missouri

Plant biologists welcome their robot overlords

Thursday, February 16, 2017

Old-school areas of plant biology are getting tech upgrades that herald more detailed, faster data collection.

by Heidi Ledford

25 January 2017
 
A robot measures the crops in an agricultural field near Columbia, Missouri (credit: DeSouza/Fritschi/Shafiekhani/Suhas/University of Missouri)
 
As a postdoc, plant biologist Christopher Topp was not satisfied with the usual way of studying root development: growing plants on agar dishes and placing them on flatbed scanners to measure root lengths and angles. Instead, he would periodically stuff his car with plants in pots dripping with water and drive more than 600 kilometres from North Carolina to Georgia to image his specimens in 3D, using an X-ray machine in a physics lab.
 

Five years later, the idea of using detailed imaging to study plant form and function has caught on. The use of drones and robots is also on the rise as researchers pursue the ‘quantified plant’ — one in which each trait has been carefully and precisely measured from nearly every angle, from the length of its root hairs to the volatile chemicals it emits under duress. Such traits are known as an organism’s phenotype, and researchers are looking for faster and more comprehensive ways of characterizing it.

From 10 to 14 February, scientists will gather in Tucson, Arizona, to compare their methods. Some will describe drones that buzz over research plots armed with hi-tech cameras; others will discuss robots that lumber through fields bearing equipment to log each plant’s growth.

The hope is that such efforts will speed up plant breeding and basic research, uncovering new aspects of plant physiology that can determine whether a plant will thrive in the field. “Phenotype is infinite,” says Topp, who now works at the Donald Danforth Plant Science Center in St Louis, Missouri. “The best we can do is capture an aspect of it — and we want to capture the most comprehensive aspect we can.”

The plummeting cost of DNA sequencing has made it much easier to find genes, but working out what they do remains a challenge, says plant biologist Ulrich Schurr of the Jülich Research Centre in Germany. “It is very easy now to sequence a lot of stuff,” he says. “But what was not developed with the same kind of speed was the analysis of the structure and function of plants.”

Plant breeders are also looking beyond the traits they used to focus on — such as yield and plant height — for faster ways to improve crops. “Those traits are useful but not enough,” says Gustavo Lobos, an ecophysiologist at the University of Talca in Chile. “To cope with what is happening with climate change and food security, some breeders want to be more efficient.” Researchers aiming to boost drought tolerance, for example, might look at detailed features of a plant’s root system, or at the arrangement of its leaves.

False-colour images of a bean-breeding trial captured by a camera mounted on a drone (credit: Lav R. Khot/Washington State University & Phillip N Miklas/USDA-ARS)

A need for speed

The needs of these researchers have bred an expanding crop of phenotyping facilities and projects. In 2015, the US Department of Energy announced a US$34-million project to generate the robotics, sensors and methods needed to characterize sorghum, a biofuel crop. Last year, the European Union launched a project to create a pan-European network of phenotyping facilities. And academic networks have sprung up around the globe as plant researchers attempt to standardize approaches and data analyses.

Large-scale phenotyping has long been used in industry, but was too expensive for academic researchers, says Fiona Goggin, who studies plant–insect interactions at the University of Arkansas in Fayetteville. Now, the falling prices of cameras and drones, as well as the rise of the ‘maker’ movement that focuses on homemade apparatus, are enticing more academics to enter the field, she says.

At Washington State University in Pullman, biological engineer Sindhuja Sankaran’s lab is preparing to deploy drones carrying lidar, the laser equivalent of radar. The system will scan agricultural fields to gather data on plant height and the density of leaves and branches. Sankaran also uses sensors to measure the volatile chemicals that plants give off, particularly when they are under attack from insects or disease. She hopes eventually to mount the sensors on robots.

A drone loaded with thermal imaging equipment flies over grapevines (credit: Lav R. Khot/Washington State University)

Sankaran’s mechanical minions return from their field season with hundreds of gigabytes of raw data, and analysing the results keeps her team glued to computers for the better part of a year, she says. Many researchers do not realize the effort and computing savvy it takes to pick through piles of such data, says Edgar Spalding, a plant biologist at the University of Wisconsin–Madison. “The pheno­typing community has rushed off to collect data and the computing is an afterthought.”

Standardizing the technology is another barrier, says Nathan Springer, a geneticist at the University of Minnesota in St Paul. The lack of equipment everyone can use means that some researchers have to rely on slower data-collection methods. Springer has been working with 45 research groups to characterize 1,000 varieties of maize (corn) grown in 20 different environments across the United States and Canada. The project has relied heavily on hand measurements rather than on drones and robots, he says.

Topp now has his own machine to collect computed tomography (CT) images, but processing samples is still a little slow for his liking. He speaks with reverence of a facility at the University of Nottingham, UK, that speeds up its scans by using robots to feed the plants through the CT machine. But he’s pleased that he no longer has to haul his soggy cargo across three states to take measurements. “It’s just endless, the number of possibilities.”

Nature 541, 445–446 (26 January 2017) | doi:10.1038/541445a

NASA-Missouri Space Grant Consortium 2017 Associates Award Competition

Event date(s): Monday, June 19, 2017


Announcement

Important Dates

Solicitation: May 1, 2017
Proposals Due: June 19, 2017
Anticipated Period of Performance: July 10, 2017 - April 30, 2018
 

Introduction

The NASA Missouri Space Grant Office is accepting proposals to extend the Consortium’s capabilities and enhance collaborations with Missouri academic institutions that are not permanent members. The Office expects to award a total of approximately $69,000 under this solicitation for proposals with anticipated funding levels ranging from $7,500 to $15,000 per proposal. This call is dependent upon availability of FY 2017 funds. Proposals for lesser amounts will be considered. Note that, excluding fellowships and scholarships, a one-to-one cost share match is required for all funds awarded as a result of this solicitation. The Missouri Space Grant Office reserves the right to partially fund proposals if deemed appropriate.
The main mission of the Consortium is to maintain and enhance, through the State's research universities and corporate partners, the Nation’s workforce capabilities in aerospace and space related science, engineering, and technology; and to aid in the dissemination of NASA related information to students, faculty, researchers, and the general public. The primary goal of the Consortium is to inspire, motivate, recruit, educate, and train students to be competent researchers at all academic levels in order to help meet Missouri’s and NASA’s need for skilled, knowledgeable, diverse, and high-performing professional scientists, engineers, technologists, and educators specializing in the fields of interest to NASA.
 

Eligibility

Eligibility is limited to accredited academic institutions and informal education providers in Missouri that are not permanent Affiliates of the Consortium.
 

Missouri Transect Webinar - Jeff Hargrove (Community Team)

Event date(s): Tuesday, November 29, 2016


Join us on November 29 at noon for a presentation by Jeff Hargrove on the Missouri Transect Community Team. Jeff is an Extension Technician at Lincoln University and he will present on his work in Scott County to build capacity for more resilient communities. All Missouri Transect participants are encouraged to join this webinar and learn more about Jeff's contribution to the Community Team.

Meeting URL: https://meetings.webex.com/collabs/#/meetings/detail?uuid=M6AQ7Z7AY1FW2SGP2YN00TFNKS-1S1Z&rnd=840854.12705

MO DIRT Soil Health Survey Training: Forest Park, St. Louis, MO

Event date(s): Tuesday, September 27, 2016
Location: Dennis & Judith Jones Visitor and Education Center, 5595 Grand Drive in Forest Park, St. Louis, MO 63112


MO DIRT - Soil Health Survey Training for Master Naturalists - Sedalia

Event date(s): Saturday, September 17, 2016
Location: Sedalia, MO


MO DIRT will offer a soil health survey training to Missouri Master Naturalists during their statewide advanced training event "Where the Ozarks Meet the Prairies." For more information, visit the event page on the MO DIRT website.