Journal of Environmental Biology

Unravelling the genetic diversity and population structure of Sitophilus oryzae L. in North India using mitochondrial COI sequences

P. Kaundal^1,5, K.G. Padwal²*, S. Chakravarty³, N. Srinivasa¹, R.M. Mahalle⁴, A.K. Singh⁵, P.S. Tripathy⁶ and C.P. Srivastava¹     

¹Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi - 221 005, India

²Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Rajiv Gandhi South Campus, Banaras Hindu University, Barkachha, Mirzapur - 231 307, India

³Department of Entomology, Bihar Agricultural University, Sabour-813 210, India

⁴Institute of Agricultural Sciences, Chungnam National University, Daejeon-34134, Republic of Korea

⁵Department of Entomology, Rani Lakshmi Bai Central Agricultural University, Jhansi-284 003, India

⁶College of Fisheries, Rani Lakshmi Bai Central Agricultural University, Datia-475 686, India

Received: 21 January 2026                   Revised: 28 March 2026                   Accepted: 16 May 2026

*Corresponding Author Email : kanchan.eaz@bhu.ac.in                 *ORCiD: https://orcid.org/0000-0002-4210-767X

Abstract

Aim: Sitophilus oryzae (Linnaeus) (Coleoptera: Curculionidae) is a notorious pest inflicting substantial economic damage to stored grains worldwide. Population genetic studies offer valuable insights into insects' evolutionary and adaptive strategies and demonstrate how environmental factors influence genetic diversity and gene flow among populations.Therefore, the present study was undertaken to study the genetic diversity of S. oryzae populations from different geographical regions of North India.

Methodology: In this study, a total of 150 samples of S. oryzae were collected from 15 different locations, representing diverse agro-climatic zones of India. The samples were then identified by utilizing taxonomic keys. Thereafter, the specimens were subjected to PCR amplification of mitochondrial cytochrome c oxidase I (COI) gene to study their genetic variation and population structure.

Results: The results revealed low values of haplotype diversity (0.178) and nucleotide diversity (0.00032). Significant negative values of neutrality tests suggested a recent demographic expansion of the population. Mantel's test revealed a weak correlation between genetic differentiation and geographical distance. Haplotype network analysis revealed a single major clade, representing the major population assumed to be the ancestral population. Moreover, low-frequency haplotypes with one or two populations suggested ongoing population divergence, possibly influenced by phosphine resistance mechanisms. The phylogenetic tree supported the genetic homogeneity of the population since there was no clustering of the population based on geographical area.

Interpretation: Based on the COI markers, it can be concluded that North Indian populations of S. oryzae exhibit low genetic diversity, which has implications for pest management strategies primarily involving the use of fumigants.

Key words: COI, Genetic homogeneity, Gene flow, Phylogeny, Sitophilus oryzae

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