State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Information Traceability for Agricultural Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
Chemosphere. 2023 Oct;338:139489. doi: 10.1016/j.chemosphere.2023.139489. Epub 2023 Jul 12.
Although Cd accumulation varies among rice varieties is recognized, the underlying mechanisms are not well clarified. In this study, comparative transcriptome analysis were performed by hydroponic culture system with two rice varieties, Y1540 (high Cd accumulator) and Y15 (low Cd accumulator) under 20 μM Cd stress. Results revealed 17,320 differentially expressed genes (DEGs) in roots of Y15 (7,655 upregulated and 9,665 downregulated) and 17,386 DEGs in roots of Y1540 (8,823 upregulated and 8,563 downregulated) expose to 20 μM Cd stress. Gene ontology (GO) analysis enriched 24 and 26 terms in Y15 and Y1540 respectively, including 23 common terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed 27 and 28 significant pathways in Y15 and Y1540 respectively, with 19 common pathways. Different responses to Cd stress between cultivars were not only reflected in differently enriched GO terms and KEGG pathways but also in different DEGs of 23 common GO terms and significant sequences represented by p-values of 19 common KEGG pathways. Both cultivars resist Cd through common processes with different weights; hence glutathione metabolism, mineral absorption, biosynthesis of secondary metabolites, and degradation of aromatic compounds could be playing a more important role in Y1540, whereas ribosome biogenesis in eukaryotes, mismatch repair, aminoacyl-tRNA biosynthesis, and the cell cycle maybe playing a more important role in Y15. Weighted gene co-expression network analysis (WGCNA) showed that five and three modules were clustered in Y15 and Y1540, respectively, with yellow and brown modules in Y15 and brown modules in Y1540 being significantly related to Cd stress. Further analysis showed that most of hub genes in Y15 were related to signal transduction or transcription factors, while most of hub genes in Y1540 were related to binding, metabolic, and secondary metabolic processes, which demonstrated their different response patterns at transcriptomic level to Cd stress.
尽管人们已经认识到不同水稻品种对镉的积累存在差异，但其中的机制尚不清楚。在这项研究中，通过水培系统，以 Y1540（高镉积累）和 Y15（低镉积累）两个水稻品种为研究对象，在 20μM Cd 胁迫下进行了比较转录组分析。结果显示，在 20μM Cd 胁迫下，Y15 的根中差异表达基因（DEGs）有 17320 个（7655 个上调，9665 个下调），Y1540 的根中差异表达基因（DEGs）有 17386 个（8823 个上调，8563 个下调）。基因本体（GO）分析分别富集了 Y15 和 Y1540 中的 24 和 26 个术语，其中包含 23 个共同术语。京都基因与基因组百科全书（KEGG）富集分别在 Y15 和 Y1540 中显示了 27 和 28 个显著途径，其中包含 19 个共同途径。不同品种对 Cd 胁迫的反应不仅反映在不同的 GO 术语和 KEGG 途径上，也反映在 23 个共同 GO 术语和 19 个显著途径中 p 值代表的不同 DEGs 上。两个品种都通过共同的过程来抵抗 Cd，只是权重不同；因此，谷胱甘肽代谢、矿物质吸收、次生代谢物合成和芳香族化合物降解可能在 Y1540 中发挥更重要的作用，而真核生物核糖体生物发生、错配修复、氨酰-tRNA 生物合成和细胞周期可能在 Y15 中发挥更重要的作用。加权基因共表达网络分析（WGCNA）显示，Y15 和 Y1540 分别聚类为 5 个和 3 个模块，其中黄色和棕色模块在 Y15 中显著相关，棕色模块在 Y1540 中显著相关。进一步分析表明，Y15 中的大多数枢纽基因与信号转导或转录因子有关，而 Y1540 中的大多数枢纽基因与结合、代谢和次生代谢过程有关，这表明它们在转录组水平对 Cd 胁迫的反应模式不同。
