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Elucidation of the population structure and genetic diversity of Bipolaris oryzae associated with rice brown spot disease using SSR markers

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Abstract

Brown spot disease, caused by Bipolaris oryzae, is one of the several disastrous diseases affecting rice. The brown spot fungus illustrates substantial pathogenic and genetic variability. To the best of our knowledge, extensive analysis utilizing specific SSR primers for B. oryzae genome is quite inadequate for the population structure and genetic diversity of Indian B. oryzae isolates. A total of 84 brown spot isolates were collected from rice-cultivating areas across southern and eastern Indian states, viz., Tamil Nadu, Andhra Pradesh, Odisha and Chhattisgarh. The pathogenicity and virulence characteristics of these isolates were assessed with the susceptible cultivar CR Dhan 201. Twelve genome-specific SSR markers of B. oryzae warranted the investigation of the population structure and genetic diversity among the isolates. These isolates were categorized based on their disease grade as highly virulent isolates (4 nos.), virulent isolates (8 nos.), moderately virulent isolates (47 nos.) and less virulent isolates (25 nos.). PCR amplification and DNA sequencing confirmed the isolates to be B. oryzae. PCR amplification and DNA sequencing confirmed the isolates to be B. oryzae. The SSR markers produced a total of 35 alleles with 1 to 4 alleles per locus with a gene diversity ranging between 0.00 and 0.687 and a major allele frequency variation of 0.425–0.975. The PIC value ranged from 0.00 to 0.638 having a mean value of 0.34. Cluster analysis technique was applied to group the brown spot isolates into four distinct clusters. Principal coordinate and structure analysis identified two genetic clusters of B. oryzae isolates for individual states with some degree of distinctness complying with their virulence. Analysis of molecular variance revealed more genetic variation within populations and less among populations. The study outcome would expedite the comprehension of genetic diversity of B. oryzae across the southern and eastern states of India. Furthermore, we anticipate its guidance in the development of more effective disease management strategies as well as in the generation of novel resistant varieties through marker-assisted breeding.

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Acknowledgements

The authors gratefully acknowledge ICAR-National Rice Research Institute, Cuttack, India for providing the necessary facilities.

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  1. U. Keerthana and M. Phalguni contributed equally to this work.

Authors and Affiliations

  1. ICAR-National Rice Research Institute, Cuttack, 753006, Odisha, India

    U. Keerthana, M. Phalguni, S. R. Prabhukarthikeyan, R. Naveenkumar, Manoj K. Yadav, C. Parameswaran, Mathew S. Baite, S. Raghu, P. Panneerselvam & P. C. Rath

  2. S.V. Agricultural College, Acharya N.G. Ranga Agricultural University, Tirupati, India

    Madem Gurivi Reddy

  3. Tamil Nadu Agricultural University, Coimbatore, India

    S. Harish

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Contributions

UK and MP contributed to conceptualization, methodology and writing––original draft; SRP was involved in writing––review and editing; RN and MKY performed data analysis and data curation; CP contributed to software and validation; MSB and SR carried out survey and methodology; MGR and SH carried out survey and processed samples; PP and PCR contributed to resources and data validation.

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Correspondence to S. R. Prabhukarthikeyan.

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Keerthana, U., Phalguni, M., Prabhukarthikeyan, S.R. et al. Elucidation of the population structure and genetic diversity of Bipolaris oryzae associated with rice brown spot disease using SSR markers. 3 Biotech 12, 281 (2022). https://doi.org/10.1007/s13205-022-03347-4

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