Comprehensive Transcriptome Analysis Uncovers Hub Long Non-coding RNAs Regulating Potassium Use Efficiency in Nicotiana tabacum

Abstract

Potassium (K) is the essential element for plant growth. It is one of the critical factors that determine crop yield, quality, and especially leaf development in tobacco. However, the molecular mechanism of potassium use efficiency (KUE), especially non-coding RNA, is still unknown. In this study, tobacco seedlings were employed, and their hydro-cultivation with K treatments of low and sufficient concentrations was engaged. Physiological analysis showed that low potassium treatment could promote malondialdehyde (MDA) accumulation and antioxidant enzyme activities such as peroxidase (POD), ascorbate-peroxidase (APX). After transcriptomic analysis, a total of 10,585 LncRNA transcripts were identified, and 242 of them were significantly differently expressed under potassium starvation. Furthermore, co-expression networks were constructed and generated 78 potential regulation modules in which coding gene and LncRNAs are involved and functional jointly. By further module-trait analysis and module membership (MM) ranking, nine modules, including 616 coding RNAs and 146 LncRNAs, showed a high correlation with K treatments, and 20 hub K-responsive LncRNAs were finally predicted. Following gene ontology (GO) analysis, the results showed potassium starvation inducing the pathway of antioxidative stress which is consistent with the physiology result mentioned above. Simultaneously, a part of detected LncRNAs, such as MSTRG.6626.1, MSTRG.11330.1, and MSTRG.16041.1, were co-relating with a bench of MYB, C3H, and NFYC transcript factors in response to the stress. Overall, this research provided a set of LncRNAs that respond to K concentration from starvation and sufficient supply. Simultaneously, the regulation network and potential co-functioning genes were listed as well. This massive dataset would serve as an outstanding clue for further study in tobacco and other plant species for nutrient physiology and molecular regulation mechanism.

Transcriptome dynamics uncovers long non-coding RNAs response to salinity stress in Chenopodium quinoa

“…TCONS_00009717 is a miRNA found in soybean that may be induced by salt stress, its potential target is cytochrome P450 ( Chen et al, 2019 ). Summarily, LncRNAs were also discovered and found to be involved in response to several abiotic stresses in plant species such as Arabidopsis thaliana , Zea may , and Nicotiana tabacum ( Liu et al, 2012 ; Lv et al, 2013 , 2019 ; Yu et al, 2019 ; Zhang et al, 2019 , 2021 ; Chen et al, 2022 ). However, as a remarkable salt tolerant crop, the LncRNAs of quinoa responding to salt stress have not been reported yet.…”

“…LncRNAs have been discovered to be involved in a variety of biological regulatory processes, and their expression patterns are more tissue-specific than mRNA ( Ponting et al, 2009 ; Rinn and Chang, 2012 ). According to their relative positions to nearby protein-coding genes in the genome, LncRNAs are generally classified into five types: sense, antisense, bidirectional, intergenic, and intronic ( Liu et al, 2012 ; Lv et al, 2019 ; Chen et al, 2022 ). Previous studies have indicated that plant LncRNAs play functional roles in signal pathway transmission and molecular regulation under abiotic stresses such as salt stress.…”

“…A nucleus-localized drought-induced LncRNA ( DRIR ), which functioned in water transport and ABA signaling, could enhance the tolerance to drought and salt stress in Arabidopsis ( Qin et al, 2017 ). Currently, stress-responsive LncRNAs have been identified in many species, such as maize ( Lv et al, 2013 , 2016 ; Chen et al, 2022 ), rice ( Zhang et al, 2014 ), Arabidopsis ( Liu et al, 2012 ), pistachio ( Jannesar et al, 2020 ), chickpea ( Kumar et al, 2021 ), and rapeseed ( Tan et al, 2020 ). However, no systematic study on salt-responsive LncRNAs in quinoa has been reported.…”

Omics-driven crop potassium use efficiency breeding

“…Epigenomics studies are mainly about non-coding RNAs and alternative mRNA splicing (AS). Long Non-coding RNAs sense environmental K concentrations and play regulatory roles in the K response network ( Chen et al., 2022 ). AS modulation is independent of transcription regulation and plays a unique regulatory role in response to low potassium ( He et al., 2021 ).…”

Transcriptome Profiling of Transposon-Derived Long Non-coding RNAs Response to Hormone in Strawberry Fruit Development

“…However, LncRNA, especially transposon-derived LncRNAs (TE-LncRNA), is still not fully understood or even illustrated. After the introduction of new generation sequencing technology, the high-through transcriptome analysis has facilitated the discovery of LncRNA greatly ( Lv et al, 2019 ; Chen et al, 2022 ; Liang et al, 2022 ). Recently, LnRNAs were predicted and verified in the transcriptome of F. vesca fruit in altering stages ( Kang and Liu, 2015 ).…”