Host-Adaptive Divergence Shapes the Genetic Architecture of <i>Magnaporthe oryzae</i> in Southern China’s Rice Agroecosystems
Rice blast disease, caused by the ascomycete fungus <i>Magnaporthe oryzae</i> (syn. <i>Pyricularia oryzae</i>), poses a severe threat to global rice production. Southern China, a major rice-growing region characterized by diverse agroecological conditions, faces substantial c...
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2025-06-01
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| author | Xin Liu Jun Fu Zhao Deng Xinwei Chen Xiaochun Hu Zhouyi Tu Qiuyi Wang Yuxuan Zhu Pengcheng Chen Zhenan Bai Tiangang Liu Xuanwen Zhang Peng Qin Kai Wang Nan Jiang Yuanzhu Yang |
| author_facet | Xin Liu Jun Fu Zhao Deng Xinwei Chen Xiaochun Hu Zhouyi Tu Qiuyi Wang Yuxuan Zhu Pengcheng Chen Zhenan Bai Tiangang Liu Xuanwen Zhang Peng Qin Kai Wang Nan Jiang Yuanzhu Yang |
| author_sort | Xin Liu |
| collection | DOAJ |
| description | Rice blast disease, caused by the ascomycete fungus <i>Magnaporthe oryzae</i> (syn. <i>Pyricularia oryzae</i>), poses a severe threat to global rice production. Southern China, a major rice-growing region characterized by diverse agroecological conditions, faces substantial challenges from blast disease, yet our understanding of the genetic structure of <i>M. oryzae</i> populations in this region remains limited. Here, we analyzed 885 <i>M. oryzae</i> strains from 18 nurseries across four rice ecological regions in Southern China using a panel of genome-wide SNP markers. Phylogenetic and principal component analyses revealed three distinct clonal lineages: lineage I (58.19%), lineage II (21.36%), and lineage III (20.45%). Lineage I exhibited a broader geographic distribution compared to the other two lineages. Host-adapted divergence was observed across rice subspecies, with lineage III predominantly associated with <i>japonica</i> growing-regions, while lineages I and II mainly colonized <i>indica</i> rice-growing regions. Genetic diversity exhibited significant spatial heterogeneity, with the nucleotide diversity (π) ranging from 0.17 in South China to 0.32 in the Middle–Lower Yangtze River region, reflecting differential cropping systems. The predominantly negative Tajima’s <i>D</i> values across populations suggested recent expansion or selective sweeps, likely driven by host resistance pressures. High genetic differentiation between lineage I and other lineages contrasted with low divergence between lineages II and III, indicating distinct evolutionary trajectories. Furthermore, an uneven distribution of mating types among three genetic lineages was observed, suggesting limited sexual recombination within clonal lineages. The information obtained in this study may be beneficial in devising suitable strategies to control rice blast disease in Southern China. |
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| institution | Matheson Library |
| issn | 2309-608X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
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| series | Journal of Fungi |
| spelling | doaj-art-bad4bbce4b1c4c8fb77c0090c3bb8af02025-07-25T13:27:17ZengMDPI AGJournal of Fungi2309-608X2025-06-0111748510.3390/jof11070485Host-Adaptive Divergence Shapes the Genetic Architecture of <i>Magnaporthe oryzae</i> in Southern China’s Rice AgroecosystemsXin Liu0Jun Fu1Zhao Deng2Xinwei Chen3Xiaochun Hu4Zhouyi Tu5Qiuyi Wang6Yuxuan Zhu7Pengcheng Chen8Zhenan Bai9Tiangang Liu10Xuanwen Zhang11Peng Qin12Kai Wang13Nan Jiang14Yuanzhu Yang15Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaKey Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, ChinaRice blast disease, caused by the ascomycete fungus <i>Magnaporthe oryzae</i> (syn. <i>Pyricularia oryzae</i>), poses a severe threat to global rice production. Southern China, a major rice-growing region characterized by diverse agroecological conditions, faces substantial challenges from blast disease, yet our understanding of the genetic structure of <i>M. oryzae</i> populations in this region remains limited. Here, we analyzed 885 <i>M. oryzae</i> strains from 18 nurseries across four rice ecological regions in Southern China using a panel of genome-wide SNP markers. Phylogenetic and principal component analyses revealed three distinct clonal lineages: lineage I (58.19%), lineage II (21.36%), and lineage III (20.45%). Lineage I exhibited a broader geographic distribution compared to the other two lineages. Host-adapted divergence was observed across rice subspecies, with lineage III predominantly associated with <i>japonica</i> growing-regions, while lineages I and II mainly colonized <i>indica</i> rice-growing regions. Genetic diversity exhibited significant spatial heterogeneity, with the nucleotide diversity (π) ranging from 0.17 in South China to 0.32 in the Middle–Lower Yangtze River region, reflecting differential cropping systems. The predominantly negative Tajima’s <i>D</i> values across populations suggested recent expansion or selective sweeps, likely driven by host resistance pressures. High genetic differentiation between lineage I and other lineages contrasted with low divergence between lineages II and III, indicating distinct evolutionary trajectories. Furthermore, an uneven distribution of mating types among three genetic lineages was observed, suggesting limited sexual recombination within clonal lineages. The information obtained in this study may be beneficial in devising suitable strategies to control rice blast disease in Southern China.https://www.mdpi.com/2309-608X/11/7/485<i>Magnaporthe oryzae</i>rice blastSNPgenetic diversitypopulation structuremating type |
| spellingShingle | Xin Liu Jun Fu Zhao Deng Xinwei Chen Xiaochun Hu Zhouyi Tu Qiuyi Wang Yuxuan Zhu Pengcheng Chen Zhenan Bai Tiangang Liu Xuanwen Zhang Peng Qin Kai Wang Nan Jiang Yuanzhu Yang Host-Adaptive Divergence Shapes the Genetic Architecture of <i>Magnaporthe oryzae</i> in Southern China’s Rice Agroecosystems Journal of Fungi <i>Magnaporthe oryzae</i> rice blast SNP genetic diversity population structure mating type |
| title | Host-Adaptive Divergence Shapes the Genetic Architecture of <i>Magnaporthe oryzae</i> in Southern China’s Rice Agroecosystems |
| title_full | Host-Adaptive Divergence Shapes the Genetic Architecture of <i>Magnaporthe oryzae</i> in Southern China’s Rice Agroecosystems |
| title_fullStr | Host-Adaptive Divergence Shapes the Genetic Architecture of <i>Magnaporthe oryzae</i> in Southern China’s Rice Agroecosystems |
| title_full_unstemmed | Host-Adaptive Divergence Shapes the Genetic Architecture of <i>Magnaporthe oryzae</i> in Southern China’s Rice Agroecosystems |
| title_short | Host-Adaptive Divergence Shapes the Genetic Architecture of <i>Magnaporthe oryzae</i> in Southern China’s Rice Agroecosystems |
| title_sort | host adaptive divergence shapes the genetic architecture of i magnaporthe oryzae i in southern china s rice agroecosystems |
| topic | <i>Magnaporthe oryzae</i> rice blast SNP genetic diversity population structure mating type |
| url | https://www.mdpi.com/2309-608X/11/7/485 |
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