Selenium nanoparticles conferred drought tolerance in tomato plants by altering the transcription pattern of microRNA-172 (miR-172), bZIP, and CRTISO genes, upregulating the antioxidant system, and stimulating secondary metabolism.

Drought stress is one of the major limiting factors for the production of tomato in Iran. In this study, the efficiency of selenate and Se nanoparticle (SeNP) foliar application on tomato plants was assessed to vestigate mitigating the risk associated with water-deficit conditions. Tomato plants were treated with SeNPs at the concentrations of 0 and 4 mg L-1; after the third sprays, the plants were exposed to water-deficit conditions. The foliar spraying with SeNPs not only improved growth, yield, and developmental switch to the flowering phase but also noticeably mitigated the detrimental risk associated with the water-deficit conditions. Gene expression experiments showed a slight increase in expression of microRNA-172 (miR-172) in the SeNP-treated plants in normal irrigation, whereas miR-172 displayed a downregulation trend in response to drought stress. The bZIP transcription factor and CRTISO genes were upregulated following the SeNP and drought treatments. Drought stress significantly increased the H2O2 accumulation that is mitigated with SeNPs. The foliar spraying with Se or SeNPs shared a similar trend to alleviate the negative effect of drought stress on the membrane integrity. The applied supplements also conferred drought tolerance through noticeable improvements in the non-enzymatic (ascorbate and glutathione) and enzymatic (catalase and peroxidase) antioxidants. The SeNP-mediated improvement in drought stress tolerance correlated significantly with increases in the activity of phenylalanine ammonia-lyase, proline, non-protein thiols, and flavonoid concentrations. SeNPs also improved the fruit quality regarding K, Mg, Fe, and Se concentrations. It was concluded that foliar spraying with SeNPs could mitigate the detrimental risk associated with the water-deficit conditions.

Synergetic effect of water deficit and arbuscular mycorrhizal symbiosis on the expression of aquaporins in wheat (Triticum aestivum L.) roots: insights from NGS RNA-sequencing.

Wheat (Triticum aestivum) is one of the most important crops in the world. This investigation was attempted to evaluate the transcriptional responses of aquaporins (AQPs) to the mycorrhizal inoculation and/or water deficit conditions in wheat to clarify how the arbuscular mycorrhizal symbiosis can contribute to the modulation of water homeostasis. The wheat seedlings were subjected to the water deficiency, and mycorrhizal inoculation using arbuscular fungus Funneliformis mosseae and Illumina RNA-Seq analyses confirmed that aquaporins expressed differentially in response to both the irrigation levels and mycorrhizal colonization. Results of this study showed that only 13% of the studied AQPs were responsive to water deficit with a tiny fraction (3%) being up-regulated. Mycorrhizal inoculation had a greater impact on the expression of AQPs with ca. 26% being responsive, ca. 4% of which were up-regulated. The samples with arbuscular mycorrhizal inoculation yielded more root and stem biomass. Water deficit and mycorrhizal inoculation caused different AQPs to be up-regulated. The effect of mycorrhizal inoculation on the expression of AQPs was intensified by applying water deficiency with 32% of studied AQPs being responsive, 6% of which up-regulated. We also found that the overexpression of three genes TaNIP1-10, TaNIP3-3, and TaNIP3-4 was chiefly triggered by mycorrhizal inoculation. Our results show that water deficit has a lower impact on the expression of aquaporins compared to what the arbuscular mycorrhizal inoculation has; water deficit and arbuscular mycorrhizal inoculation mainly cause the down-regulation of the aquaporins, and water deficit and the arbuscular inoculation have synergetic effects. These findings could improve our knowledge of how arbuscular mycorrhizal symbiosis can contribute to the modulation of water homeostasis. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01285-w.

CRISPR/Cas StNRL1 gene knockout increases resistance to late blight and susceptibility to early blight in potato.

With the development of genome editing technologies, editing susceptible genes is a promising method to modify plants for resistance to stress. NPH3/RPT2-LIKE1 protein (NRL1) interacts with effector Pi02860 of Phytophthora infestans and creates a protein complex, promoting the proteasome-mediated degradation of the guanine nucleotide exchange factor SWAP70. SWAP70, as a positive regulator, enhances cell death triggered by the perception of the P. infestans pathogen-associated molecular pattern (PAMP) INF1. Using a clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, a construct was made to introduce four guide RNAs into the potato cultivar Agria. A total of 60 putative transgenic lines were regenerated, in which 10 transgenic lines with deletions were selected and analyzed. A mutant line with a four-allelic knockdown of StNRL1 gene was obtained, showing an ~90% reduction in StNRL1 expression level, resulting in enhanced resistance to P. infestans. Surprisingly, mutant lines were susceptible to Alternaria alternata, suggesting that StNRL1 may play a role as a resistance gene; hence, silencing StNRL1 enhances resistance to P. infestans.

Genome-wide identification of StU-box gene family and assessment of their expression in developmental stages of Solanum tuberosum.

BACKGROUND: The Plant U-box (PUB), ubiquitin ligase gene, has a highly conserved domain in potato. However, little information is available about U-box genes in potato (Solanum tuberosum). In this study, 62 U-box genes were detected in the potato genome using bioinformatics methods. Further, motif analysis, gene structure, gene expression, TFBS, and synteny analysis were performed on the U-box genes. RESULTS: Based on in silico analysis, most of StU-boxs included a U-box domain; however, some of them lacked harbored domain the ARM, Pkinase_Tyr, and other domains. Based on their phylogenetic relationships, the StU-box family members were categorized into four classes. Analysis of transcription factor binding sites (TFBS) in the promoter region of StU-box genes revealed that StU-box genes had the highest and the lowest number of TFBS in MYB and CSD, respectively. Moreover, based on in silico and gene expression data, variable frequencies of TFBS in StU-box genes could indicate that these genes control different developmental stages and are involved in complex regulatory mechanisms. The number of exons in U-box genes ranged from one to sixteen. For most U-box genes, the exon-intron compositions and conserved motifs composition in most proteins in each group were similar. The intron-exon patterns and the composition of conserved motifs validated the U-box genes phylogenetic classification. Based on the results of genome distribution, StU-box genes were distributed unevenly on the 12 S. tuberosum chromosomes. The results showed that gene duplication may possess a significant role in genome expansion of S. tuberosum. Furthermore, genome evolution of S. tuberosum was surveyed using identification of orthologous and paralogous. We identified 40 orthologous gene pairs between S. tuberosum with Solanum lycopersicum, Oryza sativa, Triticum aestivum, Gossypium hirsutum, Zea maize, Coriaria mytifolia, and Arabidopsis thaliana as well as eight duplicated genes (paralogous) in S. tuberosum. StU-box 51 gene is one of the important gene among other StU-boxes in S. tuberosum under drought stress which was expressed in tuber and leaf under drought stress. Furthermore, StU-box 51 gene has the highest expression levels in four tissue-specific (stem, root, leaf, and tuber) in potato as well as it had the highest number of TFBS in promoter region. Based on our results, StU-box 51 can introduce to researcher to utilize in breeding program and genetic engineering in potato. CONCLUSIONS: The results of this survey will be useful for further investigation of the probable role and molecular mechanisms of U-box genes in response to different stresses.

Correction: Comparative efficacy of selenate and selenium nanoparticles for improving growth, productivity, fruit quality, and postharvest longevity through modifying nutrition, metabolism, and gene expression in tomato; potential benefits and risk assessment.

[This corrects the article DOI: 10.1371/journal.pone.0244207.].

Comparative efficacy of selenate and selenium nanoparticles for improving growth, productivity, fruit quality, and postharvest longevity through modifying nutrition, metabolism, and gene expression in tomato; potential benefits and risk assessment.

This study attempted to address molecular, developmental, and physiological responses of tomato plants to foliar applications of selenium nanoparticles (nSe) at 0, 3, and 10 mgl-1 or corresponding doses of sodium selenate (BSe). The BSe/nSe treatment at 3 mgl-1 increased shoot and root biomass, while at 10 mgl-1 moderately reduced biomass accumulation. Foliar application of BSe/nSe, especially the latter, at the lower dose enhanced fruit production, and postharvest longevity, while at the higher dose induced moderate toxicity and restricted fruit production. In leaves, the BSe/nSe treatments transcriptionally upregulated miR172 (mean = 3.5-folds). The Se treatments stimulated the expression of the bZIP transcription factor (mean = 9.7-folds). Carotene isomerase (CRTISO) gene was transcriptionally induced in both leaves and fruits of the nSe-treated seedlings by an average of 5.5 folds. Both BSe or nSe at the higher concentration increased proline concentrations, H2O2 accumulation, and lipid peroxidation levels, suggesting oxidative stress and impaired membrane integrity. Both BSe or nSe treatments also led to the induction of enzymatic antioxidants (catalase and peroxidase), an increase in concentrations of ascorbate, non-protein thiols, and soluble phenols, as well as a rise in the activity of phenylalanine ammonia-lyase enzyme. Supplementation at 3 mgl-1 improved the concentration of mineral nutrients (Mg, Fe, and Zn) in fruits. The bioaccumulated Se contents in the nSe-treated plants were much higher than the corresponding concentration of selenate, implying a higher efficacy of the nanoform towards biofortification programs. Se at 10 mgl-1, especially in selenate form, reduced both size and density of pollen grains, indicating its potential toxicity at the higher doses. This study provides novel molecular and physiological insights into the nSe efficacy for improving plant productivity, fruit quality, and fruit post-harvest longevity.

Impact of arbuscular mycorrhizal fungi (AMF) on gene expression of some cell wall and membrane elements of wheat (Triticum aestivum L.) under water deficit using transcriptome analysis.

Mycorrhizal symbiotic relationship is one of the most common collaborations between plant roots and the arbuscular mycorrhizal fungi (AMF). The first barrier for establishing this symbiosis is plant cell wall which strongly provides protection against biotic and abiotic stresses. The aim of this study was to investigate the gene expression changes in cell wall of wheat root cv. Chamran after inoculation with AMF, Funneliformis mosseae under two different irrigation regimes. To carry out this investigation, total RNA was extracted from the roots of mycorrhizal and non-mycorrhizal plants, and analyzed using RNA-Seq in an Illumina Next-Seq 500 platform. The results showed that symbiotic association between wheat and AMF and irrigation not only affect transcription profile of the plant growth, but also cell wall and membrane components. Of the 114428 genes expressed in wheat roots, the most differentially expressed genes were related to symbiotic plants under water stress. The most differentially expressed genes were observed in carbohydrate metabolic process, lipid metabolic process, cellulose synthase activity, membrane transports, nitrogen compound metabolic process and chitinase activity related genes. Our results indicated alteration in cell wall and membrane composition due to mycorrhization and irrigation regimes might have a noteworthy effect on the plant tolerance to water deficit.

Next generation sequencing based development of intron-targeting markers in tetraploid potato and their transferability to other Solanum species.

Intron-targeting (IT) markers were developed from next generation sequencing (NGS) derived transcript sequencing data from the potato cultivar White Lady. The applicability of the IT markers was analyzed in other potato genotypes, and their transferability was studied in other Solanum species: section Archaesolanum (5 species), sect. Solanum (6 species) and a Solanum nigrum population (11 genotypes). Out of 250 randomly chosen transcript sequences, 144 intron harboring loci could be identified for which primer pairs were designed on exons flanking the putative introns. The usefulness of the IT primers was experimentally analyzed on a subset of 40 randomly chosen loci. Statistical analysis of diversity parameters was performed using the ATETRA and POPGENE software packages. By localizing the detected 17 polymorphic loci 11 of the 12 potato chromosomes could be identified. Specificity of the designed IT primers was tested by sequence analysis of amplified IT fragments in a randomly chosen locus. The results revealed the efficiency of NGS derived IT marker development and indicated their utility in diverse molecular analyses including their applicability for cross-species studies.

Thiol-dependent serine alkaline proteases from Bacillus sp. HR-08 and KR-8102: isolation, production, and characterization.

Two Bacillus sp. strains, HR-08 and KR-8102, isolated from soil of the west and north parts of Iran were screened on gelatin agar medium for their ability to produce alkaline protease. The enzymes were active in a wide pH range (6.0-11.0) and stable in the alkaline range (7.0-12.0). The optimum temperatures for the protease from HR-08 and KR-8102 were 65 and 50 degrees C, respectively. The irreversible thermoinactivation of HR-08 and KR-8102 proteases showed that the stability of HR-08 enzyme was higher than that of KR-8102 and the half-lives of these enzymes were 95 and 32 min at 50 degrees C, respectively. In the presence of 10 mM Ca(2+), HR-08 retained 100, 90, and 20% of its initial activity after heating for 30 min at 50, 60, and 70 degrees C, respectively. Enzymes were inhibited by phenylmethylsulfonyl fluoride and iodoacetate. After inhibition by iodoacetate, both enzymes were reactivated by dithiothreitol. These data show that the enzymes seem to be thiol-dependent serine alkaline proteases. The enzymes especially from HR-08 were stable in the presence of H(2)O(2), surfactants, and local detergents; their activities were enhanced in the presence of 5 mM Fe(2+); and the presence of 5 mM metal ions such as Mg(2+), Cu(2+), and Mn(2+) produced almost no effect.