All Issue

2025 Vol.70, Issue 4 Preview Page

Original Research Article

Identification of Major QTLs Conferring Rice Blast Resistance Using an SNDH Population
Dan-Dan Zhao1†
,
Hyunjung Chung2†
,
Muhammad Farooq1
,
Nam-Gu Kim3
,
Bo-Seong Seo2
,
Soo Yeon Choi2
,
Shinhwa Kim2
,
Sang-Min Kim2
,
Jang-Ho Lee4
,
Xiao-Xuan Du5
,
Kyung-Min Kim67*
1Postdoctoral Researcher, Crop Environment Research Division, National Institute of Crop and Food Science, Rural Development Administration, Wanju 55365, Korea
2Junior Scientist, Crop Environment Research Division, National Institute of Crop and Food Science, Rural Development Administration, Wanju 55365, Korea
3Researcher, Crop Environment Research Division, National Institute of Crop and Food Science, Rural Development Administration, Wanju 55365, Korea
4Senior Scientist, Crop Environment Research Division, National Institute of Crop and Food Science, Rural Development Administration, Wanju 55365, Korea
5Professor, College of Marine and Bioengineering, YanCheng Institute of Technology, 211 Jianjun East Road, Yangcheng City, Jiangsu Province, 224051, China
6Professor, Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
7Professor, Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea
*Corresponding Author
†D.-D. Zhao and H. Chung contributed equally.
1 December 2025. pp. 248-256
PDF XML Citation
Abstract

The rice blast pathogen, Magnaporthe oryzae, remains a significant threat to global rice production, often causing substantial yield losses in regions with favorable environmental conditions. Given the limitations of chemical control and the rapid evolution of pathogen populations, developing rice varieties with durable and broad-spectrum blast resistance is crucial for long-term disease management and reducing the overall impact on rice cultivation. To address this need, a qualitative trait locus (QTL) analysis was performed using a set of representative Korean isolates and a ‘Samgang/Nagdong’ doubled haploid (SNDH) population to identify key loci associated with rice blast resistance. Two major and significant loci, qrbr2 (chromosome 2; RM318–s2038) and qrbr6 (chromosome 6; s6015–s6018), were detected with LOD values of 4.13 and 5.15, accounting for 44% and 43% of the phenotypic variation, respectively. Among the candidate genes within these regions, Os02g0674700 (Osrbrq2), which shares a strong homology with RING-type E3 ubiquitin protein ligases, has emerged as a promising gene that contributes to resistance within the qrbr2 locus. These findings underscore the importance of qrbr2 and qrbr6, along with the Osrbrq2 candidate gene, in shaping rice defense responses, and provide a valuable basis for further characterization and marker-assisted breeding to enhance rice blast resistance.

Keywords
blast resistance
QTL analysis
rice blast
rice production
References
1

Ashkani, S., M. Y. Rafii, M. Shabanimofrad, G. Miah, M. Sahebi, P. Azizi, F. A. Tanweer, M. S. Akhtar, and A. Nasehi. 2015. Molecular breeding strategy and challenges towards improvement of blast disease resistance in rice crop. Front. Plant Sci. 6 : 886.

10.3389/fpls.2015.0088626635817PMC4644793
2

Bandumula, N. 2018. Rice production in Asia: key to global food security. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 88(4) : 1323-1328.

10.1007/s40011-017-0867-7
3

Devanna, B. N., S. Sucharita, N. C. Sunitha, C. Anilkumar, P. K. Singh, D. Pramesh, S. Samantaray, L. Behera, J. L. Katara, C. Parameswaran, P. Rout, S. Sabarinathan, H. Rajashekara, and T. R. Sharma. 2024. Refinement of rice blast disease resistance QTLs and gene networks through meta-QTL analysis. Sci. Rep. 14(1) : 16458.

10.1038/s41598-024-64142-039013915PMC11252161
4

Du, Z., X. Zhou, Y. Ling, Z. Zhang, and Z. Su. 2010. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38 : W64-70.

10.1093/nar/gkq31020435677PMC2896167
5

Fakih, Z. and H. Germain. 2025. Implication of ribosomal protein in abiotic and biotic stress. Planta 261(4) : 1-26.

10.1007/s00425-025-04665-6
6

Fakih, Z., M. B. Plourde, and H. Germain. 2023. Differential participation of plant ribosomal proteins from the small ribosomal subunit in protein translation under stress. Biomolecules 13(7) : 1160.

10.3390/biom1307116037509195PMC10377644
7

Jiang, H., Y. Feng, L. Qiu, G. Gao, Q. Zhang, and Y. He. 2020. Identification of blast resistance QTLs based on two advanced backcross populations in rice. Rice 13(1) : 31.

10.1186/s12284-020-00392-632488495PMC7266886
8

Li, W., S. Zhong, G. Li, Q. Li, B. Mao, Y. Deng, H. hang, L. Zeng, F. Song, and Z. He. 2011. Rice RING protein OsBBI1 with E3 ligase activity confers broad-spectrum resistance against Magnaporthe oryzae by modifying the cell wall defence. Cell Res. 21(5) : 835-848.

10.1038/cr.2011.421221134PMC3203666
9

Liu, X., X. Hu, Z. Tu, Z. Sun, P. Qin, Y. Liu, X. Chen, Z. Li, N. Jiang, and Y. Yang. 2024. The roles of Magnaporthe oryzae avirulence effectors involved in blast resistance/susceptibility. Front. Plant Sci. 15 : 1478159.

10.3389/fpls.2024.147815939445147PMC11496149
10

Liu, Z., J. Qiu, Z. Shen, C. Wang, N. Jiang, H. Shi, and Y. Kou. 2023. The E3 ubiquitin ligase OsRGLG5 targeted by the Magnaporthe oryzae effector AvrPi9 confers basal resistance against rice blast. Plant Commun. 4(5).

10.1016/j.xplc.2023.10062637177781PMC10504590
11

Liu, Z., Y. Zhu, H. Shi, J. Qiu, X. Ding, and Y. Kou. 2021. Recent progress in rice broad-spectrum disease resistance. Int. J. Mol. Sci. 22(21) : 11658.

10.3390/ijms22211165834769087PMC8584176
12

Manly, K. F. and J. M. Olson. 1999. Overview of QTL mapping software and introduction to Map Manager QT. Mamm. Genome 10(4) : 327-334.

10.1007/s003359900997
13

McCough, S. R. and R. W. Doerge. 1995. QTL mapping in rice. Trends Genet. 11(12) : 482-487.

10.1016/S0168-9525(00)89157-X
14

Miah, G., M. Y. Rafii, M. R. Ismail, A. B. Puteh, H. A. Rahim, R. Asfaliza, and M. A. Latif. 2013. Blast resistance in rice: a review of conventional breeding to molecular approaches. Mol. Biol. Rep. 40(3) : 2369-2388.

10.1007/s11033-012-2318-0
15

Park, C. H., S. Chen, G. Shirsekar, B. Zhou, C. H. Khang, P. Songkumarn, A. J. Afzal, Y. Ning, R. Wang, M. Bellizzi, B. Valent, and G. L. Wang. 2012. The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern–triggered immunity in rice. The Plant Cell 24(11) : 4748-4762.

10.1105/tpc.112.10542923204406PMC3531864
16

Park, J. R., S. Yun, R. Jan, and K. M. Kim. 2020. Screening and identification of brown planthopper resistance genes OsCM9 in rice. Agronomy 10(12) : 1865.

10.3390/agronomy10121865
17

Pedrozo, R., A. Osakina, Y. Huang, C. P. Nicolli, L. Wang, and Y. Jia. 2025. Status on genetic resistance to rice blast disease in the post-genomic era. Plants 14(5) : 807.

10.3390/plants1405080740094775PMC11901910
18

Sakai, H., S. S. Lee, T. Tanaka, H. Numa, J. Kim, Y. Kawahara, H. Wakimoto, C. C. Yang, M. Lwamoto, T. Abe, Y. Yamada, A. Muto, H. Inokuchi, T. Ikemura, T. Matsumoto, T. Sasaki, and T. Itoh. 2013. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 54(2) : e6-e6.

10.1093/pcp/pcs18323299411PMC3583025
19

Sallaud, C., M. Lorieux, E. Roumen, D. Tharreau, R. Berruyer, P. Svestasrani, O. Garsmeur, A. Ghesquiere, and J. L. Notteghem. 2003. Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy. Theor Appl Genet 106(5) : 794-803.

10.1007/s00122-002-1088-9
20

Sato, Y., H. Takehisa, K. Kamatsuki, H. Minami, N. Namiki, H. Ikawa, H. Ohyanagi, K. Sugimoto, B. A. Antonio, and Y. Nagamura. 2013. RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. Nucleic Acids Res. 41(D1) : D1206-D1213.

10.1093/nar/gks112523180765PMC3531122
21

Sharma, S. K., D. Sharma, R. P. Meena, M. K. Yadav, R. Hosahatti, A. K. Dubey, P. Sharma, S. Kumar, D. Pramesh, S. U. Nabi, S. Bhuvaneshwari, Y. R. Anand, S. K. Dubey, and T. S. Singh. 2021. Recent insights in rice blast disease resistance. Blast Disease of Cereal Crops.: Evolution and Adaptation in Context of Climate Change. Fungal Biology. Springer, pp. 89-123.

10.1007/978-3-030-60585-8_7
22

Sharma, T. R., A. K. Rai, S. K. Gupta, J. Vijayan, B. N. Devanna, and S. Ray. 2012. Rice blast management through host-plant resistance: retrospect and prospects. Agric. Res. 1(1) : 37-52.

10.1007/s40003-011-0003-5
23

Su, J., W. Wang, J. Han, S. Chen, C. Wang, L. Zeng, A. Feng, J. Yang, B. Zhou, and X. Zhu. 2015. Functional divergence of duplicated genes results in a novel blast resistance gene Pi50 at the Pi2/9 locus. Theor Appl Genet 128(11) : 2213-2225.

10.1007/s00122-015-2579-9
24

Szklarczyk, D., A. L. Gable, D. Lyon, A. Junge, S. Wyder, J. Huerta-Cepas, M. Simonovic, N. T. Doncheva, J. H. Morris, P. Bork, L. J. Jensen, and C. V. Mering. 2019. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47(D1) : D607-D613.

10.1093/nar/gky113130476243PMC6323986
25

Tian, T., L. Chen, Y. Ai, and H. He. 2022. Selection of candidate genes conferring blast resistance and heat tolerance in rice through integration of Meta-QTLs and RNA-Seq. Genes 13(2) : 224.

10.3390/genes1302022435205268PMC8871662
26

Valent, B., L. Farrall, and F. G. Chumley. 1991. Magnaporthe grisea genes for pathogenicity and virulence identified through a series of backcrosses. Genetics 127(1) : 87.

10.1093/genetics/127.1.872016048PMC1204315
27

Vasudevan, K., W. Gruissem, and N. K. Bhullar. 2015. Identification of novel alleles of the rice blast resistance gene Pi54. Sci. Rep. 5(1) : 15678.

10.1038/srep1567826498172PMC4620502
28

Wang, J., H. Hu, X. Jiang, S. Zhang, W. Yang, J. Dong, T. Yang, Y. Ma, L. Zhou, J. Chen, S. Nie, C. Liu, Y. Ning, X. Zhu, B. Liu, J. Yang, and J. Zhao. 2024. Pangenome-wide association study and transcriptome analysis reveal a novel QTL and candidate genes controlling both panicle and leaf blast resistance in rice. Rice 17(1) : 27.

10.1186/s12284-024-00707-x38607544PMC11014823
29

Waszczak, C., M. Carmody, and J. Kangasjärvi. 2018. Reactive oxygen species in plant signaling. Annu. Rev. Plant. Biol. 69(1) : 209-236.

10.1146/annurev-arplant-042817-040322
30

Xiao, N., Y. Wu, C. Pan, L. Yu, Y. Chen, G. Liu, Y. Li, X. Zhang, Z. Wang, Z. Dai, C. Liang, and A. Li. 2017. Improving of rice blast resistances in japonica by pyramiding major R genes. Front. Plant Sci. 7 : 1918.

10.3389/fpls.2016.0191828096805PMC5206849
31

Zeng, Z. B. 1994. Precision mapping of quantitative trait loci. Genetics 136(4) : 1457.

10.1093/genetics/136.4.14578013918PMC1205924
32

Zhang, H., J. Yang, M. Liu, X. Xu, L. Yang, X. Liu, Y. Peng, and Z. Zhang. 2024. Early molecular events in the interaction between Magnaporthe oryzae and rice. Phytopathol. Res. 6(1) : 9.

10.1186/s42483-024-00226-z
33

Zhang, X., L. Tian, C. Luo, T. Ma, P. Li, J. Sun, and Y. Zhang. 2021. QTL mapping of rice blast resistance based on RIL population in rice. Journal of Henan Agricultural Sciences 50(11) : 97.

34

Zhao, D. D., H. Chung, Y. H. Jang, M. Farooq, S. Y. Choi, X. X. Du, and K. M. Kim. 2024. Analysis of rice blast fungus genetic diversity and identification of a novel blast resistance OsDRq12 gene. Phytopathology® 114(8) : 1917-1925.

10.1094/PHYTO-02-24-0050-R
35

Zhao, D. D., H. Chung, N. G. Kim, W. I. Lee, S. Y. Choi, S. Kim, S. M. Kim, J. B. Chun, N. J. Choi, J. R. Lim, B. Y. Seo, and J. Y. Yoon. 2026. ‘Disease incidence and race diversity of rice blast in Korea from 2020 to 2022. Plant Disease. (In press).

Information
  • Publisher :The Korean Society of Crop Science
  • Publisher(Ko) :한국작물학회
  • Journal Title :The Korean Journal of Crop Science
  • Journal Title(Ko) :한국작물학회지
  • Volume : 70
  • No :4
  • Pages :248-256
  • Received Date : 2025-10-30
  • Revised Date : 2025-11-25
  • Accepted Date : 2025-11-26
  • DOI :https://doi.org/10.7740/kjcs.2025.70.4.248
Journal Informaiton The Korean Journal of Crop Science The Korean Journal of Crop Science
Online Submission
  • NRF
  • KOFST
  • KISTI Current Status
  • KISTI Cited-by
  • crosscheck
  • orcid
  • open access
  • ccl
Journal Informaiton Journal Informaiton - close