Razalli Izreen Izzati, Abdullah-Zawawi Muhammad-Redha, Zainal Abidin Rabiatul Adawiah, Harun Sarahani, Che Othman Muhamad Hafiz, Ismail Ismanizan, Zainal Zamri
Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor, Malaysia.
UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia.
Sci Rep. 2025 Mar 12;15(1):8465. doi: 10.1038/s41598-025-92942-5.
Rice, a staple food consumed by half of the world's population, is severely affected by the combined impact of abiotic and biotic stresses, with the former causing increased susceptibility of the plant to pathogens. Four microarray datasets for drought, salinity, tungro virus, and blast pathogen were retrieved from the Gene Expression Omnibus database. A modular gene co-expression (mGCE) analysis was conducted, followed by gene set enrichment analysis to evaluate the upregulation of module activity across different stress conditions. Over-representation analysis was conducted to determine the functional association of each gene module with stress-related processes and pathways. The protein-protein interaction network of mGCE hub genes was constructed, and the Maximal Clique Centrality (MCC) algorithm was applied to enhance precision in identifying key genes. Finally, genes implicated in both abiotic and biotic stress responses were validated using RT-qPCR. A total of 11, 12, 46, and 14 modules containing 85, 106, 253, and 143 hub genes were detected in drought, salinity, tungro virus, and blast. Modular genes in drought were primarily enriched in response to heat stimulus and water deprivation, while salinity-related genes were enriched in response to external stimuli. For the tungro virus and blast pathogen, enrichment was mainly observed in the defence and stress responses. Interestingly, RPS5, PKG, HSP90, HSP70, and MCM were consistently present in abiotic and biotic stresses. The DEG analysis revealed the upregulation of MCM under the tungro virus and downregulation under blast and drought in resistant rice, indicating its role in viral resistance. HSP70 showed no changes, while HSP90 was upregulated in susceptible rice during blast and drought. PKG increased during drought but decreased in japonica rice under salinity. RPS5 was highly upregulated during blast in both resistant and susceptible rice. The RT-qPCR analysis showed that all five hub genes were upregulated in all treatments, indicating their role in stress responses and potential for crop improvement.
水稻是全球一半人口的主食，受到非生物和生物胁迫的综合影响，前者会增加植物对病原体的易感性。从基因表达综合数据库中检索到了四个分别针对干旱、盐度、东格鲁病毒和稻瘟病菌的微阵列数据集。进行了模块化基因共表达（mGCE）分析，随后进行基因集富集分析，以评估不同胁迫条件下模块活性的上调情况。进行了过度表达分析，以确定每个基因模块与胁迫相关过程和途径的功能关联。构建了mGCE中心基因的蛋白质-蛋白质相互作用网络，并应用最大团中心性（MCC）算法提高识别关键基因的精度。最后，使用RT-qPCR验证了涉及非生物和生物胁迫反应的基因。在干旱、盐度、东格鲁病毒和稻瘟病中分别检测到了11个、12个、46个和14个模块，包含85个、106个、253个和143个中心基因。干旱中的模块化基因主要富集在对热刺激和水分剥夺的反应中，而与盐度相关的基因则富集在对外部刺激的反应中。对于东格鲁病毒和稻瘟病菌，主要在防御和胁迫反应中观察到富集。有趣的是，RPS5、PKG、HSP90、HSP70和MCM在非生物和生物胁迫中始终存在。差异表达基因分析显示，在抗性水稻中，MCM在东格鲁病毒感染下上调，在稻瘟病和干旱下下调，表明其在病毒抗性中的作用。HSP70没有变化，而HSP90在易感水稻的稻瘟病和干旱期间上调。PKG在干旱期间增加，但在粳稻盐度处理下减少。RPS5在抗性和易感水稻的稻瘟病期间均高度上调。RT-qPCR分析表明，所有五个中心基因在所有处理中均上调，表明它们在胁迫反应中的作用以及作物改良的潜力。
