Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita

Abstract

Root-knot nematodes (RKNs) severely affect plants growth and productivity, and several commercial biocontrol bacteria can improve plants resistance to RKNs. Pseudomonas putida Sneb821 isolate was found to induce tomatoes resistance against Meloidogyne incognita. However, the molecular functions behind induced resistance remains unclear. Long non-coding RNA (lncRNA) is considered to be a new component that regulates the molecular functions of plant immunity. We found lncRNA was involved in Sneb821-induced tomato resistance to M. incognita. Compared with tomato inoculated with M. incognita, high-throughput sequencing showed that 43 lncRNAs were upregulated, while 35 lncRNAs were downregulated in tomatoes previously inoculated with Sneb821. A regulation network of lncRNAs was constructed, and the results indicated that 12 lncRNAs were found to act as sponges of their corresponding miRNAs. By using qRT-PCR and the overexpression vector pBI121, we found the expression of lncRNA44664 correlated with miR396/GRFs (growth-regulating factors) and lncRNA48734 was correlated with miR156/SPL (squamosal promoter-binding protein-like) transcription factors. These observations provided a novel molecular model in biocontrol bacteria-induced tomato resistance to M. incognita.

Sl‐lncRNA15492 interacts with Sl‐miR482a and affects Solanum lycopersicum immunity against Phytophthora infestans

“…There has recently been considerable focus on lncRNAs in plants. Accordingly, a rapid increase in the number of identified plant lncRNAs has occurred because of the rapid advances in high‐throughput sequencing technology (Zhu et al ., 2015; Wang et al ., 2016; Zaynab et al ., 2018; Sun et al ., 2020; Yang et al ., 2020). However, there are few studies on the functions of plant lncRNAs in biological processes.…”

Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non‐polyadenylated flower lncRNAs in chickpea

“…Long noncoding RNAs (lncRNAs) are emerging as key regulators of the genome that respond primarily to stress and plant development (Gelaw and Sanan‐Mishra, 2021; Huo et al ., 2021; Jain et al ., 2021). Thousands of lncRNAs have recently been discovered in plants including Arabidopsis (Wang et al ., 2021), Oryza sativa (Jain et al ., 2021), Glycine max (Zhang et al ., 2021), Medicago truncatula (Zhao et al ., 2020), Lycopersicum esculentum (Yang et al ., 2020), Camellia sinensis (Baruah et al ., 2021a; Varshney et al ., 2019), Citrus limon (Bordoloi et al ., 2022) and Capsicum annuum (Baruah et al ., 2021b) through RNA‐sequencing technology. However, lncRNAs are a large collection of highly heterogeneous transcripts with multiple features depending on their site of origin in the genome, sequence, expression level and interaction with neighbouring genes; therefore, their functional characterization remains challenging.…”

Plant growth-promoting rhizobacterium Bacillus cereus AR156 - induced systemic resistance against multiple pathogens by priming of phytoalexin synthesis and secretion

“…The plant growth-promoting rhizobacteria Bacillus amyloliquefaciens HK34 can trigger ISR against P. cactorum in Panax ginseng (Lee et al, 2015). There was a study showing that lncRNAs played an important role in biocontrol bacteria P. putidaSneb821 to induce tomato resistance against Meloidogyne incognitainfection (Yang et al, 2020). In addition to Pseudomonas , various strains of Bacillus , fungi, and viruses can also stimulate ISR, reducing the incidence and severity of crop diseases significantly.…”