Supercomputer-powered 3D imaging of root systems to help breeders develop climate-change adapted plants for farmers and ease pressure on the food supply
From:
University of Texas at Austin, Texas Advanced Computing Center
July 29, 2021 -- The shoots of plants
get all of the glory, with their fruit and flowers and visible structure. But
it's the portion that lies below the soil -- the branching, reaching arms of
roots and hairs pulling up water and nutrients -- that interests plant physiologist
and computer scientist, Alexander Bucksch, associate professor of Plant Biology
at the University of Georgia.
The health and growth of the root system
has deep implications for our future.
Our ability to grow enough food to
support the population despite a changing climate, and to fix carbon from the
atmosphere in the soil are critical to our, and other species', survival. The
solutions, Bucksch believes, lie in the qualities of roots.
"When there is a problem in the
world, humans can move. But what does the plant do?" he asked. "It
says, 'Let's alter our genome to survive.' It evolves."
Until recently, farmers and plant
breeders didn't have a good way to gather information about the root system of
plants, or make decisions about the optimal seeds to grow deep roots.
In a paper published this month in Plant
Physiology, Bucksch and colleagues introduce DIRT/3D (Digital Imaging of
Root Traits), an image-based 3D root phenotyping platform that can measure 18
architecture traits from mature field-grown maize root crowns excavated using
the Shovelomics technique.
In their experiments, the system
reliably computed all traits, including the distance between whorls and the
number, angles, and diameters of nodal roots for 12 contrasting maize genotypes
with 84 percent agreement with manual measurements. The research is supported
by the ROOTS program of the Advanced Research Projects Agency-Energy (ARPA-E)
and a CAREER award from National Science Foundation (NSF).
"This technology will make it
easier to analyze and understand what roots are doing in real field
environments, and therefore will make it easier to breed future crops to meet
human needs " said Jonathan Lynch, Distinguished Professor of Plant
Science and co-author, whose research focuses on understanding the basis of
plant adaptation to drought and low soil fertility.
DIRT/3D uses a motorized camera set-up
that takes 2,000 images per root from every perspective. It uses a cluster of
10 Raspberry Pi micro-computers to synchronize the image capture from 10 cameras
and then transfers the data to the CyVerse Data Store -- the national
cyberinfrastructure for academic researchers -- for 3D reconstruction.
The system generates a 3D point cloud
that represents every root node and whorl -- "a digital twin of the root
system," according to Bucksch, that can be studied, stored, and compared.
The data collection takes only a few
minutes, which is comparable to an MRI or X-Ray machine. But the rig only costs
a few thousand dollars to build, as opposed to half a million, making the
technology scalable to perform high-throughput measurements of thousands of
specimens, which is needed to develop new crop plants for farmers. Yet, the 3D
scanner is also enabling basic science and addresses the problem of
pre-selection bias because of sample limitations in plant biology.
"Biologists primarily look at the
one root structure that is most common -- what we call the dominant root
phenotype," Bucksch explained. "But people forgot about all of the
other phenotypes. They might have a function and a role to fulfill. But we just
call it noise," Bucksch said. "Our system will look into that noise
in 3D and see what functions these roots might have."
Individuals who use DIRT/3D to image
roots will soon be able to upload their data to a service called PlantIT that
can perform the same analyses that Bucksch and his collaborators describe in
their recent paper, providing information on a wide range of traits from young
nodal root length to root system eccentricity. This data lets researchers and
breeders compare the root systems of plants from the same or different seeds.
The framework is made possible by
massive number-crunching capabilities behind the scenes. These are provided by
the Texas Advanced Computing Center (TACC) which receives massive amounts of
data from the CyVerse Cyberinfrastructure for computing.
Though it takes only five minutes to
image a root crown, the data processing to create the point cloud and quantify
the features takes several hours and requires many processors computing in
parallel. Bucksch uses the NSF-funded Stampede2 supercomputer at TACC through
an allocation from the Extreme Science and Engineering Discovery Environment
(XSEDE) to enable his research and power the public DIRT/2D and DIRT/3D
servers.
DIRT/3D is an evolution on a previous 2D
version of the software that can derive information about roots using only a
mobile phone camera. Since it launched in 2016, DIRT/2D has proven to be a
useful tool for the field. Hundreds of plant scientists worldwide use it, including
researchers at leading agribusinesses.
The project is part of ARPA-E's ROOTS
program, which is working to develop new technologies that increase carbon
storage within the soil and root systems of plants.
"The DIRT/3D platform enables
researchers to identify novel root traits in crops, and breed plants with
deeper, more extensive roots," said ARPA-E ROOTS Program Director Dr.
David Babson. "The development of these kind of technologies will help
promote climate change mitigation and resilience while also giving farmers the
tools to lower costs and increase crop productivity. We're excited to see the
progress that the team at PSU and UGA has made over the course of their
award."
The tool has led to the discovery of
several genes responsible for root traits. Bucksch cites a recent study
of Striga hermanthica resistance in sorghum as the kind of
outcome he hopes for users of DIRT/3D. Striga, a parasitic weed, regularly
destroys sorghum harvests in huge areas of Africa.
The lead researcher, Dorota Kawa, a post-doc
at UC Davis, found that there are some forms of sorghum with Striga-resistant
roots. She derived traits from these roots using DIRT/2D, and then mapped the
traits to genes that regulate the release of chemicals in the roots that
triggers Striga germination in plants.
DIRT3D improves the quality of the root
characterizations done with DIRT/2D and captures features that are only
accessible when scanned in 3D.
The challenges facing farmers are
expected to rise in coming years, with more draughts, higher temperatures,
low-soil fertility, and the need to grow food in less greenhouse-gas producing
ways. Roots that are adapted to these future conditions will help ease pressure
on the food supply.
"The potential, with DIRT/3D, is
helping us live on a hotter planet and managing to have enough food,"
Bucksch said. "That is always the elephant in the room. There could be a
point where this planet can't produce enough food for everybody anymore, and I
hope we, as a science community, can avoid this point by developing better
drought adapted and CO2 sequestering plants."
https://www.sciencedaily.com/releases/2021/07/210729143426.htm
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