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

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.

当缺乏可用于形态学鉴定的植物组织时，植物物种鉴定极具挑战性。目前仍缺乏适用于此类场景的广谱鉴定方法，例如当根系混杂生长，或是针对腐烂、半消化植物材料的鉴定场景，此类难题便尤为凸显。此类困境同样阻碍了土壤生态学、营养生态学等生态学科的研究进展。本研究提出了一种基于聚合酶链式反应（PCR）的鉴定方案，可用于识别中欧农田中常见的多种植物类群。基于trnT-F叶绿体DNA（cpDNA）区域，研究人员开发了多项PCR扩增体系，可鉴定2个植物科（禾本科（Poaceae）、伞形科（Apiaceae））、2个植物属（车轴草属（Trifolium）、车前属（Plantago））以及9个植物物种：千叶蓍（Achillea millefolium）、普通荞麦（Fagopyrum esculentum）、多年生黑麦草（Lolium perenne）、狭叶羽扇豆（Lupinus angustifolius）、红花菜豆（Phaseolus coccineus）、白芥（Sinapis alba）、西洋蒲公英（Taraxacum officinale）、普通小麦（Triticum aestivum）及玉米（Zea mays）。这些扩增体系可通过长度介于116 bp至381 bp的特异性扩增子实现植物物种鉴定，其特异性与灵敏度始终维持在较高水平，可检测微量植物DNA，例如腐烂植物材料、草食动物肠道或粪便中的微量植物DNA。为提升大批量样本的物种鉴定效率，研究人员将特异性引物组合应用于多重PCR体系中，可在单次反应中同时筛选多个物种。本研究所述的分子鉴定体系应用场景广泛，可用于根系与叶片枯落物鉴定、植物痕迹物证分析以及植食性相关研究。