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Oct. 5, 2022
By Fred MillerU of A System Division of Agriculture@AgNews479
Related PHOTOS: https://flic.kr/s/aHsmX89coX
FAYETTEVILLE, Ark. — Researchers in Arkansas and Missouri have confirmed two genetic
pathways that lead to herbicide resistance in weedy rice, a major pest for Arkansas
Most herbicide-resistant weedy rice in Arkansas inherited the trait via gene flow
from herbicide-tolerant cultivated rice varieties, said Nilda Burgos, professor of
weed physiology and molecular biology for the Arkansas Agricultural Experiment Station.
But some weedy ride developed the resistance independently because of continuous use
of specific herbicides.
Burgos said this is important information for farmers who use weedy rice herbicides
to control the pest in other crops when they are in rotation with rice
The Agricultural Experiment Station is the research arm of the University of Arkansas
System Division of Agriculture.
Weedy rice is a major problem in Arkansas, which produces nearly half the rice grown
in the United States. In 2020, rice contributed more than $1.1 billion to the state’s
agricultural economy, according to the 2022 Agricultural Profile published by the
Division of Agriculture. It is available online: https://bit.ly/AgProfile2022.
Weedy rice infestations cause an estimated $45 million in economic losses in the U.S.
each year from yield losses and reduced grain quality, according to a research paper
co-authored by Burgos and her collaborators at Washington University. Losses amount
to hundreds of millions of dollars worldwide.
Weedy rice, once commonly called red rice, is the same species as cultivated rice,
Burgos said. Because they are so closely related, the cultivated and weedy plants
can cross pollinate in the field, an action called “outcrossing.” By this action,
also known as gene flow, weedy rice can obtain genetic traits from its more civilized
One of the changes gene flow made to the weed is that red rice is no longer always
red nor always medium grain, hence its new moniker.
The potential for outcrossing raised concern for the development of herbicide resistance
in fields commonly planted with imidazolinone herbicide-tolerant rice varieties, Burgos
said. Known as Clearfield™ varieties, they allow farmers to plant their fields and
then apply herbicides to kill weedy rice and other weeds without harming their crops.
Imidazolinone herbicides are commonly called ALS herbicides because they kill weeds
by inhibiting acetolactate synthase, a key enzyme in plant growth.
Burgos identified ALS herbicide-resistant weedy rice in some Arkansas fields at least
20 years ago, about the same year Clearfield™ technology was introduced. Those resistant
weeds were collected from a field that had never before been planted with Clearfield
Burgos collaborated with Washington University Ph.D. student Marshall Wedger, now
a post-doctoral researcher there, and his graduate advisor, Kenneth Olsen, professor
of biology, to identify the pathway to resistance for weedy rice in Arkansas. The
question they wanted to answer was whether the resistant weeds Burgos identified in
Arkansas fields resulted from outcrossing or from evolutionary pressure caused by
constant herbicide applications.
Wedger is the lead author of a research paper co-authored by Burgos and Olsen about
their findings. It has been published in the Nature online journal Communications Biology.
While a Ph.D. student, Wedger received a Graduate Fellowship Grant from the National
Science Foundation to investigate the genetic mechanisms of resistance in weedy rice.
He came to Arkansas and Burgos helped him collect seed samples from six Arkansas farms
where she had identified ALS resistance in weedy rice.
Burgos grew the seed and tested the plants for ALS resistance. She identified the
resistant weeds and scored their level of resistance. The same samples were shared
with Wedger at Washington University.
Wedger used whole-genome sequences of 48 weedy rice plants to show how herbicide resistance
evolved by gene flow from crop rice. Almost all other cases of herbicide resistance
in agricultural weeds result from selection of tolerant plants in the weed population.
Burgos said controlled crosses, using associated marker traits, and whole-genome sequencing
can also track which direction gene flow is occurring. “Research has shown that the
dominant gene flow is from the crop to the weed,” she said.
“In the past 20 years, weedy rice has gone from being very genetically distinct from
U.S. crop varieties to nowadays mostly being derived from crop-weed hybridization,”
Olsen said. “The weeds are grabbing certain traits from the crop that are beneficial
to them, including herbicide resistance.”
“As a de-domesticated weedy relative, weedy rice has always been able to outcross
with cultivated rice. Based on our results, this ability to interbreed is what led
to most of the herbicide resistance that we see today,” Wedger said.
Burgos said their findings confirm what she found in rice fields some 20 years ago.
“It’s like déjà vu. I’ve seen this before,” she said.
“Most of the resistance was determined to come from outcrossing with Clearfield™ rice,”
Burgos said. “But we discovered a low frequency of resistant weedy rice caused by
Wedger’s whole-genome sequencing was able to distinguish between resistant weedy rice
that resulted from outcrossing with cultivated rice from those that resulted from
another mechanism. Outcrossing resulted in other shared genetic mutations besides
the herbicide resistance, Burgos said. The absence of those secondary shared mutations
indicated when resistance came from herbicide pressure.
This type of herbicide pressure-induced resistance occurs when ALS herbicides are
used continuously on a field. Weedy rice that is not killed by the regular applications
spreads its seed, producing more weeds that can tolerate the herbicide applications.
The process continues until there is a stable population of herbicide-resistant weedy
Burgos said the unintentional development of herbicide-resistant weedy rice by herbicide
pressure resulted in the same mutation occurring in the weeds that gives Clearfield™
rice its resistance. However, other genetic mutations found in Clearfield™ rice were
not shared in those weedy rice plants, indicating they did not result from outcrossing.
“This means there are two pathways to the mutation that results in ALS herbicide resistance,”
Burgos said. Intensive use of ALS herbicides to control weedy rice in other crops
used in rotation with rice could lead to resistance even when ALS-resistant Clearfield™
varieties are not planted in the rotation.
The report’s authors agree that adaptation of weedy rice to herbicide application
serves as an example of the dangers of relying on single methods of control for agricultural
“How quickly a resistant weedy rice population builds up to a point where the herbicide
is no longer useful depends on how the producer manages the herbicide-tolerant rice
technology,” Burgos said. “There are best management practices guidelines that help
growers avoid resistance evolution for a long time, if implemented.”
Avoiding a buildup of herbicide-resistant weedy rice begins with zero tolerance weed
management, Burgos said. “Don’t leave anything in your field. And don’t forget the
edges of the fields.”
Growers usually clean up their fields thoroughly, but some neglect the edges and ditches,
Burgos said. The following year, weedy rice sprouts up at the borders of rice fields
and spreads in from the edges.
Also, weedy rice seed that drops in water in the ditches gets carried to other areas
and can sprout up anywhere.
Rotating Clearfield™ rice with conventional varieties can also slow gene flow and
inhibit development of herbicide-resistant weeds, Burgos said. Rotate rice with other
crops, like soybeans, and the different weed control strategies used with those plants
can help keep rice fields clean. She also advises rotating weed control strategies.
“Make sure, whatever you use, you leave no weedy rice in the field,” Burgos said.
To learn more about Division of Agriculture research, visit the Arkansas Agricultural
Experiment Station website: https://aaes.uada.edu/. Follow us on Twitter at @ArkAgResearch and on Instagram at @ArkAgResearch. To learn more about the Division of Agriculture,
visit https://uada.edu/. Follow us on Twitter at @AgInArk.
About the Division of Agriculture
The University of Arkansas System Division of Agriculture’s mission is to strengthen
agriculture, communities, and families by connecting trusted research to the adoption
of best practices. Through the Agricultural Experiment Station and the Cooperative
Extension Service, the Division of Agriculture conducts research and extension work
within the nation’s historic land grant education system.
The Division of Agriculture is one of 20 entities within the University of Arkansas
System. It has offices in all 75 counties in Arkansas and faculty on five system campuses.
The University of Arkansas System Division of Agriculture offers all its Extension
and Research programs and services without regard to race, color, sex, gender identity,
sexual orientation, national origin, religion, age, disability, marital or veteran
status, genetic information, or any other legally protected status, and is an Affirmative
Action/Equal Opportunity Employer.
Media Contact: Fred MillerU of A System Division of AgricultureArkansas Agricultural Experiment Station(479) email@example.com