Skip to main content
ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #315701

Research Project: Using Genetic Approaches to Reduce Crop Losses in Rice Due to Biotic and Abiotic Stress

Location: Dale Bumpers National Rice Research Center

Title: More than one way to evolve a weed: parallel evolution of U.S. weedy rice through independent genetic mechanisms

Author
item QI, XINSHUAI - Washington University
item LIU, YAN - University Of Arkansas
item VIGUEIRA, CYNTHIA - High Point University
item YOUNG, NELSON - University Of Massachusetts
item CAICEDO, ANA - University Of Massachusetts
item Jia, Yulin
item Gealy, David
item OLSEN, KENNETH - Washington University

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/27/2015
Publication Date: 6/15/2015
Citation: Qi, X., Liu, Y., Vigueira, C., Young, N., Caicedo, A.L., Jia, Y., Gealy, D.R., Olsen, K.M. 2015. More than one way to evolve a weed: parallel evolution of U.S. weedy rice through independent genetic mechanisms. Molecular Ecology. 24:3329–3344. DOI: 10.1111/mec.13256.

Interpretive Summary: Weedy red rice, a variant of cultivated rice (Oryza sativa) is one of the most challenging agricultural weeds in rice production. It is known that genes have been lost in rice through its domestication from ancient wild species. Little is known regarding if weedy red rice has also gone through a genetic bottleneck. In the present study, we performed comparative quantitative trait loci (QTL) mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica rice variety and representatives of each of the two major weedy rice strains found in U.S. rice fields, strawhull (S) and blackhull awned (B). Candidate genes for some weediness traits (awn length and grain pigmentation) were identified within QTL mapped regions and were associated with single genes. However, for more complex quantitative traits (heading date, panicle length, seed shattering) we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Together these findings demonstrated that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in rice to allow agricultural weed evolution through multiple genetic mechanisms. Understanding the genetic variability of weedy rice demonstrates the ability of this weed to evolve with changing environments, resulting in challenges for weed control.

Technical Abstract: Many crop species were independently selected for a shared suite of “domestication traits,” which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two major weedy rice strains found in U.S. rice fields, strawhull (S) and blackhull awned (B). Genotyping-by-sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6,016 and 13,730 SNPs mapped in F5 lines of the S and B populations, respectively. For some weediness traits (awn length and grain pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed a causal role for previously described molecular variation, with trait variation largely attributable to individual loci. However, for more complex quantitative traits (heading date, panicle length, seed shattering) we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms.