Background and aims Native grasses planted or growing on sites contaminated by heavy metals should be safe for livestock and wildlife. Plant breeders seek to identify genes and quantitative trait loci (QTLs) controlling trace element variation among these grasses. Methods QTLs controlling forage mineral concentrations were mapped in a population derived from two perennial wildrye species, Leymus cinereus and Leymus triticoides, grown in soil contaminated with arsenic, cadmium, copper, lead, zinc, and other trace elements. These QTLs were aligned to the genome sequence of barley (Hordeum vulgare) for comparison to genes or QTLs controlling trace element uptake in other species and soils, including perennial wildrye grown in fertile soil.Results A total of 25 QTLs for 14 elements were detected on contaminated soil. Three of four zinc QTLs were conserved between fertile and contaminated soils, but no other QTLs were conserved across these test soils. Two homoeologous molybdenum QTLs were closely associated with MOT1 orthogenes, which encode one of two known molybdate transporters in plants, and possible candidate gene associations were identified for other heavy metal QTLs. Conclusions Results elucidate conserved and unparalleled mechanisms controlling trace element variation among different plants and soils, showing opportunities and challenges in plant breeding.Each year, millions of tonnes of new trace metals including arsenic (As), cadmium (Cd), copper (Cu), manganese (Mn), molybdenum (Mo), lead (Pb), and zinc (Zn) are produced by mines and mobilized into the biosphere (Nriagu and Pacyna 1988;Moore and Luoma 1990). Humans, plants and animals require Cu, Mo, Mn, Zn and other trace elements including iron (Fe) and magnesium (Mg) as essential micronutrients, but these metals can be toxic to most plants and animals at higher concentrations (Welch 1995;Corah 1996;Grusak and DellaPenna 1999;He et al. 2005; White and Broadley 2005; White and Brown 2010). Other trace metals including As, Cd, and Pb are not essential Plant Soil