of 36 trials on date 2, the LSD associated with UAS image-based IDC scores was lower than the LSD associated with visual scores, indicating the image-based scores provided more precise measurements of IDC severity.

Conclusions: Overall, the UAS was able to capture differences in IDC stress and may be used for evaluations of candidate breeding lines in a soybean breeding program. This system was both more efficient and precise than traditional scoring methods.

Keywords: Image analysis; Iron deficiency chlorosis; Neural network; Random forest; Remote sensing; Soybean; Unmanned aircraft system (UAS).

Fig. 1

Soybean iron deficiency chlorosis testing field site location near Danvers, MN. The field used in this study is located in Six Grove Township, MN (45.274285, − 95.718046) in Swift County. The yellow circles highlight the nine ground control points in the field for geometric calibration and the red squares highlight the radiometric calibration panels. These panels were painted with four levels of grey for empirical line method calibration. Overlaid to the field orthomosaic is a vector file delineating the plot boundaries of 3386 soybean plots. Each plot boundary is colored based on the trial each plot belongs to. A total of 36 trials was grown

Fig. 2

Relationships between two dates of iron deficiency chlorosis (IDC) severity (a) and two separate raters scoring plots (b). IDC severity was measured on a total of 3386 plots on both July 12 and August 01. The correlation of ratings between date 1 and date 2 was found to be 0.80. A subset of 252 plots were measured by two independent raters on date 1. The correlation of ratings between raters was found to be 0.93

Fig. 3

Iron deficiency chlorosis classification. The Orthomosaic (top) is first classified into plant and soil pixels (bottom left). The plant pixels are then classified in a second step to green pixels (%G), yellow pixels (%Y), and brown pixels (%B) (bottom right). These features are then related back to ground-based visual scores through random forest and neural network models to classify tolerant and susceptible plots

Fig. 4

A total of 36 trials consisting of soybean breeding lines, each arranged in a randomized complete block design in the field, were analyzed using a linear model for both visual score and unmanned aircraft system (UAS) predicted values on both dates (July 12 and August 01). Bars indicate the least significant difference (LSD) values to separate mean scores of breeding lines for each trial in the field. In 31 of the 36 trials on date 1 (top) and 33 of 36 trials on date 2 (bottom), the LSD was decreased when using the UAS predicted IDC scores (black inside bars in the linear model compared to the visual scores (dashed outside bars)