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<p>Rice (<i>Oryza sativa</i>, Indica) is an important staple food crop and a major route for heavy metals (HMs) such as Cadmium (Cd) and Arsenic (As). These HMs disturb plant-nutrient uptake and stunt the growth and final crop yield. Being emerging regulators, the role of lncRNAs in metal toxicity remains largely unknown. The present study identified HM-responsive lncRNA in hydroponically grown Huanghuazhan (HHZ) rice. The transcriptomic analysis revealed 3,303 lncRNAs in HHZ rice treated with Cd and As. We found that 288 lncRNA transcripts were upregulated and 253 were downregulated in CK <i>vs</i> Cd. Contrastingly, CK <i>vs</i> As showed 278 up- and 314 down-regulated lncRNAs, while Cd <i>vs</i> As showed 285 and 251 were up- and down-regulated lncRNAs. In addition, WGCNA analysis showed four enriched modules correlating the protein-coding (PCs) genes with lncRNAs transcriptionally. Subsequently, the expression of selected lncRNAs-PCs targets like MSTRG.24054.4 negatively correlated with <i>LOC_Os08g15204.1</i> under Cd and As stress in the root. These results suggest that lncRNAs may regulate the expression of PCs in response to excessive Cd and As contamination. Similarly, the cis-regulatory network analysis indicated the involvement of a few lncRNAs that control the expression of As and Cd stress-related genes. Furthermore, GO and KEGG pathway analyses specified 951 GO terms in 21 pathways, respectively. Our findings pinpointed the role of lncRNAs in Cd and As tolerance, which might used as a reference for future functional-based research to mitigate Cd and/or As contamination from the environment.</p>

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The comprehensive identification of lncRNA landscape associated with cadmium and arsenic stress responses in huanghuazhan rice

  • 期刊论文

  • 发表日期：

    2025年1月5日

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  • Sana Basharat,
  • Iffat Shaheen,
  • Muhammad Waseem,
  • Pingwu Liu

摘要

Rice (Oryza sativa, Indica) is an important staple food crop and a major route for heavy metals (HMs) such as Cadmium (Cd) and Arsenic (As). These HMs disturb plant-nutrient uptake and stunt the growth and final crop yield. Being emerging regulators, the role of lncRNAs in metal toxicity remains largely unknown. The present study identified HM-responsive lncRNA in hydroponically grown Huanghuazhan (HHZ) rice. The transcriptomic analysis revealed 3,303 lncRNAs in HHZ rice treated with Cd and As. We found that 288 lncRNA transcripts were upregulated and 253 were downregulated in CK vs Cd. Contrastingly, CK vs As showed 278 up- and 314 down-regulated lncRNAs, while Cd vs As showed 285 and 251 were up- and down-regulated lncRNAs. In addition, WGCNA analysis showed four enriched modules correlating the protein-coding (PCs) genes with lncRNAs transcriptionally. Subsequently, the expression of selected lncRNAs-PCs targets like MSTRG.24054.4 negatively correlated with LOC_Os08g15204.1 under Cd and As stress in the root. These results suggest that lncRNAs may regulate the expression of PCs in response to excessive Cd and As contamination. Similarly, the cis-regulatory network analysis indicated the involvement of a few lncRNAs that control the expression of As and Cd stress-related genes. Furthermore, GO and KEGG pathway analyses specified 951 GO terms in 21 pathways, respectively. Our findings pinpointed the role of lncRNAs in Cd and As tolerance, which might used as a reference for future functional-based research to mitigate Cd and/or As contamination from the environment.