Leveraging Chloroplast Genome-wide Analysis for Enhanced ARMS-qPCR Identification of Dendrobium brymerianum

Wuhian Xenin^*
*Correspondence: Wuhian Xenin, Department of Genetics, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland, Email:

Keywords

Chloroplast genome • Single-Nucleotide Polymorphism (SNP) • Botanical research • Conservation

Introduction

D. brymerianum, a member of the Orchidaceae family, holds immense significance in traditional medicine, particularly in Southeast Asia. However, precise identification of this species remains a challenge due to its morphological similarities with other Dendrobium species. Traditional methods relying solely on morphology often lead to misidentification, hindering conservation efforts and pharmaceutical research. To overcome these challenges, molecular techniques such as Amplification Refractory Mutation System quantitative PCR (ARMS-qPCR) coupled with genomic analysis have emerged as powerful tools. In this article, we elucidate the recent breakthroughs in chloroplast genome-wide analysis, highlighting their pivotal role in uncovering novel Single-Nucleotide Polymorphism (SNP) resources for the accurate identification of D. brymerianumvia ARMS-qPCR [1].

Literature Review

Chloroplasts, the organelles responsible for photosynthesis in plants, harbor their own genome known as the chloroplast genome. With a relatively conserved structure and high copy number per cell, chloroplast genomes serve as invaluable resources for phylogenetic studies, species identification, and evolutionary analyses. Recent advancements in next-generation sequencing technologies have revolutionized chloroplast genome sequencing, enabling rapid and cost-effective acquisition of whole chloroplast genome sequences [2].

Single-Nucleotide Polymorphisms (SNPs), the most abundant form of genetic variation, play crucial roles in genotype-phenotype associations, population genetics, and evolutionary studies. In the context of species identification, SNPs serve as robust molecular markers due to their high abundance, stability, and inheritance. Through comprehensive chloroplast genome-wide analysis of D. brymerianum and closely related species, researchers have identified a plethora of species-specific SNPs distributed across the chloroplast genome. The integration of these SNPs into ARMS-qPCR assays has revolutionized the identification of D. brymerianum. ARMS-qPCR exploits the specificity of SNP-containing primers to selectively amplify target DNA sequences. By designing allele-specific primers targeting the identified SNPs, researchers can achieve highly sensitive and specific detection of D. brymerianum DNA, even in complex mixtures or degraded samples. Moreover, the quantitative nature of qPCR enables accurate quantification of target DNA, further enhancing the reliability of species identification [3].

Discussion

The development of SNP-based ARMS-qPCR assays holds immense promise across various domains. In botanical research, these assays facilitate rapid and accurate species identification, aiding in taxonomic revisions, biodiversity assessments, and conservation efforts. By accurately delineating species boundaries, researchers can devise targeted conservation strategies to protect endangered species like D. brymerianum and their habitats [4].

Furthermore, the pharmaceutical industry stands to benefit significantly from SNP-based identification methods. D. brymerianum, renowned for its medicinal properties, serves as a valuable source of bioactive compounds with potential therapeutic applications. Accurate species identification ensures the authenticity and quality of herbal products derived from D. brymerianum, thereby enhancing consumer confidence and regulatory compliance [5]. ARMS-qPCR, a highly sensitive molecular technique, relies on the selective amplification of target sequences based on Single Nucleotide Polymorphisms (SNPs) or insertions/deletions (indels). By designing primers that specifically recognize the unique sequence variants in D. brymerianum, ARMS-qPCR assays can be tailored to selectively amplify DNA from this species while minimizing non-specific amplification from closely related species.

The integration of chloroplast genome-wide analysis with ARMS-qPCR offers several advantages. Firstly, it enhances the specificity of molecular assays, ensuring accurate discrimination of D. brymerianum from closely related species. Secondly, it improves the sensitivity of detection, enabling the reliable identification of D. brymerianum even in complex sample matrices. Moreover, this approach provides a rapid and cost-effective means of species identification compared to traditional morphological methods or whole-genome sequencing [6].

Conclusion

In conclusion, the integration of chloroplast genome-wide analysis with SNP-based ARMS-qPCR represents a paradigm shift in the identification of D. Brymerianum and other plant species. By harnessing the power of molecular markers and high-throughput sequencing technologies, researchers can overcome the limitations of traditional morphological approaches, paving the way for more robust and reliable species identification methods. As we continue to unravel the complexities of plant genomes and refine molecular techniques, the potential for innovation and discovery in botanical research and pharmacology remains boundless. The combination of high-throughput sequencing technologies for chloroplast genome analysis with the precision and sensitivity of ARMS-qPCR represents a powerful toolkit for plant species identification and molecular diagnostics. As genomic data continue to accumulate and molecular techniques advance, the scope and accuracy of species identification methods are expected to further improve, offering valuable tools for biodiversity conservation, sustainable resource management and biotechnological applications.

Acknowledgement

None.

Conflict of Interest

There are no conflicts of interest by author.

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