Advances in Plant Molecular Taxonomy: Techniques, Challenges, and Applications
Rahul G. Shelke *
Agrinucleon Biosciences LLP, Achalpur, Amravati, Maharashtra, India.
Yogesh Lahane *
Botanical Survey of India, Botanic Garden of Indian Republic, Noida, 201301, India.
Priyanka Ingle
Botanical Survey of India, Botanic Garden of Indian Republic, Noida, 201301, India.
Prashant Pusalkar
Botanical Survey of India, Western Regional Centre, Pune, 411001, India.
Sandeep Chauhan
Botanical Survey of India, Botanic Garden of Indian Republic, Noida, 201301, India.
Praful Pardhi
School of Computer Science and Engineering Shri. Ramdeobaba College of Engineering & Management, Ramdeobaba University, Nagpur, India.
Ravi Chandrabhan Nirmal
ICAR-Indian Agricultural Research Institute, New Delhi, India.
Sunil Kumar Prajapati
ICAR-Indian Agricultural Research Institute, New Delhi, India.
*Author to whom correspondence should be addressed.
Abstract
Advances in plant molecular taxonomy have revolutionized species identification and classification, overcoming the limitations of traditional morphology-based approaches. These challenges include cryptic species, hybridization, and phenotypic plasticity complicate the distinction of closely related taxa. Molecular techniques, including DNA barcoding and plastid genome analysis, have emerged as powerful tools to address these issues. DNA barcoding, utilizing standardized genetic markers such as rbcL, matK, and ITS regions, has become indispensable for species identification, biodiversity assessment, and conservation efforts. The integration of NGS technologies has further enhanced molecular taxonomy, enabling large-scale genomic and transcriptomic studies. Plastid genome sequencing has provided deeper insights into plant phylogenetics, resolving complex evolutionary relationships and taxonomic ambiguities. Despite challenges like limited marker variability and incomplete databases, advancements in NGS, third-generation sequencing, and bioinformatics are expanding the frontiers of molecular taxonomy. Emerging technologies, including SNP analysis, RAD-seq, and machine learning are offering new opportunities for exploring plant diversity. Future directions will focus on expanding genomic databases, integrating phenotypic and molecular data, and applying these tools for large-scale biodiversity monitoring. These efforts will ensure continued progress in plant taxonomy, systematics, and conservation, particularly in the face of global environmental change.
Keywords: DNA barcoding, Phylogenomics, molecular markers, next-generation sequencing, plastid genomics