Improved imaging technology advances the way we measure traits in crop species – sciencedaily

The measurement of plant phenotypes, a term used to describe the observable characteristics of an organism, is an essential aspect of studying and improving economically important crops. Phenotypes central to the breeding process include characteristics such as the number of kernels in corn, the size of seeds in wheat, or the color of fruit in grapes. These characteristics are visible to the naked eye, but are actually induced by microscopic molecular and cellular processes in the plant. Three-dimensional (3D) imaging is a recent innovation in plant biology to capture phenotypes at the scale of the “whole plant”: from tiny cells and organelles from roots, to leaves and flowers. However, current 3D imaging processes are limited by the tedious preparation of samples and the depth of imaging, typically reaching only a few layers of cells in plant tissue. New research led by Christopher Topp, PhD, associate member at Donald Danforth Plant Science Center, and Keith Duncan, researcher in his lab, pioneered x-ray microscope technology to image plant cells, whole tissues and even organs at unprecedented speed. depths with cellular resolution. The work, supported by Valent BioSciences LLC and Sumitomo Chemical Corporation, was recently published in the scientific journal Plant Physiology, titled X-ray microscopy enables high-resolution multi-scale 3D imaging of plant cells, tissues and organs. This work will enable plant scientists around the world to study aerial and subterranean features with revolutionary clarity.

“This article focuses on multiscale,” says corresponding author Chris Topp, “because plants are multiscale. A corn cob begins as a microscopic group of cells called a meristem. form all visible parts of the corn plant through division and growth. Their improved 3D X-ray microscopy (XRM) technology allows researchers to relate the plant’s developmental microstructure, such as meristemic cells, to traits visible as they mature, for example leaves and flowers.In other words, 3D XRM provides resolution at the cellular level of whole plant organs and tissues.

In addition, their XRM methodology can also image underground structures at exceptional resolution, including roots, fungi and other microbes. “The roots of plants are responsible for many important biological processes; they feed the microbes in the soil and, in return, the plants receive phosphorus and nitrogen, ”Topp explains. “We know that the interaction between roots and microbes is important because it was the main source of phosphorus and nitrogen before chemical fertilizers were invented.” Our reliance on chemical fertilizers in standard farming practices has, in turn, made major contributions to global climate change. “Half of all biologically available nitrogen has been made in a factory over the past 100 years,” Topp continues. “It is estimated that this process uses 3% of all available energy and generates 3% of greenhouse gas emissions on planet Earth each year. Therefore, a critical part of the sustainable agriculture movement is reducing chemical inputs and fostering natural interactions between roots and underground microbes. “We didn’t have the tools to understand these interactions until recently,” says Topp. “3D XRM can help unlock the potential to reestablish these natural alliances in our farming systems. “

The 3D XRM methodology is unique from other imaging approaches in plant biology because of its ability to produce essentially perfect 3D clarity of plant structure. Other common methods, such as photon-based tomography, are limited by shallow imaging depths and are optimized for a few selected plant species. In contrast, using 3D XRM, the team led by Topp and Duncan are able to image “thick tissues that are recalcitrant to typical optical methods”, in a multitude of economically important crops, including corn, foxtail millet. , soybeans, teff, and grapes. “This article is the first of its kind to show the extent of what XRM 3D can do,” notes Topp.

A major goal of the article is to establish a reproducible protocol for other plant scientists interested in 3D XRM imaging. To achieve this, lead author Keith Duncan has spent a lot of time – and trial and error – preparing samples to optimize the contrast between the plant and its background. X-ray imaging works by differential absorption, where dense material (like minerals in the soil) absorbs more X-rays and appears darker in an image. However, biological material like plant tissue has poor X-ray absorption, and the team was in danger of completely eliminating the material they were interested in imaging. “Solving this problem for one type of sample – like a root tip – is one thing,” says Topp, “but the idea of ​​the article was to give plant scientists working on a variety of tissues and relevant plant species access to these methods. We want to apply 3D XRM widely to both above and below ground plant systems. “As such, their published methodologies dramatically advance the number of plant species. and the types of plant tissue that can be imaged at near perfect resolution.

Keith Duncan continues to lead Topp Lab’s partnership with Valent Biosciences and Sumitomo Chemical, focusing on enhancing 3D XRM capabilities. He often collaborates with Kirk Czymmek, PhD, director of the Advanced Bioimaging Laboratory at the Danforth Center, who was also the author of the article.

The next step on the horizon is to image the 3D structures of fungal networks in the soil. Part of this work includes improving machine learning approaches, so that a computer is trained to recognize what in an image is a root, soil, or spore (the reproductive cells of a fungus). Their work will continue to develop new technological approaches to improve our multi-scale understanding of the “whole plant”, from the microscopic to the visible.

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