Samarina Lidiia S, Koninskaya Natalia G, Shkhalakhova Ruset M, Simonyan Taisiya A, Kuzmina Daria O
Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia.
Int J Mol Sci. 2025 Jul 16;26(14):6808. doi: 10.3390/ijms26146808.
DNA barcoding of intraspecific diversity of agricultural crops is important to develop the genetic passports of valuable genotypes and cultivars. The advantage of DNA-barcoding as compared to traditional genotyping of cultivars is that the procedure can be unified and applied for the broad range of accessions. This not only makes it cost efficient, but also allows to develop open access genetic databases to accumulate information of the world's germplasm collections of different crops. In this regard, the aim of the review was to analyze the latest research in this field, including the selection of loci, universal primers, strategies of amplicons analysis, bioinformatic tools, and the development of databases. We reviewed the advantages and disadvantages of each strategy with the focus of cultivars identification. The data indicates that following chloroplast loci are the most prominent for the intraspecific diversity analysis: (trnE-UUC/trnT-GUU, rpl23/rpl2.l, psbA-trnH, trnL-trnF, trnK, rpoC1, ycf1-a, rpl32-trnL, trnH-psbA and matK). We suggest that the combination of three or four of these loci can be a sufficient DNA barcode for cultivar-level identification. This combination has to be selected for each crop. Advantages and disadvantages of different approaches of amplicons analysis are discussed. The bioinformatic tools and databases for the plant barcoding are reviewed. This review will be useful for selecting appropriate strategies for barcoding of intraspecific diversity of agricultural crops to develop genetic passports of valuable cultivars in germplasm collections worldwide.
对农作物种内多样性进行DNA条形码分析，对于构建珍贵基因型和品种的遗传谱系至关重要。与传统的品种基因分型相比，DNA条形码技术的优势在于其操作流程可以统一，适用于广泛的种质资源。这不仅降低了成本，还能建立开放获取的遗传数据库，以积累不同作物的全球种质资源信息。在这方面，本综述的目的是分析该领域的最新研究，包括位点选择、通用引物、扩增子分析策略、生物信息学工具以及数据库的开发。我们以品种鉴定为重点，综述了每种策略的优缺点。数据表明，以下叶绿体位点在种内多样性分析中最为突出：（trnE-UUC/trnT-GUU、rpl23/rpl2.l、psbA-trnH、trnL-trnF、trnK、rpoC1、ycf1-a、rpl32-trnL、trnH-psbA和matK）。我们建议，将其中三到四个位点组合起来，就足以作为品种水平鉴定的DNA条形码。每种作物都必须选择这样的组合。文中还讨论了不同扩增子分析方法的优缺点。对植物条形码的生物信息学工具和数据库进行了综述。本综述将有助于为农作物种内多样性条形码分析选择合适的策略，以构建全球种质资源库中珍贵品种的遗传谱系。
