Genetic diversity and population structure of Cnaphalocrocis medinalis across India and South Asia: Insights from COI and ITS2 gene analyses

Abstract

Rice leaffolder, Cnaphalocrocis medinalis, a major pest of rice, poses a significant threat to crop yield across Asia. This is why the spread of this pest across Southeast Asia needs to be studied to understand its population dynamics, genetic diversity, and potential impact on regional rice cultivation. In this study, the genetic diversity and population structure of C. medinalis were examined using mitochondrial COI and nuclear ITS2 gene sequences collected from 15 Indian states and several South Asian countries. A total of 100 COI and 63 ITS2 sequences were analyzed, including new and publicly available data on NCBI, to assess nucleotide diversity, haplotype variation, and phylogenetic relationships. The DNA extraction, PCR amplification, sequencing, and bioinformatics analyses were done. Results revealed higher haplotype and nucleotide diversity in Indian populations compared to other Asian regions, indicating genetic variations and potential historical bottlenecks followed by population expansions. Median-joining haplotype networks showed widespread haplotypes, suggesting gene flow, while region-specific haplotypes indicated localized adaptation. AMOVA highlighted substantial genetic differentiation among populations for COI (62.51% variation), whereas ITS2 showed moderate differentiation (43.86%). Phylogenetic analyses identified polyphyletic and monophyletic clades, emphasizing complex population dynamics. Neutrality tests and mismatch distributions suggested demographic expansions in Indian populations. These findings underscore the evolutionary history, possible migration pattern and genetic structure of C. medinalis, providing insights into pest management strategies. Future research should explore environmental and anthropogenic factors driving genetic differentiation to enhance integrated pest management practices, ensuring sustainable rice production across diverse agro-climatic regions.