Molecular marker technology is a genetic analysis method based on organism genome, and is widely used in identification, genetic variability analysis, genetic diversity and population structure research, and genetic Linkage Group (LG) and marker-assisted selection. SRAP is a newly developed and widely used molecular marker technology, with a great potential in studies of genetic resources of medicinal plants due to its simplicity, numerous makers, and high reproducibility. Recently, it is popular to use the molecular marker technology to construct Dendrograms, clarify the relationship between germplasm and herb quality, assist the selection of herb and analyze the herb's quality. In this paper, the principle and protocol of SRAP and SCAR are discussed; some optimized SRAP reaction systems are compared with a summative list of common primes of SRAP; the applications of SRAP in germplasm genetic diversity analysis, genuineness analysis, genetic map construction are reviewed. In addition, the applications of SCAR and its role in the identification of Chinese herbal medicines are also discussed. The current status and prospect of applying the combination of SRAP and SCAR in the study of herbal medicines are commented.
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