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Journal of Integrative Agriculture  2022, Vol. 21 Issue (9): 2588-2602    DOI: 10.1016/j.jia.2022.07.022
Special Issue: 园艺-分子生物合辑Horticulture — Genetics · Breeding
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
A novel long non-coding RNA, DIR, increases drought tolerance in cassava by modifying stress-related gene expression

DONG Shi-man1, 4, XIAO Liang3, LI Zhi-bo1, 4, SHEN Jie1, 4, YAN Hua-bing3, LI Shu-xia1, 2, LIAO Wen-bin1, 2, PENG Ming1, 2

1 Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, P.R.China

2 Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, P.R.China

3 Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, P.R.China

4 College of Tropical Crops, Hainan University, Haikou 570228, P.R.China

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本研究鉴定了一个新的lncRNA,命名为干旱诱导型lncRNA(DIRDROUGHT-INDUCED INTERGENIC lncRNA)。基因表达分析表明,干旱胁迫显著诱导了DIR的表达,而植物激素脱落酸和茉莉酸处理不影响DIR的表达。此外,过表达DIR基因可增强转基因木薯脯氨酸的积累从而提升抗旱性。RNA测序分析发现,DIR优先影响与干旱相关的转录基因和代谢相关基因。利用RNA下拉技术(RNA pull-down)联合质谱分析发现DIR与325个蛋白存在相互作用。蛋白-蛋白互作分析(Protein-protein interaction analysis,PPI)发现,mRNA胞质运输和蛋白质翻译质控通路相关的蛋白质被显著富集。这些结果表明,DIR与其互作蛋白可通过调控mRNAs或蛋白质的代谢来响应干旱胁迫。因此,干旱胁迫下通过调节DIR的表达有提高木薯产量的潜力


Cassava is an important tropical cash crop.  Severe drought stresses affect cassava productivity and quality, and cause great economic losses in agricultural production.  Enhancing the drought tolerance of cassava can effectively improve its yield.  Long non-coding RNAs (lncRNAs) are present in a wide variety of eukaryotes.  Recently, increasing evidence has shown that lncRNAs play a critical role in the responses to abiotic stresses.  However, the function of cassava lncRNAs in the drought response remains largely unknown.  In this study, we identified a novel lncRNA, DROUGHT-INDUCED INTERGENIC lncRNA (DIR).  Gene expression analysis showed that DIR was significantly induced by drought stress treatment, but did not respond to abscisic acid (ABA) or jasmonic acid (JA) treatments.  In addition, overexpression of the DIR gene enhanced proline accumulation and drought tolerance in transgenic cassava.  RNA-seq analysis revealed that DIR preferentially affected drought-related genes that were linked to transcription and metabolism.  Moreover, RNA pull-down mass spectrometry analysis showed that DIR interacted with 325 proteins.  A protein–protein interaction (PPI) analysis found a marked enrichment in proteins associated with the mRNA export and protein quality control pathways.  Collectively, these results suggest that DIR and its interacting proteins that regulate mRNA or protein metabolism are involved in mediating the drought stress response.  Thus, regulating DIR expression has potential for improving cassava yield under drought conditions.

Keywords:  lncRNA        RNA-seq        drought stress        cassava        DIR  
Received: 16 November 2021   Accepted: 06 May 2022
Fund: This work was supported by the National Key Research and Development Program of China (2018YFD1000500, 2019YFD1000500, and 2019YFD1001105), the Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (1630052021026 and 1630052022008), the National Natural Science Foundation of China (31960440), the Hainan Provincial Natural Science Foundation of China (320MS097), and the Natural Science Foundation of China (31701484).  

About author:  Correspondence PENG Ming, E-mail:; LIAO Wen-bin, E-mail:; LI Shu-xia, E-mail:; YAN Hua-bing, E-mail:

Cite this article: 

DONG Shi-man, XIAO Liang, LI Zhi-bo, SHEN Jie, YAN Hua-bing, LI Shu-xia, LIAO Wen-bin, PENG Ming. 2022. A novel long non-coding RNA, DIR, increases drought tolerance in cassava by modifying stress-related gene expression. Journal of Integrative Agriculture, 21(9): 2588-2602.

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