MOLECULAR PROFILING OF BLAST RESISTANCE GENES IN LOCAL MALAYSIAN RICE (Oryza sativa L.)

Nur Amalia Amira Roslizan; Amira Adilah Kamaruddin; Mohammad Malek Faizal Azizi; Faiz Ahmad; Nor'Aishah Hasan

doi:10.18006/2025.13(2).284.298

Authors

Nur Amalia Amira Roslizan Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia
Amira Adilah Kamaruddin Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia
Mohammad Malek Faizal Azizi Agrotechnology & Biosciences Division, Malaysian Nuclear Agency,Bangi, 43000 Kajang, Selangor, Malaysia https://orcid.org/0000-0002-8963-7934
Faiz Ahmad Agrotechnology & Biosciences Division, Malaysian Nuclear Agency,Bangi, 43000 Kajang, Selangor, Malaysia https://orcid.org/0000-0002-8819-0747
Nor'Aishah Hasan Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia https://orcid.org/0000-0003-1945-1170

DOI:

https://doi.org/10.18006/2025.13(2).284.298

Keywords:

Blast resistance gene, SSR markers, Indica rice, Genetic diversity, Gene pyramiding

Abstract

Paddy fields in Malaysia have been affected by rice blast disease since the early years of rice cultivation, and it continue to suffer from its devastating effects due to the rapid evolution of the causal pathogen Magnaporthe oryzae. Although Malaysia is home to various local indica rice, the potential for resistance among these resources remains limited. This study aims to investigate the distribution of blast resistance genes in Malaysian rice cultivars and to categorize them into clusters based on genetic similarities. We extracted DNA from 75 rice accessions and performed molecular genotyping for four blast resistance genes (denoted as Pi) using allele-specific functional markers: the major genes Pi33 (RM72) and Pi27(t) (RM259), as well as the minor genes pi21 (RM1359) and Pi26 (RM413). The results of this profiling analysis were used to construct a hierarchical dendrogram for cluster analysis. The findings revealed that Pi33 had the highest distribution frequency at 60.00%, followed by Pi27(t) at 49.33%, Pi26 at 34.67%, and pi21 at 21.33%. All rice accessions were grouped into eight clusters, with four accessions, viz., Malinja, Bahagia, Serendah, and Bario, classified together in Cluster 8 for harboring 100% of the Pi genes. Meanwhile, Cluster 1 included 17 candidates with the highest similarity to the widely used resistant variety IR64. In conclusion, this study provides a framework for marker-assisted breeding to develop blast-resistant rice cultivars with multigenic resistance, contributing to sustainable rice production in Malaysia.

Author Biographies

Nur Amalia Amira Roslizan, Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia

Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia

Amira Adilah Kamaruddin, Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia

Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia

Mohammad Malek Faizal Azizi, Agrotechnology & Biosciences Division, Malaysian Nuclear Agency,Bangi, 43000 Kajang, Selangor, Malaysia

Agrotechnology & Biosciences Division, Malaysian Nuclear Agency,Bangi, 43000 Kajang, Selangor, Malaysia

Faiz Ahmad, Agrotechnology & Biosciences Division, Malaysian Nuclear Agency,Bangi, 43000 Kajang, Selangor, Malaysia

Agrotechnology & Biosciences Division, Malaysian Nuclear Agency,Bangi, 43000 Kajang, Selangor, Malaysia

Nor'Aishah Hasan, Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia

Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia

References

Ab Razak, S., Kamaruzaman, R., Saidon, S. A., Nor Azman, N. H. E., Misman, S. N., & Abd Majid, A. M. (2019). Molecular screening of blast resistance genes in selected Southeast Asia rice varieties. Journal of Biotech Research, 10, 293-299.

Ali, A. H. A., AbdEl-khalek, S. M., Emira, A. B., & Aboulila, A. A. (2023). Molecular profiling of some blast resistance genes and analysis of physiological variability in rice plants produced by anther culture and hybridization. Physiological and Molecular Plant Pathology, 126, 102051. https://doi.org/10.1016/ J.PMPP.2023.102051 DOI: https://doi.org/10.1016/j.pmpp.2023.102051

Aljumaili, S. J., Rafii, M. Y., Sakimin, S. Z., Ahmad, K., & Al-Jumaily, A. (2023). Backcrossing with marker assistance to introduce broad-spectrum bacterial leaf blight resistance in the Malaysian elite variety MR297. Agriculture, 13(2), 372. DOI: https://doi.org/10.3390/agriculture13020372

Anh, T. T. T., Khanh, T. D., Dat, T. D., & Xuan, T. D. (2018). Identification of Phenotypic Variation and Genetic Diversity in Rice (Oryza sativa L.) Mutants. Agriculture, 8(2), 30. https://doi.org/10.3390/AGRICULTURE8020030. DOI: https://doi.org/10.3390/agriculture8020030

Berruyer, R., Adreit, H., Milazzo, J., Gaillard, S., Berger, A., Dioh, W., Lebrun, M. H., & Tharreau, D. (2003). Identification and fine mapping of Pi33, the rice resistance gene corresponding to the Magnaporthe grisea avirulence gene ACE1. Theoretical and Applied Genetics, 107(6), 1139–1147. https://doi.org/10.1007/ S00122-003-1349-2/METRICS DOI: https://doi.org/10.1007/s00122-003-1349-2

Caguiat, X. G. I., &Yabes, J. C. (2016). Phylogenetic Similarity of Popular Rice Varieties from Different Sources. Journal of Phylogenetics & Evolutionary Biology, 4(3).1000171. https://doi.org/10.4172/2329-9002.1000171. DOI: https://doi.org/10.4172/2329-9002.1000171

Department of Statistics Malaysia (2023). Selected Agricultural Indicators. Printer for Department of Statistics. ISSN 2289-2257.

Dev, A., Kumar, A., Singh, K., Khan, N. A., Dwivedi, D. K., & Dixit, S. (2022). Corresponding Author: Genetic divergence and cluster analysis for yield and yield contributing traits in rice (Oryza sativa L.) genotypes. The Pharma Innovation Journal, 11(7), 2612–2617.

Fatah, T. (2015). Development of blast resistant rice variety derived from crossing between MR219 and PongsuSeribu 2 through marker-assisted backcross breeding. PhD thesis submitted to the Faculty of Agriculture, Universiti Putra Malaysia. Retrieved from http://psasir.upm.edu.my/id/eprint/59181.

Food and Agriculture Organization of the United Nations (2024). GIEWS Country Brief: Malaysia. GIEWS Global Information and Early Warning System on Food and Agriculture. Retrieved from https://www.fao.org/giews/countrybrief/index.jsp.

Fukuoka, S., Saka, N., Koga, H., Ono, K., Shimizu, T., Ebana, K., Hayashi, N., Takahashi, A., Hirochika, H., Okuno, K., & Yano, M. (2009). Loss of function of a proline-containing protein confers durable disease resistance in rice. Science (New York, N.Y.), 325(5943), 998–1001. https://doi.org/10.1126/science.1175550 DOI: https://doi.org/10.1126/science.1175550

Fukuoka, S., Saka, N., Mizukami, Y., Koga, H., Yamanouchi, U., Yoshioka, Y., Hayashi, N., Ebana, K., Mizobuchi, R., & Yano, M. (2015). Gene pyramiding enhances durable blast disease resistance in rice. Scientific Reports, 5(1), 1–7. https://doi.org/10.1038/srep07773. DOI: https://doi.org/10.1038/srep07773

Gebrie, G., & Abebe, D. (2022). Determining the level of genotypic variability of upland rice genotypes using cluster analysis. International Journal of Scholarly Research and Reviews, 01(01), 001–008. DOI: https://doi.org/10.56781/ijsrr.1.1.0021

Hashim, M. F. C., Nurulhuda, K., Haidar, A. N., Muharam, F. M., Nurulhuda, K., et al. (2022). Physiological and Yield Responses of Five Rice Varieties to Nitrogen Fertilizer Under Farmer's Field in IADA Ketara, Terengganu, Malaysia. Sains Malaysiana, 51(2), 359-368. https://doi.org/10.17576/JSM-2022-5102-03 DOI: https://doi.org/10.17576/jsm-2022-5102-03

Jagadeesh, D., & Devaki, N. S. (2020). Magnaporthe oryzae in Karnataka. India. International Journal of Agricultural Technology, 16(4), 799–818.

Kanyange, L., Fan, Y. Y., Zhang, Z. H., Huang, D. R., Huang, T. X., Zhuang, J.Y., & Zhu, Y. J. (2022). Genetic Association between Blast Resistance and Yield Traits in Rice Detected Using a High-Density Bin Map. Agronomy, 12(5), 1173. https://doi.org/10.3390/agronomy12051173. DOI: https://doi.org/10.3390/agronomy12051173

Kim, S., Kim, C. Y., Park, S. Y., Kim, K. T., Jeon, J., Chung, H., Choi, G., Kwon, S., Choi, J., Jeon, J., Jeon, J. S., Khang, C. H., Kang, S., & Lee, Y. H. (2020). Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming. Nature communications, 11(1), 5845. https://doi.org/10.1038/s41467-020-19624-w. DOI: https://doi.org/10.1038/s41467-020-19624-w

Lin, H. A., Chen, S. Y., Chang, F. Y., Tung, C. W., Chen, Y. C., Shen, W. C., Chen, R. S., Wu, C. W., & Chung, C. L. (2018). Genome-wide association study of rice genes and loci conferring resistance to Magnaporthe oryzae isolates from Taiwan. Botanical Studies, 59(1), 1–14. https://doi.org/10.1186/s40529-018-0248-4. DOI: https://doi.org/10.1186/s40529-018-0248-4

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(4), 394–401. https://doi.org/10.1007/S00438-005-0032-5 DOI: https://doi.org/10.1007/s00438-005-0032-5

Mandal, N., Adak, S., Das, D. K., Sahoo, R. N., Mukherjee, J., Kumar, A., Chinnusamy, V., Das, B., Mukhopadhyay, A., Rajashekara, H., & Gakhar, S. (2023). Spectral characterization and severity assessment of rice blast disease using univariate and multivariate models. Frontiers in plant science, 14, 1067189. https://doi.org/10.3389/fpls.2023.1067189 DOI: https://doi.org/10.3389/fpls.2023.1067189

Manojkumar, H. B., Deepak, C. A., Harinikumar, K. M., Rajanna, M. P., & Chethana, B. (2020). Molecular profiling of blast resistance genes and evaluation of leaf and neck blast disease reaction in rice. Journal of Genetics, 99(1), 1–10. https://doi.org/10.1007/S12041-020-01212-Y/METRICS. DOI: https://doi.org/10.1007/s12041-020-01212-y

Miah, G., Rafii, M. Y., Ismail, M. R., Puteh, A. B., Rahim, H. A., & Latif, M. A. (2017). Marker-assisted introgression of broad-spectrum blast resistance genes into the cultivated MR219 rice variety. Journal of the Science of Food and Agriculture, 97(9), 2810–2818. https://doi.org/10.1002/jsfa.8109. DOI: https://doi.org/10.1002/jsfa.8109

Misman, S. N., & Zakaria, L. (2019). Pathotype Identification of Rice Blast Pathogen, Pyriculariaoryzae Using Differential Varieties in Peninsular Malaysia. Tropical Life Sciences Research, 30(2), 181–190. https://doi.org/10.21315/TLSR2019.30.2.13 DOI: https://doi.org/10.21315/tlsr2019.30.2.13

Mynbayeva, D., Amirova, A., Usenbekov, B., Dubina, E., Zhunusbayeva, Z., Zeinalov, Z., & Berkimbay, K. (2024). Development of rice lines by pyramiding of major blast resistance genes. 10.20944/preprints202406.1091.v2. DOI: https://doi.org/10.20944/preprints202406.1091.v1

Nihad, S. A. I., Hasan, M. K., Kabir, A., Hasan, M. A. I., Bhuiyan, M. R., Yusop, M. R., & Latif, M. A.(2022). Linkage of SSR markers with rice blast resistance and development of partial resistant advanced lines of rice (Oryza sativa) through marker-assisted selection. Physiology and Molecular Biology of Plants, 28(1), 153–169. https://doi.org/10.1007/s12298-022-01141-3. DOI: https://doi.org/10.1007/s12298-022-01141-3

Nurulnahar, E., Adam, P., Mazidah, M., Roslan, I., &Rafii, Y. M. (2020). Rice blast disease in Malaysia: Options for its control (Penyakitkarah di Malaysia: Kaedah untuk pengawalan). Journal of Tropical Agriculture and Food Science, 48(1): 11 – 23.

Pedrozo, R., Osakina, A., Huang, Y., Nicolli, C. P., Wang, L., & Jia, Y. (2025). Status on Genetic Resistance to Rice Blast Disease in the Post-Genomic Era. Plants (Basel, Switzerland), 14(5), 807. https://doi.org/10.3390/plants14050807 DOI: https://doi.org/10.3390/plants14050807

Pohan, S. D. P., Sukiran, N. L., Jamsari, J., Mohd Yusir, N. S., Mohammad Nahar, S., & Shamsudin, N. A. A. S. (2024). The Evaluation of Blast Resistance and Submergence Tolerance of New Breeding Rice (Oryza sativa L.) Lines Developed Through 4-Way Marker-Assisted Breeding. Malaysian Applied Biology, 53(5), 141–157. https://doi.org/10.55230/mabjournal.v53i5.3186. DOI: https://doi.org/10.55230/mabjournal.v53i5.3186

Qi, Z., Du, Y., Yu, J., Zhang, R., Yu, M., Cao, H., Song, T., Pan, X., Liang, D., & Liu, Y. (2023). Molecular Detection and Analysis of Blast Resistance Genes in Rice Main Varieties in Jiangsu Province, China. Agronomy, 13(1), 157. https://doi.org/10.3390/ AGRONOMY13010157/S1. DOI: https://doi.org/10.3390/agronomy13010157

Raboin, L. M., Ballini, E., Tharreau, D., Ramanantsoanirina, A., Frouin, J., Courtois, B., & Ahmadi, N. (2016). Association mapping of resistance to rice blast in upland field conditions. Rice, 9(1), 59. https://doi.org/10.1186/S12284-016-0131-4 DOI: https://doi.org/10.1186/s12284-016-0131-4

Rezk, A. A., Mohamed, H. I., & El-Beltagi, H. S. (2024). Genetic variability and diversity analysis in Oryza sativa L. genotypes using quantitative traits and SSR markers. Saudi Journal of Biological Sciences, 31(3), 103944. https://doi.org/10.1016/ J.SJBS.2024.103944 DOI: https://doi.org/10.1016/j.sjbs.2024.103944

Sabri, S., Ab Wahab, M. Z., Sapak, Z., & Mohd Anuar, I. S. (2023). A review of bacterial diseases of rice and its management in Malaysia. Food Research, 7 (Suppl. 2), 120-133. https://doi.org/10.26656/fr.2017.7(S2).20. DOI: https://doi.org/10.26656/fr.2017.7(S2).20

Singh, A., Kumar, D., Gemmati, D., Ellur, R., Singh, A., et al. (2024). Investigating Genetic Diversity and Population Structure in Rice Breeding from Association Mapping of 116 Accessions Using 64 Polymorphic SSR Markers. Crops, 4(2),180–194. https://doi.org/10.3390/CROPS4020014/S1 DOI: https://doi.org/10.3390/crops4020014

Sunian, E., Jamal, M. S., Saidon, S. A., Mokhtar, A., Kamaruzaman, R., et al. (2021). Varietipadibaharu MARDI: MR 315 (New MARDI Rice Variety: MR 315). Buletin Teknologi MARDI, 23, 1–14.

Surapaneni, M., Balakrishnan, D., Mesapogu, S., Krishnam Raju, A., Rao, Y. V., & Neelamraju, S. (2016). Genetic characterization and population structure of Indian rice cultivars and wild genotypes using core set markers. 3 Biotech, 6 (1), 95. https://doi.org/10.1007/S13205-016-0409-7 DOI: https://doi.org/10.1007/s13205-016-0409-7

Szulczyk, K. R. (2022). Estimating the economic costs and mitigation of rice blast infecting the Malaysian paddy fields. SN Business & Economics, 3(1), 16. http://dx.doi.org/10.2139/ssrn.4624433 DOI: https://doi.org/10.1007/s43546-022-00389-x

Tian, D., Deng, Y., Yang, X., Li, G., Li, Q., Zhou, H., Chen, Z., Guo, X., Su, Y., Luo, Y., & Yang, L.(2022). Association analysis of rice resistance genes and blast fungal avirulence genes for effective breeding resistance cultivars. Frontiers in Microbiology, 13, 1007492. https://doi.org/10.3389/fmicb.2022.1007492. DOI: https://doi.org/10.3389/fmicb.2022.1007492

Wang, L., Ma, Z., Zhao, J., Gu, S., Gao, L., Mukhina, Z., Ma, D., & Zheng, W. (2022). Progress on mapping, cloning, and application of rice blast resistance genes. Pakistan Journal of Botany, 54(6), 2363–2375. https://doi.org/10.30848/PJB2022-6(6). DOI: https://doi.org/10.30848/PJB2022-6(6)

Wang, X., Lee, S., Wang, J., Ma, J., Bianco, T., & Ji, Y. (2014). Current advances on genetic resistance to rice blast disease. In W. Yan, & J. Bao (Eds.) Rice - Germplasm, Genetics and Improvement. IntechOpen Publication. https://doi.org/10.5772/56824. DOI: https://doi.org/10.5772/56824

Wengler, M. R., & Talbot, N. J. (2025). Mechanisms of regulated cell death during plant infection by the rice blast fungus Magnaporthe oryzae. Cell Death & Differentiation, 1-9. https://doi.org/10.1038/s41418-024-01442-y. DOI: https://doi.org/10.1038/s41418-024-01442-y

Wu, Y., Xiao, N., Chen, Y., Yu, L., Pan, C., Li, Y., Zhang, X., Huang, N., Ji, H., Dai, Z., Chen, X., & Li, A. (2019). Comprehensive evaluation of resistance effects of pyramiding lines with different broad-spectrum resistance genes against Magnaporthe oryzae in rice (Oryza sativa L.). Rice, 12(1), 1–13. https://doi.org/10.1186/S12284-019-0264-3/TABLES/2 DOI: https://doi.org/10.1186/s12284-019-0264-3

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), e0213566. https://doi.org/10.1371/journal.pone.0211061. DOI: https://doi.org/10.1371/journal.pone.0213566

Yang, Q., Lin, F., Wang, L., & Pan, Q. (2009). Identification and mapping of Pi41, a major gene conferring resistance to rice blast in the Oryza sativa sub sp. indica reference cultivar, 93-11.TAG. Theoretical and Applied Genetics, 118(6), 1027–1034. https://doi.org/10.1007/S00122-008-0959-0. DOI: https://doi.org/10.1007/s00122-008-0959-0

Yasmin, I., Adhikary, S., Hassan, L., & Sagor, G. H. M. (2023). Biochemical changes of rice genotypes against blast (Magnaporthe

oryzae) disease and SSR marker validation for resistance genes. Journal of Phytology, 15, 63–69. https://doi.org/10.25081/ jp.2023.v15.7397.

Yasuda, N., Mitsunaga, T., Hayashi, K., Koizuma, S., & Koizumi, S. (2015). Effects of Pyramiding Quantitative Resistance Genes pi21, Pi34, and Pi35 on Rice Leaf Blast Disease. Plant Disease, 99, 904-909. https://doi.org/10.1094/PDIS-02-14-0214-RE DOI: https://doi.org/10.1094/PDIS-02-14-0214-RE

Zhang, Y., Zhao, J., Li, Y., Yuan, Z., He, H., Yang, H., Qu, H., Ma, C., & Qu, S. (2016). Transcriptome analysis highlights defense and signaling pathways mediated by rice pi21 gene with partial resistance to Magnaporthe oryzae. Frontiers in Plant Science, 7, 1834. https://doi.org/10.3389/FPLS.2016.01834/FULL DOI: https://doi.org/10.3389/fpls.2016.01834

Zhu, M., Wang, L., & Pan, Q. (2004). Identification and characterization of a new blast resistance gene located on rice chromosome 1 through linkage and differential analyses. Phytopathology, 94(5), 515–519. https://doi.org/10.1094/phyto.2004.94.5.515 DOI: https://doi.org/10.1094/PHYTO.2004.94.5.515

Zuraida, A. R., Zulkifli, A., Habibuddin, H., & Naziah, B. (2011). Regeneration of Malaysian rice variety MR 219 via somatic embryogenesis. Journal of Tropical Agriculture and Food Science, 39 (2), http://jtafs.mardi.gov.my/jtafs/39-2/MR%20219.pdf.