Intraspecific phylogenetic analysis of rice leaf folder, Cnaphalocrocis medinalisGuenee (Lepidoptera: Crambidae) populations across five agro-ecological units in Kerala

SEENA R  SUBHAGAN; BERIN  PATHROSE; MANI  CHELLAPPAN; SMITA  NAIR; DHALIN  D

doi:10.56093/ijas.v95i9.154431

Authors

SEENA R SUBHAGAN Kerala Agricultural University, Vellanikkara, Kerala 680 656, India
BERIN PATHROSE Kerala Agricultural University, Vellanikkara, Kerala 680 656, India
MANI CHELLAPPAN Kerala Agricultural University, Vellanikkara, Kerala 680 656, India
SMITA NAIR Kerala Agricultural University, Vellanikkara, Kerala 680 656, India
DHALIN D Kerala Agricultural University, Vellanikkara, Kerala 680 656, India

https://doi.org/10.56093/ijas.v95i9.154431

Keywords:

Agro-ecological units (AEU), Cnaphalocrocis medinalis, Intraspecific phylogeny, Mitochondrial cytochrome oxidase subunit 1(mtCO1)

Abstract

The present study was carried out during 2023–2024 at College of Agriculture, Vellanikkara, Kerala to investigate the intraspecific molecular phylogeny by utilizing mtCO1 gene sequences of the rice leaf folder, Cnaphalocrocis medinalis Guenee (Lepidoptera: Crambidae), across five major rice (Oryza sativa) growing agroecological units (AEUs), viz. AEU 3- Onattukara Sandy plains, AEU 4-Kuttanad, AEU 6-Kole lands Thrissur, AEU 20-Wayanad Central Plateau and AEU 23-Palakkad Eastern Plains in Kerala. While all populations clustered within the same clade, medinalis from Onattukara exhibited separate branching, albeit sharing similarities with Kuttanad populations. In contrast, populations from Thrissur and Wayanad displayed a closer resemblance, while those from Palakkad exhibited similarities with populations from China and Jharkhand in India. Moreover, the observed genetic structuring suggested regional differences in population dynamics, with populations from Southern Kerala (Onattukara and Kuttanad) exhibiting closer genetic grouping compared to those from Northern Kerala (Wayanad, Palakkad, and Thrissur). Analysis of percent identity matrices unveiled a high level of genetic similarity among C. medinalis populations across Kerala's AEUs, ranging from 98–99%. Notably, Kuttanad populations shared 99.85% of their identity with those from Onattukara and Wayanad, while Wayanad populations shared the same level of identity as Thrissur. Despite the regional differences, our study did not observe an apparent "barcode gap" typical of COI sequences. These findings shed light on the possibility of seasonal migration patterns, inbreeding events, and the subsequent distribution dynamics of the rice leaf folder across Kerala. Moreover, the potential impact of migration on disseminating resistant alleles among insect populations is a critical issue that warrants comprehensive investigation.

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References

Alvi S M, Ali M A, Chaudhary S and Iqbal S. 2003. Population trends and chemical control of rice leaf folder, Cnaphalocrocis medinalis on rice crop. International Journal of Agriculture and Biology 5(4): 615–17.

An B, Deng X, Shi H, Ding M, Lan J, Yang J and Li Y. 2014. Development and characterization of microsatellite markers for rice leaf folder, Cnaphalocrocis medinalis (Guenee) and cross-species amplification in other Pyralididae. Molecular Biology Reports 41(2): 1151–56. doi: 10.1007/s11033-013-2961-0 DOI: https://doi.org/10.1007/s11033-013-2961-0

Babendreier D, Maolin H, Rui T, Zhang F, Vongsabouth T, Win K K, Min K, Peng H, Song K, Annamalai S and Horgan F G. 2020. Biological control of Lepidopteran pests in rice: A multi-nation case study from Asia. Journal of Integrated Pest Management 11: 1–11. https://doi.org/10.1093/jipm/pmaa002 DOI: https://doi.org/10.1093/jipm/pmaa002

Balasubramani V, Sridharan S and Sadakathulla S. 2000. Effect of shade on leaf folder incidence in hybrid rice. Insect Environment 6: 15–16.

Barrion A T, Litsinger J A, Medina E B, Aguda R M, Bandong J P, Pantua Jr. P C, Viajante V D, Cruz C D and Vega C R. 1991. The rice Cnaphalocrocis and Marasmia (Lepidoptera: Pyralidae) leaf folder complex in the Philippines: Taxonomy, bionomics and control. Philippine Entomology 8: 987–1074.

Chang S S, Lo Z C, Keng C G, Li G Z, Chen X L and Wu X W. 1980. Studies on the migration of rice leafroller Cnaphalocrocis medinalis Guenee. Acta Entomologica Sinica 23: 130–40.

Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783–91. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x DOI: https://doi.org/10.1111/j.1558-5646.1985.tb00420.x

Folmer O, Black M, Hoeh W, Lutz R and Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3(5): 294–99.

Georghiou G P, Ariaratanam V, Pasternak M E and Lin S C. 1975. Organophosphorus multi-resistance in Culex pipiens quinquefasciatus in California. Journal of Economic Entomology 68: 461–67. DOI: https://doi.org/10.1093/jee/68.4.461

Georghiou G P, Pasteur N and Hawley M K. 1980. Linkage relationships between organophosphate resistance and a highly active esterase B in Culex pipiens quinquefasciatus Say from California. Journal of Economic Entomology 73: 301–05. DOI: https://doi.org/10.1093/jee/73.2.301

Hebert P D N, Cywinska A, Ball S L and de Waard J R. 2003a. Biological identifications through DNA barcodes. (In) Proceedings of the Royal Society B: Biological Sciences 270 (1512): 313–21. https://doi.org/10.1098/rspb.2002.2218 DOI: https://doi.org/10.1098/rspb.2002.2218

Hebert P D N, Ratnasingham S and de Waard J R. 2003b. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society B: Biological Sciences 270: 96–99. https://doi.org/10.1098/ rsbl.2003.0025 DOI: https://doi.org/10.1098/rsbl.2003.0025

Hsieh C, Guo T, Tu K, Liao C and Chuang W. 2023. Genetic structure of the rice leaf folder, Cnaphalocrocis medinalis (Lepidoptera: Crambidae) in Taiwan. Taiwania 68(4): 451‒57. 10.6165/tai.2023.68.451

Huang X and Madan A. 1999. CAP3: A DNA sequence assembly program. Genome Research 9(9): 868–77. https://doi.org/10.1101/gr.9.9.868 DOI: https://doi.org/10.1101/gr.9.9.868

Jiang W B, Zhu J Q, Song C, Li X Y, Yang Y and Yu W D. 2013. Molecular phylogeny of the butterfly genus Polytremis (Hesperiidae, Hesperiinae, Baorini) in China. PLoS One 8: e84098. https://doi.org/10.1371/journal.pone.0084098 DOI: https://doi.org/10.1371/journal.pone.0084098

Jindal V. 2019. Genetic diversity of rice leaf folder using mitochondrial cytochrome oxidase 1 gene. Indian Journal of Entomology 81(1): 75–81. http://dx.doi.org/10.5958/0974-8172.2019.00027.0 DOI: https://doi.org/10.5958/0974-8172.2019.00027.0

Joshi R C, Heinrichs E A and Venugopal M S. 1986. A rice leaf folder, Marasmia patnalis Bradley: Escaped attention of rice entomologists. Pesticides 20: 51.

Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16(2): 111–20. https://doi.org/10.1007/BF01731581 DOI: https://doi.org/10.1007/BF01731581

Litsinger J A, Bandong J P, Canapi B L, Dela-Cruz C G, Pantua P C, Alviola A L and Batay-An E H. 2006. Evaluation of action thresholds for chronic rice insect pests in the Philippines: III. Leaf folders. International Journal of Pest Management 52: 181–94. DOI: https://doi.org/10.1080/09670870600664490

Luo S J. 2010. Occurrence of rice leaf roller in China and its identification and prevention. Plant Diseases and Pests 1: 13–18.

Mashhoor K, Ramesh N, Lazar K V and Shanas S. 2019. Molecular phylogeny of rice leaf folder (Cnaphalocrocis medinalis). Research Journal of Biotechnology 14(8): 1–7.

Mohapatra S D. 2008. Participatory appraisal for biointensive IPM research in basmati rice: A case study. Oryza 45(2): 157–77. Padmavathi C, Gururaj K, Padmakumari A P and Pasalu I C. 2006. Comparative bionomics of leaf folders, Cnaphalocrocis medinalis Guenee and Marasmia patnalis Bradley in rice. Entomon 31: 1–8.

Pan X X. 1985. Studies on migratory law and control strategies of rice leaf roller (Cnaphalocrocis medinalis Guenee) in Sichuan Basin. Journal of Nanjing Agricultural University 3: 32–40.

Park Y C, Kitade O, Schwarz M, Kim J P and Kim W. 2006. Intraspecific molecular phylogeny, genetic variation and phylogeography of Reticulitermes speratus (Isoptera: Rhinotermitidae). Molecules and Cells 21(1): 89–103. DOI: https://doi.org/10.1016/s1016-8478(23)12906-2

Pasteur N, Iseki A and Georghiou G P. 1981. Genetic and biochemical studies on the highly active esterases A and B associated with organophosphate resistance in the Culex pipiens complex. Biochemical Genetics 19: 9099919. https:// doi.org/10.1007/bf00504256 DOI: https://doi.org/10.1007/BF00504256

Qi G J. 2008. Occurrence of the third and fourth generations of Cnaphalocrocis medinalis in the mixed cropping rice region in Anqing, Anhui Province. Chinese Journal of Rice Science 22: 513–18.

Rautaray B K, Bhattacharya S, Panigrahi D and Dash S R. 2019. Studied on species diversity of rice leaf folder and their natural enemies in north-eastern coastal plains of Odisha. International Journal of Current Microbiology and Applied Sciences 8(10): 634–45. DOI: https://doi.org/10.20546/ijcmas.2019.810.072

Raymond M and Marquine M. 1994. Evolution of insecticide resistance in Culex pipiens populations: The Corsican paradox. Journal of Evolutionary Biology 7(3): 315–37. http://dx.doi. org/10.1046/j.1420-9101.1994.7030315.x DOI: https://doi.org/10.1046/j.1420-9101.1994.7030315.x

Saitou N and Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4): 406–25. https://doi.org/10.1093/ oxfordjournals.molbev.a040454

Salgueiro P, Restrepo-Zabaleta J, Costa M, Galardo A K R, Pinto J, Gaborit P, Guidez A, Martins A J and Dusfour I. 2019. Liaisons dangereuses: Cross-border gene flow and dispersal of insecticide resistance-associated genes in the mosquito Aedes aegypti from Brazil and French Guiana. DOI: https://doi.org/10.1590/0074-02760190120

Memorias do Instituto Oswaldo Cruz 114: e190120. https://doi.org/10.1590%2F0074-02760190120

Samui R P, Chattopadhyay N, Sabale J P, Kartikeyan K and Balachandran P V. 2007. Weather based forewarning of leaf folder attack on kharif rice and operational crop protection at Pattambi, Kerala. Mausam 58(4): 525–36. https://doi. org/10.54302/mausam.v58i4.1436 DOI: https://doi.org/10.54302/mausam.v58i4.1436

Singh A, Jaswal A and Kashyap L. 2019. Consequences of nutrient management on the incidence of leaf folder insect. Annals of Agri-Bio Research 23(2): 156–60.

Sun Y, Liu T, Ling Y, Wang L, Ni H, Guo D, Dong B B, Huang Q, Long L P, Zhang S, Wu S F, and Gao C F. 2023. Insecticide resistance monitoring of Cnaphalocrocis medinalis (Lepidoptera: Pyralidae) and its mechanism to chlorantraniliprole. Pest Management Science 79: 3290–99. https://doi.org/10.1002/ps.7512 DOI: https://doi.org/10.1002/ps.7512

Tamura K, Nei M and Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. (In) Proceedings of the National Academy of Sciences of the United States of America 101: 11030–35. https://doi.org/10.1073/pnas.0404206101 DOI: https://doi.org/10.1073/pnas.0404206101

Tamura K, Stecher G and Kumar S. 2021. MEGA 11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution 38(7): 3022–27. https://doi.org/10.1093/molbev/msab120 DOI: https://doi.org/10.1093/molbev/msab120

Tanwar R K, Singh S, Singh S P, Kanwar V K, Kumar R, Khokar M K and Mohapatra S D. 2019 Implementing the systems approach in rice pest management: India context. Oryza 56 (Special Issue): 136–42. DOI: https://doi.org/10.35709/ory.2019.56.s.6

Thompson J D, Higgins D G and Gibson T J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673–80. https://doi.org/10.1093/nar/22.22.4673 DOI: https://doi.org/10.1093/nar/22.22.4673

Tu C W. 1983. Recent advances in research on the insect pests of rice that migrate long distances in China. Scientia Agricultura Sinica 6: 76–82.

Wada T. 1979. Influence of the temperature and the growing stages of the rice plant on the number of larval instars in the rice leafroller, Cnaphalocrocis medinalis Guenée. Japanese Journal of Applied Entomology and Zoology 23: 178–82.

Wang F, Yang F, Lu M, Luo S, Zhai B, Lim K, McInerney C E and Hu G. 2017. Determining the migration duration of rice leaf folder [Cnaphalocrocis medinalis (Guenee)] moths using a trajectory analytical approach. Scientific Reports 7(1): 1–8. https://doi.org/10.1038/srep39853 DOI: https://doi.org/10.1038/srep39853

Wheeler W C. 1989. The systematics of insect ribosomal DNA. The Hierarchy of Life: Molecules and Morphology in Phylogenetic Analysis, pp. 307–321. Fernholm B, Bremer K and Jornvall H (Eds). Elsevier, Amsterdam, The Netherlands.

Yaakop S, David-Dass A, Shaharuddin U S, Sabri S, Badrulisham A S and Che-Radziah C M. 2020. Species richness of leaf roller and stem borers (Lepidoptera) associated with different paddy growth and first documentation of its DNA barcode. Pertanika Journal of Tropical Agricultural Science 43(4): 523–35. DOI: https://doi.org/10.47836/pjtas.43.4.08