RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping.

Anand Seethepalli,Felix B Fritschi,Alina Zare,Marcus Griffiths,Shuyu Liu,Hussien Almtarfi,Larry M York,Xue-Feng Ma,Zenglu Li,Xiuwei Liu,Haichao Guo,Elison B Blancaflor

doi:10.34133/2020/3074916

Abstract

Root crown phenotyping measures the top portion of crop root systems and can be used for marker-assisted breeding, genetic mapping, and understanding how roots influence soil resource acquisition. Several imaging protocols and image analysis programs exist, but they are not optimized for high-throughput, repeatable, and robust root crown phenotyping. The RhizoVision Crown platform integrates an imaging unit, image capture software, and image analysis software that are optimized for reliable extraction of measurements from large numbers of root crowns. The hardware platform utilizes a backlight and a monochrome machine vision camera to capture root crown silhouettes. The RhizoVision Imager and RhizoVision Analyzer are free, open-source software that streamline image capture and image analysis with intuitive graphical user interfaces. The RhizoVision Analyzer was physically validated using copper wire, and features were extensively validated using 10,464 ground-truth simulated images of dicot and monocot root systems. This platform was then used to phenotype soybean and wheat root crowns. A total of 2,799 soybean (Glycine max) root crowns of 187 lines and 1,753 wheat (Triticum aestivum) root crowns of 186 lines were phenotyped. Principal component analysis indicated similar correlations among features in both species. The maximum heritability was 0.74 in soybean and 0.22 in wheat, indicating that differences in species and populations need to be considered. The integrated RhizoVision Crown platform facilitates high-throughput phenotyping of crop root crowns and sets a standard by which open plant phenotyping platforms can be benchmarked.

Highlights

Roots serve as the interface between the plant and the complex soil environment with key functions of water and nutrient extraction from soils [1, 2]
In order to account for the three-dimensional shape of root crowns, small aperature settings with deeper depths of field are recommended
In order to ensure that the correct physical units can be determined by the integrated platform, copper wires of known diameters ranging from 0.20 to 2.57 mm were imaged with the RhizoVision Crown hardware, and the correct pixels per mm conversion factor was supplied to the Analyzer for analysis

Summary

Introduction

Roots serve as the interface between the plant and the complex soil environment with key functions of water and nutrient extraction from soils [1, 2]. Root system architecture (RSA) refers to the shape and spatial arrangement of root systems within the soil, which plays an important role in plant fitness, crop performance, and agricultural productivity [1, 3, 4]. RSA is shaped by the interactions between genetic and environmental components and influences the total volume of soil that roots can explore [3]. Understanding the contribution of RSA phenes to crop performance is of key importance in food security and for breeding of more productive and resilient varieties in a changing environment. Because roots are hidden underground and require considerable effort to characterize, research on plant roots lags behind that of the aboveground organs [8], and the genetic and functional basis of RSA remains obscured [9].

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