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<p>Rice yellow stem borer (YSB), <i>Scirpophaga incertulas</i> (Walker), is one of the most destructive insect pests of rice across diverse rice ecosystems. The pest damages the rice crop at both the seedling and maturity stages, resulting in severe yield losses. Host Plant Resistance (HPR) is the economical, sustainable, and eco-friendly component of integrated pest management (IPM). A comprehensive understanding of population genetics and the genetic diversity of YSB is essential for identifying tolerant donors and strengthening the resistance breeding programmes. In the present study, the genetic diversity of YSB populations collected from different locations of India was analysed using the mitochondrial <i>Cytochrome c oxidase subunit I</i> (<i>COX1</i>) gene, and compared with global YSB populations. Phylogenetic analysis revealed the presence of two major clades among the global YSB populations. Nucleotide sequence analysis detected 60 mutations and 56 variable sites (polymorphic sites) in the <i>COX1</i> sequences, with Indian populations exhibiting a comparatively higher number of variable sites. Haplotype analysis identified 38 haplotypes, among which three are major haplotypes (haplotype 24, 32, and 34). The overall haplotype diversity (Hd) and the nucleotide diversity (π) were 0.964 and 0.02182, respectively, while Indian populations exhibited Hd of 0.952 and π of 0.01235, indicating high haplotype diversity with moderate nucleotide divergence. Neutrality tests for Indian populations yielded significantly negative values of Tajima’s D (-2.21303), Fu and Li’s D (-4.40753), and Fu and Li’s F (-4.05701), suggesting an excess of low-frequency polymorphisms and/or localized mutational events. Overall, mitochondrial <i>COX1</i> gene-based analysis revealed considerable genetic variation among YSB populations in India and across global regions. This study represents one of the first comprehensive reports summarising the genetic variation of YSB populations using the mitochondrial <i>COX1</i> gene sequences, providing valuable insights for resistance breeding and long-term YSB pest management.</p>

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Genetic diversity of rice yellow stem borer, Scirpophaga incertulas (Walker) from different locations of India based on mitochondrial COX1 gene

  • 期刊论文

  • 发表日期：

    2026年5月18日

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  • M Annamalai,
  • Swagat Mohanty,
  • Swarnali Bhattacharya,
  • Shyamaranjan Das Mohapatra,
  • C Parameswaran,
  • Prakash Chandra Rath

摘要

Rice yellow stem borer (YSB), Scirpophaga incertulas (Walker), is one of the most destructive insect pests of rice across diverse rice ecosystems. The pest damages the rice crop at both the seedling and maturity stages, resulting in severe yield losses. Host Plant Resistance (HPR) is the economical, sustainable, and eco-friendly component of integrated pest management (IPM). A comprehensive understanding of population genetics and the genetic diversity of YSB is essential for identifying tolerant donors and strengthening the resistance breeding programmes. In the present study, the genetic diversity of YSB populations collected from different locations of India was analysed using the mitochondrial Cytochrome c oxidase subunit I (COX1) gene, and compared with global YSB populations. Phylogenetic analysis revealed the presence of two major clades among the global YSB populations. Nucleotide sequence analysis detected 60 mutations and 56 variable sites (polymorphic sites) in the COX1 sequences, with Indian populations exhibiting a comparatively higher number of variable sites. Haplotype analysis identified 38 haplotypes, among which three are major haplotypes (haplotype 24, 32, and 34). The overall haplotype diversity (Hd) and the nucleotide diversity (π) were 0.964 and 0.02182, respectively, while Indian populations exhibited Hd of 0.952 and π of 0.01235, indicating high haplotype diversity with moderate nucleotide divergence. Neutrality tests for Indian populations yielded significantly negative values of Tajima’s D (-2.21303), Fu and Li’s D (-4.40753), and Fu and Li’s F (-4.05701), suggesting an excess of low-frequency polymorphisms and/or localized mutational events. Overall, mitochondrial COX1 gene-based analysis revealed considerable genetic variation among YSB populations in India and across global regions. This study represents one of the first comprehensive reports summarising the genetic variation of YSB populations using the mitochondrial COX1 gene sequences, providing valuable insights for resistance breeding and long-term YSB pest management.