Differentiation between Setaria pumila (yellow foxtail) and Setaria parviflora (knotroot foxtail) via morphological characteristics and genetic markers

Abstract

Yellow foxtail and knotroot foxtail are problematic weed species in turfgrass that are often mistaken for one another due to their similar morphology. Yellow foxtail and knotroot foxtail have phenotypic plasticity inter- and intraspecies, which can bias their identification. Accurate identification in the early growth stage is challenging as key traits like rhizomes appear late or are absent. Previous research showed they responded differently to several herbicides within the limited options for selective control in warm-season turfgrass. Research was conducted to evaluate the use of genetic markers for differentiating biotypes of yellow foxtail, knotroot foxtail, giant foxtail, green foxtail, and some unknown foxtails collected in Alabama. Extracted DNA was amplified with polymerase chain reaction targeting trnH-psbA, atpB-rbcL, maturase K (matK), and internal transcribed spacer (ITS) regions. Sanger sequencing, except for trnH-psbA, revealed single-nucleotide polymorphisms distinguishing the two species. Evolutionary analysis of the concatenation of those DNA regions revealed that yellow foxtail and knotroot foxtail cluster in one clade, while green foxtail and giant foxtail belong to two distinct clades. This study demonstrated that applying these DNA barcodes except trnH-psbA is relevant in accurately identifying early, aiding proper identification before herbicide selection.