Genomic Structure and Contemporary Evolution of Weediness in Red Rice

01 Oct 2010 31 Jan 2017

Ana Caicedo (PI) , Kenneth M Olsen (CoPI), Yulin Jia (CoPI)


PI: Ana L. Caicedo (University of Massachusetts Amherst)

CoPIs: Kenneth M. Olsen (Washington University) and Yulin Jia (University of Arkansas/USDA-ARS Dale Bumpers National Rice Research Center)

Key Collaborators: David Gealy (University of Arkansas/USDA-ARS Dale Bumpers National Rice Research Center) and Nilda Burgos (University of Arkansas)

Red rice is an aggressive, weedy form of cultivated rice that infests crop fields and is a primary factor limiting rice productivity in the U.S. and worldwide. As the weedy relative of a genomic model species, red rice is supremely suited to serve as a model for understanding the processes by which weediness emerges in agricultural settings. Previous work by this research group has revealed that red rice in the U.S. has arisen twice independently, in both cases from Asian domesticated rice. This project will further examine several complementary aspects of red rice evolution in three broad aims. First, leveraging current information about U.S. red rice origins, the project will examine the genetic basis by which weedy traits emerge. Candidate weedy genomic regions will be identified through comparison of whole-genome sequences of U.S. weedy rice strains with their putative cultivated ancestors, and through genetic analyses of weed-crop crosses. Second, the project will determine how the weed's origin and population structure compare among four world regions (South Asia, Southeast Asia, Northeast Asia, North America) that differ in the presence/absence of reproductively compatible wild species and in the predominant locally cultivated rice variety. Third, the project will assess how recent shifts in U.S. agriculture towards the use of imidazolinone (IMI) herbicide-resistant rice varieties are affecting the emergence of herbicide-resistant red rice. Specifically, the project will determine the relative roles of crop-weed gene flow versus spontaneous mutation in the creation of IMI-resistant weedy rice.

Weedy crop relatives are a leading cause of crop losses worldwide, and this research will provide the first detailed examination of the genetic mechanisms and demographic processes by which weediness can evolve. The work will also provide basic insights into the impact of recent shifts to herbicide resistant rice farming on weed evolution, thereby providing critical data for devising effective weed control strategies. Other broader impacts of the project will involve training of a teacher summer intern through collaboration with the nationally recognized Washington University Science Outreach (WUSO); the teacher intern will create a "red rice" lab activity for classroom use, which will be made available on the web, publicized through science outreach programs, and supported locally through the WUSO materials warehouse. Teacher mentoring will also take the form of biotechnology research training to science faculty at the University of Arkansas at Pine Bluff, a historically African-American institution. The project will also participate in the annual Rice Research and Extension Center Field Day held in Stuttgart (AR). This popular event attracts a diverse cross-section of the public that include families, stake holders, state and regional rice research and extension specialists, industry representatives, congressional aides, and international visitors, providing an excellent opportunity to disseminate information about the the project and its relevance to rice agriculture. All sequence data generated will be available through through a project website (to be established) and long-term at public repositories that include GenBank and Gramene.