title: The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice.
abstract: The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.).
authors.forename: Nilda Roma
authors.initials: NR
authors.lastname: Burgos
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.).
authors.forename: Vijay
authors.initials: V
authors.lastname: Singh
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.).
authors.forename: Te Ming
authors.initials: TM
authors.lastname: Tseng
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.).
authors.forename: Howard
authors.initials: H
authors.lastname: Black
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.).
authors.forename: Nelson D
authors.initials: ND
authors.lastname: Young
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.).
authors.forename: Zhongyun
authors.initials: Z
authors.lastname: Huang
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.).
authors.forename: Katie E
authors.initials: KE
authors.lastname: Hyma
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.).
authors.forename: David R
authors.initials: DR
authors.lastname: Gealy
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.) caicedo@bio.umass.edu.
authors.forename: Ana L
authors.initials: AL
authors.lastname: Caicedo
mesh_terms: D018556:Crops, Agricultural; D003710:Demography; D019143:Evolution, Molecular; D014644:Genetic Variation; D005838:Genotype; D006239:Haplotypes; D053209:Herbicide Resistance; D006540:Herbicides / Q000494:pharmacology*; D012275:Oryza / Q000235:genetics / Q000502:physiology*; D010641:Phenotype; D017422:Sequence Analysis, DNA; D014481:United States
chemical_list: D006540:Herbicides