Caicedo, Colleagues Probe Genomic Structure of Weedy Rice

Weedy rice, in the foreground, growing with cultivated rice. Photo by Ana Caicedo.
Weedy rice, in the foreground, growing with cultivated rice. Photo by Ana Caicedo.

In a new study of how weeds evolve, in particular weedy rice – one of the prime threats to rice production worldwide and in the United States – Ana Caicedo, biology, and colleagues elsewhere found that “relatively few genetic changes are required for the emergence of weediness traits.”

The authors report that “de-domestication” from ancestral cultivated plants has repeatedly played a major role in weedy rice evolution. However, the genetic processes that undermine cultivated characteristics in ancestor plants seem to occur easily. Caicedo is the co-corresponding author on the paper that appears this month in Nature Genetics.

She and colleagues state, “Crop domestication provided the calories that fueled the rise of civilization. For many crop species, domestication was accompanied by the evolution of weedy crop relatives, which aggressively outcompete crops and reduce harvests. Understanding the genetic mechanisms that underlie the evolution of weedy crop relatives is critical for agricultural weed management and food security.”

In the U.S., they add, weedy rice is estimated to be present in 30 percent of rice fields and leads to annual crop losses of over $50 million.

Caicedo says this research into the genomic structure of aggressive weedy rice strains could lead tonew ways of controlling weeds, which threaten a basic food staple relied upon by millions. Her research team included investigators at the Dale Bumpers National Rice Research Center in Arkansas, two Chinese institutions and Washington University, St. Louis, and was supported by a Plant Genome Research Program grant from the National Science Foundation.

Weedy rice is more aggressive than cultivated rice, with several undesirable characteristics, Caicedo says. For example, it ripens at widely different times instead of all at once like cultivated rice, and it disperses or scatters its seeds rather than retaining them on the plant until they can be harvested, a trait particularly difficult for farmers.

Once established, weedy rice is very hard to get rid of, as seeds can persist in the soil for years. Previous work had shown that weedy rice in the U.S. had multiple origins and likely descended from common cultivated rice groups, Caicedo notes, making it an ideal model for understanding the genetic changes by which evolution produces a weed from a domesticated ancestor.

She and colleagues sequenced the genomes of two U.S. weedy rice strains with different genetic backgrounds, 18 strawhull weeds and 20 blackhull weeds, and compared them to 145 previously published genomes of crop rice and wild varieties. Their analysis showed that the two weeds evolved from two different crop varieties at different stages in the domestication process, and, crucially, the genetic basis for weediness differs between the two strains.

Co-author Kenneth Olsen of Washington University says the findings show that rice has a tendency toward weediness, and that “the evolution of weedy crop relatives is an under-recognized part of the domestication process.”

Further, a shift toward mechanized production aids the weeds: When rice is planted by hand, planters study each seedling and discard the weedy ones, but mechanized, direct-seeded farming has eliminated this step, the authors point out.

Caicedo and colleagues conclude that “the apparent ease with which this aggressive agricultural weed can repeatedly evolve should sound a note of caution as global rice agriculture continues shifts toward the mechanized production practices that promote its persistence and proliferation.”