Transcriptomic Response of In Vitro Potato (Solanum tuberosum L.) to Piezoelectric Ultrasound

Abstract

As part of a wider project to assess the impact of ultrasound on in vitro plant growth, this paper aimed to determine whether the application of piezoelectric ultrasound (PE-US) would induce changes to the transcriptome of in vitro potato (Solanum tuberosum L.). After exposing explants (single-node segments with a single leaf) to PE-US (35 kHz; 70 W) for 20 min, the effect of this stressor was determined at 0 h, 24 h, 48 h, 1 week, and 4 weeks to assess the possible immediate and residual effects of PE-US on the potato transcriptome. After mRNA was isolated, bioinformatic processing and analysis of RNA-seq datasets, KEGG analysis revealed that 24% of up-regulated biological processes were a response to stress immediately after the application of PE-US (reducing to 11% and 9% at 48 h and 4 weeks, respectively). After assessing a total of 40,430 genes for expression intensity at these five time intervals, it was found that 138, 72, 18, 5, and 59 differentially expressed genes (DEGs), respectively, were significantly up-regulated, while 6, 82, 96, 172, and 107 DEGs, respectively, were down-regulated. DEGs coding for universal stress protein, chitinase, catalase, zinc finger proteins, 21 transcription factors, glutathione S-transferase, and 17 heat shock proteins, mainly Hsp70, Hsp20, and Hsp90 proteins, and possibly the first of such discovery in US-based plant stress research, was detected. Following the validation of RNA-seq data by RT-qPCR, between SeqMonk LFC and RT-qPCR LFC, the Spearman and Pearson correlation coefficients were 0.86 and 0.90, respectively. Plantlets exposed to PE-US had significantly shorter shoots but significantly longer roots as well as higher shoot and root fresh weight, while chl b and total chl were significantly lower but the chl a/b ratio was significantly higher in plantlets exposed to PE-US. PE-US thus constituted an acute abiotic stress, but by 4 weeks, in vitro potato plantlets managed to mitigate the stress through the production of antioxidant enzyme systems and other functional metabolic changes.Key Message Piezoelectric ultrasound (PE-US) constitutes a nonfatal abiotic stress to in vitro potato. A notable discovery was the expression of 17 heat shock proteins in response to this abiotic stress.Electronic supplementary material The online version of this article (https://doi.

Transcription Profile of Potato (Solanum tuberosum L.) Growing In Vitro

“…Plant material as well as culture and growth conditions follow those employed by Dobránszki et al (2017Dobránszki et al ( , 2019 and Teixeira da Silva et al ( , 2020. Briefly, singlenode segments containing a single leaf were excised from 4-week-old in vitro potato plantlets of 'Desirée' and plated for 4 weeks on plant growth regulator-free Murashige and Skoog (1962) medium.…”

“…Total RNA was purified from the samples as three biological replicates. Total RNA isolation and removal of rRNA were made as described earlier (Dobránszki et al 2019;Teixeira da Silva et al 2019, 2020. The 15 mRNA libraries derived from the three biological replicates of five treatments were pooled into five qualified libraries.…”

“…The 15 mRNA libraries derived from the three biological replicates of five treatments were pooled into five qualified libraries. Deep sequencing (150 bp paired-end reads, expected data volume was 100 M reads/ sample) was conducted as in our earlier studies (Dobránszki et al 2019;Teixeira da Silva et al 2019, 2020.…”

“…Bioinformatic processing and analysis of RNA-seq datasets, as well as subsequent functional annotation of significant DEGs were implemented in the same way and using the same databases and software as reported earlier (Dobránszki et al 2019;Teixeira da Silva et al 2019, 2020, namely: SolTub 3.0 (https ://plant s.ensem bl.org/Solan um_tuber osum/Info/Index ); FastQC v0.11.7 (https ://githu b.com/sandre ws/FastQ C) for quality check of the FastQ files and to decide the trimming parameters; TrimGalore v0.5.0 (https ://githu b.com/Felix Krueg er/TrimG alore ); HISAT2 v2.1.0 (Kim et al 2015); SeqMonk v1.42.0 program (https ://githu b.com/s-andre ws/SeqMo nk); NCBI database using BlastX-fast in Blast2GO v5.2 (Götz et al 2008); Gene3D, SFLD, SuperFamily, Coils, MobiDBLite, CDD, HAMAP, HMMPanther, HMMPfam, FprintScan, BlastProDom, Pro-fileScan, HMMTigr, PatternScan; KEGG maps (Kanehisa Laboratories; https ://www.kegg.jp/kegg/kegg1 .html; Kanehisa et al 2017). Only those DEGs with a p value ≥ 0.05 for the intensity difference filter in SeqMonk were considered for the statistical analysis.…”

“…Recent advances using this model plant revealed that when a stem explant is cut, 189 genes are up-regulated, including the increased production of products related to defense, stress response, and wound healing (Teixeira da . Although several stress-related genes were up-regulated in response to ultrasound (US), even during a 4-week developmental period following explant plating, resulting plantlets survived, both after US transmitted by air (Dobránszki et al 2019) and liquid-transmitted US (PE-US; Teixeira da Silva et al 2020). A better understanding of the transcriptomic profile would also allow for the developmental fate to be better understood if the same explants were to be placed on different media with different plant growth regulators, thereby inducing different organs.…”