Please wait a minute...
Journal of Integrative Agriculture
Advanced Online Publication | Current Issue | Archive | Adv Search
An approach integrating molecular markers and differential strains of Pyricularia oryzae for identifying functional major blast-resistant genes in rice

Fengrui Zhang1, Xue Dong1, Zhiqin Lun1, Jingfeng Zhang1, Yuxin Zhang1, Houxiang Kang2, Juntao Ma3, Guomin Zhang3, Han Yan4, Wensheng Zhao1, You-Liang Peng1, Jun Yang1#

1 State Key Laboratory of Agricultural and Forestry Biosecurity, MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China

2 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China

3 Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China

4 Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China


 Highlights 

• develop molecular markers for five major blast-resistant genes in the Piz/Pi9 locus.

• screen out one P. oryzae differential strain containing only the avirulence gene Avr-Pizt.

• integrate molecular markers and P. oryzae differential strains for identifying functional major blast-resistant genes in rice.

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
摘要  

快速、准确的鉴定水稻中功能性的主效抗瘟基因是抗瘟育种的关键环节。本研究以水稻主效抗瘟位点Piz/Pi9为例,基于一套包含24个主效抗瘟基因的水稻单基因系以及一个含有Pigm的品种谷梅4,开发了PizPi2Pi9PiztPigm5个主效抗瘟基因的分子标记,并筛选出一个仅含单个无毒基因Avr-Pizt的稻瘟菌鉴别菌株。利用这些分子标记对黑龙江省193个水稻品种进行扩增,鉴定出42个品种中含有Pizt54个品种中含有Piz。同时利用仅含Avr-Pizt的稻瘟菌鉴别菌株,确认龙粳31、龙粳3013、龙粳161429个品种中存在功能性的Pizt。综上所述,本研究建立了一种整合分子标记和稻瘟菌鉴别菌株的方法来高效且精准的鉴定水稻中功能性的主效抗瘟基因。



Abstract  

The rapid and accurate identification of functional major blast-resistance genes represents a crucial and essential step in rice blast-resistance breeding. This study focused on five major blast-resistance genes at the Piz/Pi9 locus: Piz, Pi2, Pi9, Pizt, and Pigm. Molecular markers were developed for each gene, and one Pyricularia oryzae differential strain containing only the avirulence gene Avr-Pizt was identified through screening. This screening utilized a set of rice monogenic lines containing 24 major blast-resistance genes and a landrace Gumei 4 containing the major blast-resistance gene Pigm. Analysis of 193 rice varieties from Heilongjiang province using the molecular markers identified 42 varieties containing Pizt and 54 ones containing Piz. Subsequently, using the differential strain of Avr-Pizt, 29 varieties, including Longgeng 31, Longgeng 3013, and Longgeng 1614, were confirmed to contain functional Pizt. This research establishes an approach that combines molecular markers and P. oryzae differential strains for efficient and precise identification of functional major blast-resistance genes in rice.

Keywords:  rice blast       Magnaporthe oryzae              avirulent gene              Piz/Pi9 locus              Pizt  
Online: 21 October 2025  
Fund: 

This work was supported by the China Agricultural Research System (CARS-01-38), the Natural Science Foundation of China (32293244), the Natural Science Foundation of Heilongjiang Province, China (TD2022C004), and the National Key Research and Development Plan, China (2024YFD1401001). 

About author:  #Correspondence Jun Yang, E-mail: yangj@cau.edu.cn

Cite this article: 

Fengrui Zhang, Xue Dong, Zhiqin Lun, Jingfeng Zhang, Yuxin Zhang, Houxiang Kang, Juntao Ma, Guomin Zhang, Han Yan, Wensheng Zhao, You-Liang Peng, Jun Yang. 2025. An approach integrating molecular markers and differential strains of Pyricularia oryzae for identifying functional major blast-resistant genes in rice. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.10.008

Ashkani S, Rafii M Y, Shabanimofrad M, Ghasemzadeh A, Ravanfar S A, Latif M A. 2016. Molecular progress on the mapping and cloning of functional genes for blast disease in rice (Oryza sativa L.): Current status and future considerations. Critical Reviews in Biotechnology36, 353-367.

Chen Z, Bu Q, Liu G, Wang M, Wang H, Liu H, Li X, Li H, Fang J, Liang Y, Teng Z, Kang S, Yu H, Cheng Z, Xue Y, Liang C, Tang J, Li J, Chu C. 2023. Genomic decoding of breeding history to guide breeding-by-design in rice. National Science Review, 10, nwad029.

Deng Q Y, Luo J T, Zheng J M, Pu Z J. 2025. Development and breeding application of efficient KASP markers for wheat scab resistance genes based on high-throughput chips. Acta Agriculturae Boreali-sinica, 40, 175-184. (in Chinese)

Deng Y, Zhai K, Xie Z, Yang D, Zhu X, Liu J, Wang X, Qin P, Yang Y, Zhang G, Li Q, Zhang J, Wu S, Milazzo J, Mao B, Wang E, Xie H, Tharreau D, He Z. 2017. Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance. Science, 355, 962-965.

Fang W W, Liu C C, Zhang H W, Xu H, Zhou S, Fang K X, Peng Y L, Zhao W S. 2018. Selection of differential isolates of Magnaporthe oryzae for postulation of blast resistance genes. Phytopathology, 108, 878-884.

Li W, Wang B, Wu J, Lu G, Hu Y, Zhang X, Zhang Z, Zhao Q, Feng Q, Zhang H, Wang Z, Wang G, Han B, Wang Z, Zhou B. 2009. The Magnaporthe oryzae avirulence gene AvrPiz-t encodes a predicted secreted protein that triggers the immunity in rice mediated by the blast resistance gene Piz-t. Molecular Plant-Microbe Interactions, 22, 411-420.

Ling Z Z, Jiang W R, Wang J L, Lei C L. 2001. Study and utilization of the common sensibility of rice variety Lijiang Xintuan Heigu. Scientia Agricultura Sinica, 34, 1-4. (in Chinese)

Liu H, Zhuo F Y, Guo R, Si Z S, Zhu F, Cao S W, Zhu X X, Qin B R, Xu X, Liu W C. 2023. Evaluation report on the contribution rate for rice pest and disease control of plant protection in 2022. Plant Medicine, 2, 18-26. (in Chinese)

Liu J T, Zhang F R, Zhao W S, Liu J F, Chen Q, Peng Y L, Yang J. 2025. Research progress on green prevention and control of rice blast disease. Acta Phytopathologica Sinica, 55, 1-20. (in Chinese)

Miah G, Rafii M Y, Ismail M R, Puteh A B, Rahim H A, Asfaliza R, Latif M A. 2013. Blast resistance in rice: A review of conventional breeding to molecular approaches. Molecular Biology Reports, 40, 2369-2388.

Newton C R, Graham A, Heptinstall L E, Powell S J, Summers C, Kalsheker N, Smith J C, Markham A F. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Research, 17, 2503-2516.

Qu S, Liu G, Zhou B, Bellizzi M, Zeng L, Dai L, Han B, Wang G L. 2006. The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice. Genetics, 172, 1901-1914.

Ren H, Lv X H, Du M. 2017. Molecular marker assisted breeding method for multi resistant rice. Jiangsu Agricultural Sciences, 45, 154-158. (in Chinese)

Sahu P K, Sao R, Choudhary D K, Thada A, Kumar V, Mondal S, Das B K, Jankuloski L, Sharma D. 2022. Advancement in the breeding, biotechnological and genomic tools towards development of durable genetic resistance against the rice blast disease. Plants (Basel), 11, 2386.

Shen R, Yao Q, Zhong D, Zhang X, Li X, Cao X, Dong C, Tian Y, Zhu J K, Lu Y. 2023. Targeted insertion of regulatory elements enables translational enhancement in rice. Frontiers in Plant Science, 14, 1134209.

Silue D, Notteghem J L, Tharreau D. 1992. Evidence of a gene-for-gene relationship in the Oryza sativa-Magnaporthe grisea pathosystem. Phytopathology, 82, 577-580.

Sorensen P L, Christensen G, Karki H S, Endelman J B. 2023. A KASP marker for the potato late blight resistance gene RB/Rpi-blb1. American Journal of Potato Research, 100, 240-246.

Tian D G, Chen Z J, Chen Z Q, Zhou Y C, Wang Z H, Wang F, Chen S B. 2016. Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi2 and Pi9 have not been widely deployed in Chinese indica rice cultivars. Rice (N Y), 9, 19.

Tian D G, Lin Y, Chen Z Q, Chen Z J, Yang F, Wang F, Wang Z H, Wang M. 2020. Exploring the distribution of blast resistance alleles at the Pi2/9 locus in major rice-producing areas of China by a novel Indel marker. Plant Disease, 104, 1932-1938.

Tsunematsu H, Yanoria M J, Ebron L A, Hayashi N, Ando I, Kato H, Imbe T, Khush G S. 2000. Development of monogenic lines of rice for blast resistance. Breeding Science, 50, 229-234.

Valent B, Chumley F G. 1991. Molecular genetic analysis of the rice blast fungus, Magnaporthe grisea. Annual Review of Phytopathology, 29, 443-467.

Wang F Q, Chen Z H, Xu Y, Wang J, Li W Q, Fan F J, Chen L Q, Tao Y J, Zhong W G, Yang J. 2019. Development and application of the functional marker for the broad-spectrum blast resistance gene PigmR in rice. Scientia Agricultura Sinica, 52, 955-967. (in Chinese)

Wang G L, Valent B. 2017. Durable resistance to rice blast. Science, 355, 906-907.

Wang J Y, Wang R Y, Fang H, Zhang C Y, Zhang F, Hao Z Y, You X M, Shi X T, Park C H, Hua K YHe F, Bellizzi M, Xuan Vo K T, Jeon J S, Ning Y S, Wang G L. 2021. Two VOZ transcription factors link an E3 ligase and an NLR immune receptor to modulate immunity in rice. Molecular Plant, 14, 253-266.

Wang Y, Zhao J M, Zhang LX, Wang P, Wang S W, Wang H, Wang X X, Liu Z H, Zheng W J. 2016. Analysis of the diversity and function of the alleles of the rice blast resistance genes Piz-t, Pita and Pik in 24 rice cultivars. Journal of Integrative Agriculture, 15, 1423-1431.

Xiao N, Pan C, Li Y, Wu Y, Cai Y, Lu Y, Wang R, Yu L, Shi W, Kang H, Zhu Z, Huang N, Zhang X, Chen Z, Liu J, Yang Z, Ning Y, Li A. 2021. Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice. Genome Biology, 22, 283.

Yang H, Huang Y Y, Yi C L, Shi J, Tan C T, Ren W R, Wang W M. 2023. Development and application of specific molecular markers for six rice blast resistance genes at Pi9 locus in rice. Scientia Agricultura Sinica, 56, 4219-4233. (in Chinese)

Yang L, Zhao M, Sha G, Sun Q, Gong Q, Yang Q, Xie K, Yuan M, Mortimer J C, Xie W, Wei T, Kang Z, Li G. 2022. The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains. Computational and Structural Biotechnology Journal, 20, 1012-1026.

Ye J, Wang K, Wang Y, Zhao Z, Yan Y, Yang H, Zhang L, Hu Z, Shi Z, Sun D, Bai J, Cao L, Wu S. 2025. Improving panicle blast resistance and fragrance in a high-quality japonica rice variety through breeding. Frontiers in Plant Science, 15, 1507827.

Zhai K, Deng Y, Liang D, Tang J, Liu J, Yan B, Yin X, Lin H, Chen F, Yang D, Xie Z, Liu J Y, Li Q, Zhang L, He Z. 2019. RRM transcription factors interact with NLRs and regulate broad-spectrum blast resistance in rice. Molecular Cell, 74, 996-1009.

Zhang A, Liu Y, Wang F, Kong D, Bi J, Zhang F, Luo X, Wang J, Liu G, Luo L, Yu X. 2022. Molecular breeding of water-saving and drought-resistant rice for blast and bacterial blight resistance. Plants (Basel), 11, 2641.

Zhang G M, Ma J T, Xiao J L, Liu Y X, Xin A H, Ren Y. 2010. The blast resistance of 24 monogenic rice lines to prevalence physiologic races of Heilongjiang and analysis of pathogenicity association. Chinese Agricultural Science Bulletin, 26, 233-237. (in Chinese)

Zhang H W, Fang W W, Liu C C, Zhao W S, Peng Y L. 2014. Identification of the pathotype of Pyricularia oryzae by inoculating on scratched rice leaves in vitro. Plant Protection, 40, 121-125. (in Chinese)

Zhou B, Qu S, Liu G, Dolan M, Sakai H, Lu G, Bellizzi M, Wang G L. 2006. The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity to Magnaporthe grisea. Molecular Plant-Microbe Interactions, 19, 1216-1228.

Zhou W M, Dong L Y, Liu S F, Liu P, Zhang X W, Li X D, Huang L Y, Yang Q Z. 2021. Development of specific molecular markers for rice blast resistance genes and their application in Yunnan japonica rice. Molecular Plant Breeding, 25, 1-25. (in Chinese)

[1] Niu Wang, Weidong Zhang, Zhenyu Zhong, Xiongbo Zhou, Xinran Shi, Xin Wang. FGF7 secreted from dermal papillae cell regulates the proliferation and differentiation of hair follicle stem cell[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3583-3597.
[2] Lichao Zhai, Shijia Song, Lihua Zhang, Jinan Huang, Lihua Lv, Zhiqiang Dong, Yongzeng Cui, Mengjing Zheng, Wanbin Hou, Jingting Zhang, Yanrong Yao, Yanhong Cui, Xiuling Jia. Subsoiling before winter wheat alleviates the kernel position effect of densely grown summer maize by delaying post-silking root–shoot senescence[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3384-3402.
[3] Tiantian Chen, Lei Li, Dan Liu, Yubing Tian, Lingli Li, Jianqi Zeng, Awais Rasheed, Shuanghe Cao, Xianchun Xia, Zhonghu He, Jindong Liu, Yong Zhang. Genome wide linkage mapping for black point resistance in a recombinant inbred line population of Zhongmai 578 and Jimai 22[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3311-3321.
[4] Zuxian Chen, Bingbing Zhao, Yingying Wang, Yuqing Du, Siyu Feng, Junsheng Zhang, Luxiang Zhao, Weiqiang Li, Yangbao Ding, Peirong Jiao. H5N1 avian influenza virus PB2 antagonizes duck IFN-β signaling pathway by targeting mitochondrial antiviral signaling protein[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3614-3625.
[5] Yang Sun, Yu Liu, Li Zhou, Xinyan Liu, Kun Wang, Xing Chen, Chuanqing Zhang, Yu Chen. Activity of fungicide cyclobutrifluram against Fusarium fujikuroi and mechanism of the pathogen resistance associated with point mutations in FfSdhB, FfSdhC2 and FfSdhD[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3511-3528.
[6] Yufeng Xiao, Meiqi Dong, Xian Wu, Shuang Liang, Ranhong Li, Hongyu Pan, Hao Zhang. Enrichment, domestication, degradation, adaptive mechanism, and nicosulfuron bioremediation of bacteria consortium YM2[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3529-3545.
[7] Yuxin He, Fei Deng, Chi Zhang, Qiuping Li, Xiaofan Huang, Chenyan He, Xiaofeng Ai, Yujie Yuan, Li Wang, Hong Cheng, Tao Wang, Youfeng Tao. Wei Zhou, Xiaolong Lei, Yong Chen, Wanjun Ren. Can a delayed sowing date improve the eating and cooking quality of mechanically transplanted rice in the Sichuan Basin, China?[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3368-3383.
[8] Dili Lai, Md. Nurul Huda, Yawen Xiao, Tanzim Jahan, Wei Li, Yuqi He, Kaixuan Zhang, Jianping Cheng, Jingjun Ruan, Meiliang Zhou. Evolutionary and expression analysis of sugar transporters from Tartary buckwheat revealed the potential function of FtERD23 in drought stress[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3334-3350.
[9] Zishuai Wang, Wangchang Li, Zhonglin Tang. Enhancing the genomic prediction accuracy of swine agricultural economic traits using an expanded one-hot encoding in CNN models[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3574-3582.
[10] Yunji Xu, Xuelian Weng, Shupeng Tang, Weiyang Zhang, Kuanyu Zhu, Guanglong Zhu, Hao Zhang, Zhiqin Wang, Jianchang Yang. Untargeted lipidomic analysis of milled rice under different alternate wetting and soil drying irrigation regimes[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3351-3367.
[11] Minghui Li, Yilan Chen, Siqiao Wang, Xueke Sun, Yongkun Du, Siyuan Liu, Ruiqi Li, Zejie Chang, Peiyang Ding, Gaiping Zhang. Plug-and-display nanoparticle immunization of the core epitope domain induces potent neutralizing antibody and cellular immune responses against PEDV[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3598-3613.
[12] Jing Zhou, Bingshuai Du, Yibo Cao, Kui Liu, Zhihua Ye, Yiming Huang, Lingyun Zhang. Genome-wide identification of sucrose transporter genes in Camellia oleifera and characterization of CoSUT4[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3494-3510.
[13] Yuheng Wang, Furong Kang, Bo Yu, Quan Long, Huaye Xiong, Jiawei Xie, Dong Li, Xiaojun Shi, Prakash Lakshmanan, Yueqiang Zhang, Fusuo Zhang. Magnesium supply is vital for improving fruit yield, fruit quality and magnesium balance in citrus orchards with increasingly acidic soil[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3641-3655.
[14] Mingxin Feng, Ying Hu, Xin Yang, Jingwen Li, Haochen Wang, Yujia Liu, Haijun Ma, Kai Li, Jiayin Shang, Yulin Fang, Jiangfei Meng. Uncovering the miRNA-mediated regulatory network involved in postharvest senescence of grape berries[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3465-3483.
[15] Li Liu, Yifeng Feng, Ziqi Han, Yaxiao Song, Jianhua Guo, Jing Yu, Zidun Wang, Hui Wang, Hua Gao, Yazhou Yang, Yuanji Wang, Zhengyang Zhao. Functional analysis of the xyloglucan endotransglycosylase/hydrolase gene MdXTH2 in apple fruit firmness formation[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3418-3434.
No Suggested Reading articles found!