title: Distinguishing between weedy Amaranthus species based on intron 1 sequences from the 5-enolpyruvylshikimate-3-phosphate synthase gene.
abstract: BACKGROUND
  Hybridization between Amaranthus species and the potential for herbicide resistance to be transferred by hybridization are of growing concern in the weed science community. Early detection of evolved herbicide resistance and hybrids expressing resistance to single or multiple herbicides is important to develop an effective control strategy.
  
  
  RESULTS
  A PCR test was developed for quick identification of weedy amaranths and any hybrids. The sequences of intron 1 for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19) gene were determined for Amaranthus palmeri, A. spinosus, A. retroflexus, A. blitoides, A. viridis, A. tuberculatus and A. hybridus. These sequences were aligned and primers were developed in areas where the sequence differed between species. Species-specific primers and cycle conditions were successfully developed. These primers produce a single robust band only for the species for which they were designed.
  
  
  CONCLUSIONS
  The PCR techniques described here allow identification of a weedy amaranth or suspect hybrid in a few hours. Using a similar target, it may be possible to design simple PCR tests to identify even more difficult to distinguish weed species or weeds prone to interspecific hybridization. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
authors.affiliation: Crop Production Systems Research Unit, USDA-ARS, Stoneville, MS, USA.
authors.forename: Alice A
authors.initials: AA
authors.lastname: Wright
authors.affiliation: Crop Production Systems Research Unit, USDA-ARS, Stoneville, MS, USA. william.molin@ars.usda.gov.
authors.forename: William T
authors.initials: WT
authors.lastname: Molin
authors.affiliation: Crop Production Systems Research Unit, USDA-ARS, Stoneville, MS, USA.
authors.forename: Vijay K
authors.initials: VK
authors.lastname: Nandula
mesh_terms: D051229:3-Phosphoshikimate 1-Carboxyvinyltransferase / Q000235:genetics*; D027721:Amaranthus / Q000235:genetics*; D017931:DNA Primers; D014644:Genetic Variation; D006824:Hybridization, Genetic; D007438:Introns; D010940:Plant Proteins / Q000235:genetics; D057685:Plant Weeds / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*
chemical_list: D017931:DNA Primers; D010940:Plant Proteins; D051229:3-Phosphoshikimate 1-Carboxyvinyltransferase
keywords: PCR; hybrids