Gene coexpression analysis reveals dose-dependent and type-specific networks responding to ionizing radiation in the aquatic model plant Lemna minor using public data

Differentiation between chemo- and radiotoxicity of 137Cs and 60Co on Lemna minor

The uptake and effects of stable Cs and Co on L.minor were extensively studied, together with the effects of gamma radiation using a 137Cs or 60Co source. Innovative is that we combined external irradiation (from 137Cs or 60Co sources) with the direct uptake of certain amounts of stable Cs or Co to simulate the impact of the same mass of a radioisotope compared with that of the stable element. Such approach allows to differentiate between chemo- and radiotoxicity of 137Cs or 60Co, permitting to study the 137Cs and 60Co uptake by L. minor without using high concentrations of these elements in solution. Our results indicate that radiotoxicity of both 137Cs and 60Co has a greater importance compared to their chemotoxicity. This was also supported by the independent action and concentration addition concepts. Both concepts resulted in a good prediction of the dose-response curve of the combination exposure. The maximal removal of 137Cs or 60Co per gram dry matter of L. minor was lower compared with the removal of the corresponding stable isotope. The toxicity of 60Co was higher compared to 137Cs based on EC50 values and uptake data. With respect to the effects on photosynthetic pigments, starch and soluble sugars contents, only starch increased in a concentration- and dose-dependent manner.

The Mutational, Epigenetic, and Transcriptional Effects Between Mixed High-Energy Particle Field (CR) and 7Li-Ion Beams (LR) Radiation in Wheat M1 Seedlings

Ionizing radiation (IR) is an effective approach for mutation breeding. Understanding the mutagenesis and transcriptional profiles induced by different mutagens is of great significance for improving mutation breeding efficiency. Here, using RNA sequencing and methylation-sensitive amplification polymorphism (MSAP) approaches, we compared the genetic variations, epigenetics, and transcriptional responses induced by the mixed high-energy particle field (CR) and ⁷Li-ion beam (LR) radiation in M₁ seedlings of two wheat genotypes (Yangmai 18 and Yangmai 20). The results showed that, in both wheat genotypes, CR displayed significantly a higher mutation efficiency (1.79 × 10^-6/bp) than that by LR (1.56 × 10^-6/bp). The induced mutations were not evenly distributed across chromosomes and varied across wheat genotypes. In Y18 M₁, the highest number of mutations were detected on Chr. 6B and Chr. 6D, whilst in Y20 M₁, Chr. 7A and Chr. 3A had the highest mutations. The transcript results showed that total of 4,755 CR-regulated and 1,054 LR-regulated differentially expressed genes (DEGs) were identified in the both genotypes. Gene function enrichment analysis of DEGs showed that these DEGs overlapped or diverged in the cascades of molecular networks involved in "phenylpropanoid biosynthesis" and "starch and sucrose metabolism" pathways. Moreover, IR type specific responses were observed between CR an LR irradiation, including specific TFs and response pathways. MSAP analysis showed that DNA methylation level increased in LR treatment, while decreased at CR. The proportion of hypermethylation was higher than that of hypomethylation at LR, whereas a reverse pattern was observed at CR, indicating that DNA methylation plays critical roles in response to IR irradiation. All these results support that the response to different IRs in wheat includes both common and unique pathways, which can be served as a useful resource to better understand the mechanisms of responses to different IRs in other plants.

Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed

Background

Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been characterized, however, the roles of long noncoding RNAs (lncRNAs) remain unknown.

Results

In this work, totally 2815 novel lncRNAs were discovered in S. polyrhiza by strand-specific RNA sequencing, of which 185 (6.6%) were expressed differentially under salinity condition. Co-expression analysis indicated that the trans-acting lncRNAs regulated their co-expressed genes functioning in amino acid metabolism, cell- and cell wall-related metabolism, hormone metabolism, photosynthesis, RNA transcription, secondary metabolism, and transport. In total, 42 lncRNA-mRNA pairs that might participate in cis-acting regulation were found, and these adjacent genes were involved in cell wall, cell cycle, carbon metabolism, ROS regulation, hormone metabolism, and transcription factor. In addition, the lncRNAs probably functioning as miRNA targets were also investigated. Specifically, TCONS_00033722, TCONS_00044328, and TCONS_00059333 were targeted by a few well-studied salt-responsive miRNAs, supporting the involvement of miRNA and lncRNA interactions in the regulation of salt stress responses. Finally, a representative network of lncRNA-miRNA-mRNA was proposed and discussed to participate in duckweed salt stress via auxin signaling.

Conclusions

This study is the first report on salt-responsive lncRNAs in duckweed, and the findings will provide a solid foundation for in-depth functional characterization of duckweed lncRNAs in response to salt stress.