Skip to main content
SpringerLink
Log in

Genetic diversity and population structure of blast resistance genes in Thai upland rice germplasm

  • Published:
European Journal of Plant Pathology Aims and scope Submit manuscript

Abstract

Rice blast is the most devastating disease of rice (Oryza sativa L.) causing yield losses worldwide. It had been shown that partially resistant rice varieties are a useful way to control rice blast disease. Landraces are a rich source of traits governing resistance/ tolerance to biotic and abiotic stresses. Therefore, 94 upland rice varieties were used to assess the genetic diversity and population structure of nine major rice blast resistance genes (Pib, Pid2, Pigm(t), Pi9, Pi-36(t), Pi54, Pi1, Pi-2(t), and Pita). The allele frequencies of the nine major R genes varied from 4.26% to 72.34%. The 94 varieties contained a range of one to seven genes with a blast resistance allele. One variety (12CR071) had the maximum seven blast resistance genes. The polymorphism information content (PIC) value among varieties varied from 0.0815 (R36STS CAPS) to 0.5000 (pB8) with an average of 0.3784 indicating moderate genetic diversity for rice blast resistance in upland rice varieties. Cluster analysis grouped 94 varieties into two major clusters. Population structure was analyzed to understand the evolution of blast resistance genes in rice. The population structure classified the upland rice into two distinct subpopulations. Interestingly, analysis of molecular variance (AMOVA) showed that much of the variability was found within subpopulation (95%), indicating a high gene exchange between the two subpopulations. In addition, eight varieties of upland rice and two control varieties were evaluated against leaf rice blast disease using four isolates of Pyricularia oryzae. The results showed that four upland rice varieties were resistant to all isolates used. Disease reactions were negatively correlated with the genotype scores of Pib, Pigm(t), Pi54, Pi-2(t), and Pita. In addition, based on the spearman rank correlation analysis, it revealed that the Pigm(t) were positively correlated to the leaf blast resistance. These findings provide important information for new sources of resistance genes for designing future breeding program of leaf blast resistant rice varieties.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Anderson, J. A., Churchill, G. A., Autrique, J. E., Tanksley, S. D., & Sorrells, M. E. (1993). Optimizing parental selection for genetic linkage maps. Genome, 36, 181–186.

    Article  CAS  Google Scholar 

  • Asibi, A. E., Chai, Q., & Coulter, J. A. (2019). Rice blast: A disease with implications for global food security. Agronomy, 9, 451.

    Article  CAS  Google Scholar 

  • Botstein, D., White, R. L., Skolinick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Society of Human Genetics, 32(3), 314–331.

    CAS  Google Scholar 

  • Bundo, M., & Coca, M. (2016). Enhancing blast disease resistance by overexpression of the calcium-dependent protein kinase OsCPK4 in rice. Plant Biotechnology Journal, 14(6), 1357–1367.

    Article  CAS  Google Scholar 

  • Castroagudín, V. L., Ceresini, P. C., de Oliveira, S. C., Reges, J. T. A., Maciel, J. L. N., Bonato, A. L. V., Dorigan, A. F., & McDonald, B. A. (2015). Resistance to QoI fungicides is widespread in Brazilian populations of the wheat blast pathogen Magnaporthe oryzae. Phytopathology, 105, 284–294.

    Article  Google Scholar 

  • Chen, X., Shang, J., Chen, D., Lei, C., Zou, Y., Zhai, W., Liu, G., Xu, J., Ling, Z., Cao, G., Ma, B., Wang, Y., Zhao, X., Li, S., & Zhu, L. (2006). A B-lectin receptor kinase gene conferring rice blast resistance. Plant Journal, 46(5), 794–804.

    Article  CAS  Google Scholar 

  • Cho, Y. C., Kwon, S. W., Choi, I. S., Lee, S. K., Jeon, J. S., Oh, M. K., Roh, J. H., Hwang, H. G., Yang, S. J., & Kim, Y. G. (2007). Identification of major blast resistance genes in Korean rice varieties (Oryza sativa L.) using molecular markers. Journal of Crop Science and Biotechnology, 10(4), 265–76.

  • Chomnunti, P., Hongsanan, S., Hudson, B. A., Tian, Q., Peršoh, D., Dhami, M. K., Alias, A. S., Xu, J., Liu, X., Stadler, M., & Hyde, K. D. (2014). The sooty moulds. Fungal Diversity, 66, 1–36.

    Article  Google Scholar 

  • Das, G., Rao, G. J. N., Varier, M., Prakash, A., & Prasad, D. (2018). Improved Tapaswini having four BB resistance gene pyramided with six genes/QTLs, resistance/tolerance to biotic and abiotic stresses in rice. Scientific Reports, 8, 2413.

    Article  Google Scholar 

  • Deng, Y., Zhu, X., Shen, Y., & He, Z. (2006). Genetic characterization and fine mapping of the blast resistance locus Pigm(t) tightly linked to Pi2 and Pi9 in a broad-spectrum resistant Chinese variety. Theoretical and Applied Genetics, 113, 705–713.

    Article  CAS  Google Scholar 

  • Doyle, J. J., & Doyle, L. J. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bull, 19(13), 11–15.

    Google Scholar 

  • Elert, E. (2014). Rice by the numbers: A good grain. Nature, 514, 50–S51.

    Article  Google Scholar 

  • Eltaher, S., Sallam, A., Belamkar, V., Emara, H. A., Nower, A. A., Salem, K. F. M., Poland, J., & Baenziger, P. S. (2018). Genetic diversity and population structure of F3:6 Nebraska winter wheat genotypes using genotyping-by-sequencing. Frontier in Genetics, 9(76). Advance online publication. https://doi.org/10.3389/fgene.2018.00076.

  • Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14, 2611–2620.

    Article  CAS  Google Scholar 

  • Fjellstrom, R., Conaway-Bormans, C. A., McClung, A. M., Marchetti, M. A., Shank, A. R., & Park, W. D. (2004). Development of DNA markers suitable for marker assisted selection of three Pi genes conferring resistance to multiple Pyricularia grisea pathotypes. Crop Science, 44(5), 1790–1798.

    Article  CAS  Google Scholar 

  • Flor, H. H. (1971). Current status of the gene-for-gene concept. Annual Review of Phytopathology, 9, 275–296.

    Article  Google Scholar 

  • Fuentes, J. L., Correa-Victoria, F. J., Escobar, F., Prado, G., Aricapa, G., Duque, M. C., & Tohme, J. (2008). Identification of microsatellite markers linked to the blast resistance gene Pi-1(t) in rice. Euphytica, 160, 295–304.

    Article  CAS  Google Scholar 

  • Hartl, D. L. (1980). Principles of population genetics (1st ed.). Sinauer Associates.

    Google Scholar 

  • Imam, J., Alam, S., Mandal, N,P., Variar, M., & Shukla, P. (2014a) Molecular screening for identification of blast resistance genes in north east and eastern Indian Rice germplasm (Oryza sativa L.) with PCR based markers. Euphytica, 196, 199–211.

  • Imam, J., Mahto, D., Prasad, M., Mait, D., Shukla, P., & Variar, M. (2014b). Molecular analysis of Indian rice germplasm accessions with resistance to blast pathogen. Journal of Crop Improvement, 28, 729–739.

    Article  CAS  Google Scholar 

  • Jia, Y., Wang, Z., & Singh, P. (2002). Development of dominant Rice blast Pi-ta resistance gene markers. Crop Science, 42, 2145–2149.

    Article  CAS  Google Scholar 

  • Jiang, J., & Wang, S. (2002). Identification of a 118-kb DNA fragment containing the locus of blast resistance gene Pi-2(t) in rice. Molecular Genetics and Genome, 268(2), 249–252.

    Article  CAS  Google Scholar 

  • Khan, M. A., Sen, P. P., Bhuiyan, R., Kabir, E., Chowdhury, A. K., Fukuta, Y., Ali, A., & Latif, M. A. (2014). Phenotypic screening and molecular analysis of blast resistance in fragrant rice for marker assisted selection. Comptes Rendus Biologies, 337(5), 318–324.

    Article  Google Scholar 

  • Khush, G. S., & Jena, K. K. (2009). Current status and future prospects for research on blast resistance in rice (Oryza sativa L.). In G. L. Wang & B. Valent (Eds.), Advances in genetics, genomics and control of Rice blast disease (pp. 1–10). Springer.

    Google Scholar 

  • Liu, H., Meil, H., Yu, X., Zoul, G., Liu, G., & Luo, L. (2002). Towards improving the drought tolerance of rice in China. Plant Genetic Resources, 4(1), 47–53.

    Article  Google Scholar 

  • Liu, J., Wang, X., Mitchell, T., Hu, Y., Liu, X., Dai, L., & Wang, G. L. (2010). Recent progress and understanding of the molecular mechanismsof the rice–Magnaporthe oryzae interaction. Molecular Plant Pathology, 11(3), 419–427.

    Article  CAS  Google Scholar 

  • Liu, X. Q., Wang, L., Chen, S., Lin, F., & Pan, Q. H. (2005). Genetic and physical mapping of Pi36(t), a novel rice blast resistance gene located on rice chromosome 8. Molecular Genetics and Genomics, 274, 394–401.

  • Luo, Z., Brock, J., Dyer, J. M., Kutchan, T., Schachtman, D., Augustin, M., Ge, Y., Fahlgren, N., & Abdel-Haleem, H. (2019). Genetic diversity and population structure of a Camelina sativa spring panel. Frontiers in Plant Science, 10. Advance online publication. https://doi.org/10.3389/fpls.2019.00184.

  • Mackill, D. J., & Bonman, J. M. (1992). Inheritance of blast resistance in near-isogenic lines of rice. Phytopathology, 82(7), 746–749.

    Article  Google Scholar 

  • Mohammadi, S. A., & Prasanna, B. M. (2003). Analysis of genetic diversity in crop plants—Salient statistical tools and considerations. Crop Science, 43(4), 1235–1248.

    Article  Google Scholar 

  • Ning, X., Yunyu, W., & Aihong, L. (2020). Strategy for use of rice blast resistance genes in rice molecular breeding. Rice Science, 27, 263–277.

    Article  Google Scholar 

  • Peakall, R., & Smouse, P. E. (2012). GenAlEx 6.5: Genetic analysis in excel. Population genetic software for teaching and research-an update. Bioinformatics, 28, 2537–2539.

    Article  CAS  Google Scholar 

  • Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus geneotype data. Genetics, 155, 945–959.

    Article  CAS  Google Scholar 

  • Ramkumar, G., Srinivasarao, K., Madhan Mohan, K., Sudarshan, I., Sivaranjani, A. K. P., Gopalakrishna, K., Neeraja, C. N., Balachandran, S. M., Sundaram, R. M., Prasad, M. S., Shobha Rani, N., Rama Prasad, A. M., Viraktamath, B. C., & Madhav, M. S. (2011). Development and validation of functional marker targeting an InDel in the major rice blast disease resistance gene Pi54 (Pikh). Molecular Breeding, 27, 129–135.

    Article  Google Scholar 

  • Roumen, E., Levy, M., & Nottéghem, J.-L. (1997). Characterization of the European pathogen population of Magnaporthe grisea by DNA fingerprinting and pathotype analysis. European Journal of Plant Pathology, 103(4), 363–371.

    Article  CAS  Google Scholar 

  • Shete, S., Tiwari, H., & Elsto, R. C. (2000). On estimating the heterozygosity and polymorphism information content value. Theoretical Population Biology, 57, 265–271.

    Article  CAS  Google Scholar 

  • Singh, A. K., Sing, P. K., Arya, M., Singh, N. K., & Singh, U. S. (2015). Molecular screening of blast resistance genes in rice using SSR markers. The Plant Pathology Journal, 31(1), 12–24.

    Article  CAS  Google Scholar 

  • Su, J., Wang, W. J., Han, J. L., Chen, S., Wang, C. Y., Zeng, L. X., Feng, A., Yang, J., Zhou, B., & Zhu, X. (2015). Functional divergence of duplicated genes results in a novel blast resistance gene Pi50 at the Pi2/9/locus. Theory Applied Genetics, 128, 2213–2225.

    Article  CAS  Google Scholar 

  • Team, R. C. (2015). R a language and environment for statistical computing. Retrieved 15 March 2018, from http://www.r-project.org.

  • Valent, B. (1997). The rice blast fungus, Magnaporthe grisea. In G.C. Carroll and P. Tudzynoski (ed.) Plant relationships. The Mycota V part B. Springer-Verlag. Berlin Journal, 37-54.

  • Wongsaprom, C., Sirithunya, P., Vanavichit, A., Pantuwan, G., Jongdee, B., Sidhiwogn, N., Lanceras-Siangliwa, J., & Toojindaa, T. (2010). Two introgressed quantitative trait loci confer a broad-spectrum resistance to blast disease in the genetic background of the cultivar RD6 a Thai glutinous jasmine rice. Field Crops Research, 119, 245–251.

    Article  Google Scholar 

  • Xiao, W. M., Yang, Q. Y., Wang, H., Guo, T., Liu, Y. Z., Zhu, X. Y., & Chen, Z. (2010). Identification and fine mapping of a resistance gene to Magnaporthe oryzae in a space-induced rice mutant. Molecular Breeding, 28, 303–312.

    Article  Google Scholar 

  • Yadav, M. K, Aravindan, S., Ngangkham, U., Subudhi, H. N., Bag, M. K., Adak, T., Munda, S., Samantaray, S., & Jena, M. (2017). Use of molecular markers in identification and characterization of resistance to rice blast in India. PLoS ONE, 12(6). Advance online publication. https://doi.org/10.1371/journal.pone.0179467, 12.

  • Yadav, M. K., Aravindan, S., Ngangkham, U., Raghu, S., Prabhukarthikeyan, S. R., Keerthana, U., Marndi, B. C., Adak, T., Munda, S., Deshmukh, R., Pramesh, D., Samantaray S., & Rath, P. C. (2019). Blast resistance in Indian rice landraces: Genetic dissection by gene specific markers. PLoS ONE, 14(1). Advance online publication. https://doi.org/10.1371/journal.pone.0211061, 2019.

  • Yan, L., Yuan, Y. B., Liang, P. Y., Juan, J. Z., Xiang, Z. Y., Lin, W. H., & Deng, Y. C. (2017). Molecular screening of blast resistance genes in rice germplasms resistant to Magnaporthe oryzae. Rice Science, 24(1), 41–47.

    Article  Google Scholar 

  • Yang, Y., Zhang, H., Xuan, N., Chen, G., Liu, X., Yao, F., & Ding, H. (2017). Identification of blast resistance genes in 358 rice germplasms (Oryza sativa L.) using functional molecular markers. European Journal of Plant Pathology, 148, 567–576.

    Article  CAS  Google Scholar 

  • Zhen, W., Wang, Y., Wang, L., Ma, Z., Zhao, J., Wang, P., Zhang, L., Liu, Z., & Lu, X. (2016). Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing. Theoretical and Applied Genetics, 129, 1035–1044.

    Article  Google Scholar 

  • Zhu, D., Kang, H., Li, Z., Liu, M., Zhu, X., Wang, Y., Wang, D., Wang, Z., Liu, W., & Wang, G. L. (2016). A genome-wide association study of field resistance to Magnaporthe oryzae in rice. Rice, 9, 44.

    Article  Google Scholar 

Download references

Acknowledgements

This work was financially supported by The National Research Council of Thailand and Mae Fah Luang University, Thailand.

Author information

Authors and Affiliations

  1. School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand

    Chayaphathra Sooklim, Putarak Chomnunti, Ekachai Chukeatirote, Rungrote Nilthong & Somrudee Nilthong

  2. Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand

    Chatchawan Jantasuriyarat

Authors
  1. Chayaphathra Sooklim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Putarak Chomnunti
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chatchawan Jantasuriyarat
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ekachai Chukeatirote
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rungrote Nilthong
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Somrudee Nilthong
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Somrudee Nilthong.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

No human and/or animal participants were involved in this study.

Informed consent

Not applicable.

Supplementary Information

ESM 1

(DOCX 24 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sooklim, C., Chomnunti, P., Jantasuriyarat, C. et al. Genetic diversity and population structure of blast resistance genes in Thai upland rice germplasm. Eur J Plant Pathol 163, 587–599 (2022). https://doi.org/10.1007/s10658-022-02499-6

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10658-022-02499-6

Keywords

Search

Navigation