Rapid Plant Identification Using Species- and Group-Specific Primers Targeting Chloroplast DNA

Abstract

Plant identification is challenging when no morphologically assignable parts are available. There is a lack of broadly applicable methods for identifying plants in this situation, for example when roots grow in mixture and for decayed or semi-digested plant material. These difficulties have also impeded the progress made in ecological disciplines such as soil- and trophic ecology. Here, a PCR-based approach is presented which allows identifying a variety of plant taxa commonly occurring in Central European agricultural land. Based on the trnT-F cpDNA region, PCR assays were developed to identify two plant families (Poaceae and Apiaceae), the genera Trifolium and Plantago, and nine plant species: Achillea millefolium, Fagopyrum esculentum, Lolium perenne, Lupinus angustifolius, Phaseolus coccineus, Sinapis alba, Taraxacum officinale, Triticum aestivum, and Zea mays. These assays allowed identification of plants based on size-specific amplicons ranging from 116 bp to 381 bp. Their specificity and sensitivity was consistently high, enabling the detection of small amounts of plant DNA, for example, in decaying plant material and in the intestine or faeces of herbivores. To increase the efficacy of identifying plant species from large number of samples, specific primers were combined in multiplex PCRs, allowing screening for multiple species within a single reaction. The molecular assays outlined here will be applicable manifold, such as for root- and leaf litter identification, botanical trace evidence, and the analysis of herbivory.

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

“…Where most molecular studies target single predators or a few species only, a small but growing number of studies have developed molecular tools to resolve smaller and larger modules within food webs, from plant-herbivore interactions (Staudacher et al 2011;Wallinger et al 2012;Garcia-Robledo et al 2013a, 2013bKitson et al 2013;Kajtoch et al 2015) to plant -leaf minerparasitoid networks (Derocles et al 2015). The food webs of soils offer a particular challenge-and particular scope for new insights-as species diversity is relatively high, trophic relations complex, and direct feeding interactions oftentimes impossible to observe.…”

Plant diversity affects behavior of generalist root herbivores, reduces crop damage, and enhances crop yield

“…All wireworm/regurgitate samples were screened for plant DNA applying multiplex PCR assays described in Wallinger et al (2012). Each sample was tested with a duplex PCR to detect DNA of wheat and maize (duplex ''TZ''), while samples stemming from the MIX treatment were additionally tested with another duplex PCR for lupine and buckwheat (duplex ''LF'') and a multiplex PCR to detect DNA fragments of buckwheat, ryegrass, beans, and mustard (multiplex ''FLPS'').…”

Evaluation of pyrosequencing for large-scale identificationof plant species (grasses as a model)

“…Wallinger et al (2012) also revealed that an overall reliable sequence alignment of all studied species, including grasses, was impossible due to the great length differences in noncoding regions even within closely related taxa. Should the SNP markers developed here prove to be species-specific, they would provide a valuable tool for reliable diagnosis of grasses.…”