Transcriptome profiling uncovers the lncRNA-mediated regulatory networks associated with tolerance to cadmium stress in barley

• Published in: Environmental and experimental botany 2023-02, Vol.206, p.105156, Article 105156
• Main Authors: Zhou, Xue-Yi, Wang, Nian-Hong, Qiu, Cheng-Wei, Luo, Liming, Zhang, Mian, Zhang, Shuo, Gao, Zi-Feng, Ahmed, Imrul Mosaddek, Wu, Feibo
• Format: Article
• Language: English
• Subjects: Antioxidant defense; Cadmium stress; Gene silencing; Hordeum vulgare L; HvGAMYB; Long non-coding RNA; Transcriptome
• ISSN: 0098-8472; 1873-7307
• DOI: 10.1016/j.envexpbot.2022.105156

Cadmium (Cd) is one of the most harmful and widespread toxic heavy metal contaminants. Long non-coding RNAs (lncRNAs) play vital roles in response to abiotic stress by participating in the gene regulatory network. Here, we performed a transcriptome analysis of lncRNAs in roots of the two contrasting barley genotypes, namely Zhenong8 (ZN, Cd-tolerant) and W6nk2 (Cd-sensitive). In total, 9937 novel lncRNAs were identified, and 5758 lncRNA-target pairs were predicted to be cis-acting and 4159 to be trans-acting. Further comparison of genotypic differences revealed 195 novel lncRNAs as differentially expressed between the two genotypes in response to Cd stress. The miRanda prediction and expression relationship analyses among miRNA, lncRNA, and mRNA revealed that 8 lncRNAs may act as target mimics of miRNAs in barley. Among them, HvGAMYB was predicted to be the target gene of miR319a_1 and miR319b-3p, with LTCONS_00177709 and LTCONS_00185175 acting as endogenous competitors. Barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) of HvGAMYB in ZN8 led to hypersensitivity to Cd stress with significantly increased Cd concentration in both roots and shoots as well as Cd accumulation in shoots. Moreover, silencing HvGAMYB suppressed photosynthesis and antioxidant-related genes but stimulated the production of reactive oxygen species (ROS) after Cd exposure, leading to exacerbated Cd-induced MDA accumulation and cell death. Our findings provide new knowledge and insights into the regulatory functions of lncRNAs in plant Cd tolerance. •Barley Cd-responsive lncRNAs firstly studied by comparing two barley genotypes ZN8 (Cd-tolerant) and W6nk2 (Cd-sensitive).•Identified 195 novel lncRNAs differently expressed in the two genotypes, including 21 Cd tolerance-associated lncRNAs.•lncRNA-miRNA-mRNA-based interaction analysis revealed 8 Cd tolerance-related key lncRNAs with targets such as HvGAMYB.•Silencing of HvGAMYB led to increased Cd concentration in barley and hypersensitivity to Cd stress.