Two genetic pathways that lead to ‘weedy rice’ identified by researchers

Weedy rice, commonly referred to as red rice, is a costly problem that impacts producers in Arkansas each growing season. Weeds reduce grain quality and impact yield which can lead to millions of dollars of lost revenue each growing season.

Scientists may have now made headway in determining why some varieties of rice are more herbicide-resistant than others which leads to more weeds. Researchers in Arkansas and Missouri have confirmed two genetic pathways that lead to herbicide resistance in weedy rice.

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 rice developed the resistance independently due to continuous use of specific herbicides.

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 U.S. 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.

Arkansas produces about half the nation’s rice. But this year’s crop is projected to be down from recent years due to input cost hikes and other factors. Planted acreage this growing season topped 1.11 million acres, according to the U.S. Department of Agriculture’s National Agricultural Statistical Service (NASS).

All rice production for the state is forecast at 81.2 million hundredweight, down 5% from the August forecast and down 11% from last year’s production of 91.1 million hundredweight, NASS reported. The all-rice yield for 2022 is forecast at 7,500 pounds per acre, down 50 pounds from August and down 130 pounds from last year.

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 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 relative.

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 rice.

Burgos collaborated with Washington University Ph.D. student Marshall Wedger, now a postdoctoral 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 herbicide pressure.”

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 rice.

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 pests.

“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.