Abstract
BackgroundGrass stalks architecturally support leaves and reproductive structures, functionally support the transport of water and nutrients, and are harvested for multiple agricultural uses. Research on these basic and applied aspects of grass stalks would benefit from improved capabilities for measuring internal anatomical features. In particular, methods suitable for phenotyping populations of plants are needed.ResultsTo meet the need for large-scale measurements of stalk anatomy features, we developed custom image processing software that utilized a variety of global thresholding, local filtering, and feature detection methods to measure rind thickness, pith area, vascular bundle counts, and individual vascular bundle size from digital images of hand-cut transections of stalks collected with a flatbed document scanner. The tool determined vascular bundle number with an average accuracy of 90% across maize genotypes that varied five-fold for this trait. The method is demonstrated on maize, sorghum, and Miscanthus stalks. The computer source code is staged for download.ConclusionsSimplicity of sample preparation and semi-automated analyses enabled by this tool greatly increase measurement throughput relative to standard microscopy-based techniques while maintaining high accuracy. The tool is expected to be useful in genetic and physiological studies of the relationships between stalk anatomy and traits such as biofuel suitability, water use efficiency, or nutrient transport.
Highlights
The stalks of widely cultivated grass species such as maize and sorghum support multiple architectural and physiological functions, while contributing the most to aerial non-grain biomass
The goal of the present work was to create an image analysis tool that could operate on images of hand-cut stem transections obtained on a flatbed scanner to measure anatomical features in high throughput
The tool to be described here operates on such images to measure stalk diameter, rind thickness, number of vascular bundles, density of vascular bundles, and vascular bundle size from such images
Summary
The stalks of widely cultivated grass species such as maize and sorghum support multiple architectural and physiological functions, while contributing the most to aerial non-grain biomass. Visible in transections of such stalks are the many vascular bundles scattered throughout the parenchymatous pith. Surrounding the pith is a layer rich in collenchyma that is usually visibly distinct and commonly called the rind. Water movement through the plant may relate to the number and size of xylem-bearing vascular bundles. Grass stalks architecturally support leaves and reproductive structures, functionally support the transport of water and nutrients, and are harvested for multiple agricultural uses. Research on these basic and applied aspects of grass stalks would benefit from improved capabilities for measuring internal anatomical features. Methods suitable for phenotyping populations of plants are needed
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