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IntroductionRecent advancements in agricultural technology have highlighted the potential of eco-friendly innovations, such as plasma-activated water (PAW), for enhancing seed germination, growth, and biomass production.MethodsIn this study, we investigated the effects of PAW irrigation on young sorghum seedlings through phenotypic and transcriptional analyses. We measured growth parameters, including seedling height, stem thickness, and biomass, across five sorghum varieties: BTx623, Sodamchal, Noeulchal, Baremae, and Hichal. Additionally, we performed detailed analyses of stem cross-sections to evaluate the structural changes induced by PAW. Whole transcriptome analysis was conducted to identify differentially expressed genes (DEGs) and to perform Gene Ontology (GO) analysis.ResultsPhenotypic analysis revealed significant growth enhancements in PAW-treated seedlings compared to the control group, with notable increases in seedling height, stem thickness, and biomass. Stem cross-section analysis confirmed that PAW treatment led to the enlargement of primordia tissue, leaf sheath (LS1 and LS2), and overall stem tissue area. Transcriptomic analysis revealed that 78% of the DEGs were upregulated in response to PAW, indicating that PAW acts as a positive regulator of gene expression. Gene Ontology (GO) analysis further showed that PAW treatment predominantly upregulated genes associated with transmembrane transport, response to light stimulus, oxidoreductase activity, and transcriptional regulation. Additionally, an enriched AP2/EREBP transcription binding motif was identified.ConclusionThese findings suggest that PAW not only enhances sorghum seedling growth through transcriptional regulation but also has the potential to optimize agricultural practices by increasing crop yield. The upregulation of genes involved in critical biological processes underscores the need for further exploration of PAW’s potential in improving the productivity of sorghum and possibly other crops.

Abstract Solanum nigrum, known as black nightshade, is a medicinal plant that contains many beneficial metabolites in its fruit. The molecular mechanisms underlying the synthesis of these metabolites remain uninvestigated due to limited genetic information. Here, we identified 47,470 unigenes of S. nigrum from three different tissues by de novo transcriptome assembly, and 78.4% of these genes were functionally annotated. Moreover, gene ontology (GO) analysis using 18,860 differentially expressed genes (DEGs) revealed tissue-specific gene expression regulation. We compared gene expression patterns between S. nigrum and tomato (S. lycopersicum) in three tissue types. The expression patterns of carotenoid biosynthetic genes were different between the two species. Comparison of the expression patterns of flavonoid biosynthetic genes showed that 9 out of 14 enzyme-coding genes were highly upregulated in the fruit of S. nigrum. Using CRISPR-Cas9-mediated gene editing, we knocked out the R2R3-MYB transcription factor SnAN2 gene, an ortholog of S. lycopersicum ANTHOCYANIN 2. The mutants showed yellow/green fruits, suggesting that SnAN2 plays a major role in anthocyanin synthesis in S. nigrum. This study revealed the connection between gene expression regulation and corresponding phenotypic differences through comparative analysis between two closely related species and provided genetic resources for S. nigrum.

Rice cultivation needs extensive amounts of water. Moreover, increased frequency of droughts and water scarcity has become a global concern for rice cultivation. Hence, optimization of water use is crucial for sustainable agriculture. Here, we characterized Loose Plant Architecture 1 (LPA1) in vasculature development, water transport, drought resistance, and grain yield. We performed genetic combination of lpa1 with semi-dwarf mutant to offer the optimum rice architecture for more efficient water use. LPA1 expressed in pre-vascular cells of leaf primordia regulates genes associated with carbohydrate metabolism and cell enlargement. Thus, it plays a role in metaxylem enlargement of the aerial organs. Narrow metaxylem of lpa1 exhibit leaves curling on sunny day and convey drought tolerance but reduce grain yield in mature plants. However, the genetic combination of lpa1 with semi-dwarf mutant (dep1-ko or d2) offer optimal water supply and drought resistance without impacting grain-filling rates. Our results show that water use, and transports can be genetically controlled by optimizing metaxylem vessel size and plant height, which may be utilized for enhancing drought tolerance and offers the potential solution to face the more frequent harsh climate condition in the future.

Fuji, a major apple cultivar in Korea, is susceptible to white rot. Apple white rot disease appears on the stem and fruit; the development of which deteriorates fruit quality, resulting in decreases in farmers' income. Thus, it is necessary to characterize molecular markers related to apple white rot resistance. In this study, we screened for differentially expressed genes between uninfected apple fruits and those infected with Botryosphaeria dothidea, the fungal pathogen that causes white rot. Antimicrobial tests suggest that a gene expression involved in the synthesis of the substance inhibiting the growth of B. dothidea in apples was induced by pathogen infection. We identified seven transcripts induced by the infection. The seven transcripts were homologous to genes encoding a flavonoid glucosyltransferase, a metallothionein-like protein, a senescence-induced protein, a chitinase, a wound-induced protein, and proteins of unknown function. These genes have functions related to responses to environmental stresses, including pathogen infections. Our results can be useful for the development of molecular markers for early detection of the disease or for use in breeding white rot-resistant cultivars.

Inflorescence architecture affects crop grain yield. Here, the authors deploy whole-genome sequencing-based bulk segregant analysis to identify the causal gene of a sorghum multi-seeded (msd) mutant and suggest MSD1 regulating the fertility of the pedicellate spikelets through jasmonic acid pathway.

Peanut (Arachis hypogaea L.) seeds were germinated to investigate the effect of the fermentation period of oak tree sawdust on germination viability and seedling characteristics. Its germination rate, seedling weight, length, and total vigor index were assessed. The seeds were sown in oak tree sawdust fermented for 0, 30, 45, and 60 days. The germination rates of the seeds in fermented sawdust were significantly different. The seeds in the 45-day fermented sawdust produced the heaviest biomass weight (4.6 g) with the longest true leaf (1.7 cm) and hypocotyl (3.4 cm) resulting in the highest total vigor index (925.8). In contrast, seeds in 0-day fermented sawdust had the lowest total vigor index (18.3). Microbiome analysis showed that the microbial community in the sawdust changed as the fermentation progressed, indicating that the microbial community seems to affect seed germination physiology. Taken together, 45-day fermented sawdust is recommended for optimal peanut seed germination and seedling growth.

Low-temperature atmospheric pressure plasma technology has been used in agriculture and plant science by direct and indirect treatment of bio-samples. However, the cellular and molecular mechanisms affected by plasma-activated water (PAW) are largely unexplored. In this study, PAW generated from a surface dielectric barrier discharge (SDBD) device was used for plant development. Physicochemical analysis was performed to confirm the PAW properties that correlated with the plasma treatment time. Arabidopsis thaliana L. was utilized to study the effect of the PAW treatment in the early developmental stage. The plasma-activated water samples are denoted as PAW5 time in minutes (min), PAW7 min, PAW12 min, PAW19 min and PAW40 min with the plasma treatment time. Seedlings grown in the PAW5, PAW7 and PAW12 had increased root lengths while the root lengths were decreased in the PAW19 and PAW40. In the cellular level observation, the PAW treatment specifically increased the root hair numbers per unit of the root but suppressed the root hair length in the PAW, indicating that PAW mainly modulates the root hair cell density in the root. Furthermore, we found that the root hair density and length at PAW5 in maximal observed conditions were positively regulated by root developmental-related genes including COBRA-LIKE9 (COBL9), XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE9 (XTH9), XTH17, AUXIN1 (AUX1) and LIKE-AUXIN (LAX3).

The control of flowering time is a major contributing factor to the improvement of crop yield by optimizing plant growth in a crop cycle. Genetic variants that determine flowering time can provide insights into optimizing flowering time for higher yields and other beneficial traits in tomato crops. Here, we examined a collection of flowering time variants to assess their effects on biomass and total tomato yields. Five late flowering (lf), thirteen large plant (lp), and seven floral homeotic (fh) mutants were identified as flowering time variants that could be rearranged according to leaf production in the primary shoot meristem (PSM). A flowering time continuum of mutants was translated into a positive continuum of biomass yield with more leaves, branches, and floral organs. The flowering time continuum showed an optimal curve of fruit yield, indicating a certain late flowering time as optimal for fruit yield, with the yield gradually decreasing in both directions with earlier or later flowering times. We isolated lf1, lf10, lp22, and fh13 as high-yielding genotypes with optimal flowering time, showing a new balance between the vegetative and flowering phases of tomato. Additionally, lp8, fh8, and fh15 produced extremely high biomass in leaves, axillary shoots, and floral organs due to late flowering in shoot apices with additional production of floral organs and lateral shoot. Our new late-flowering variants provide new genetic resources that can be used to optimize crop yield by fine-tuning flowering time, and future molecular studies could be conducted by revisiting our yield model.

Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.

The endoplasmic reticulum (ER) is the main site of protein synthesis, folding, and secretion to other organelles. The capacity of the ER to process proteins is limited, and excessive accumulation of unfolded and misfolded proteins can induce ER stress, which is associated with plant diseases. Here, a transgenic Arabidopsis system was established to express anti-cancer monoclonal antibodies (mAbs) that recognize the tumor-associated antigen GA733-2. Monoclonal antibody (mAb) CO17-1A recognize a tumor-associated epitope expressed on the colorectal cancer cell surface. The ER retention Lys-Asp-Glu-Leu (KDEL) motif sequence was added to the C-terminus of the heavy chain to retain anti-colorectal cancer mAbs in the ER, consequently boosting mAb production. Agrobacterium-mediated floral dip transformation was used to generate T1 transformants, and homozygous T4 seeds obtained from transgenic Arabidopsis plants expressing anti-colorectal cancer mAbs were used to confirm the physiological effects of KDEL tagging. Germination rates were not significantly different between both plants expressing mAb CO without KDEL mAb CO (CO plant) and mAb CO with KDEL mAb COK (COK plant). However, COK plants primary root lengths were shorter than those of CO plants and non-transgenic Arabidopsis plants in in vitro media. Most ER stress-related genes, with the exception of bZIP28 and IRE1a, were upregulated in COK plants compared to CO plants. Western blot and SDS-PAGE analyses showed that COK plants exhibited up to five times higher expression and mAb amounts than plants. Enhanced expression in mAb COK plants was confirmed by immunohistochemical analyses. mAb COK was distributed across most of the area of leaf tissues, whereas mAb CO was mainly distributed in extracellular areas. Surface plasmon resonance analyses revealed that mAb CO and mAb COK possessed equivalent or slightly better binding activities to antigen EpCAM compared to a commercially available parental antibody. N-glycosylation analysis showed that mAb CO had plant specific residues whereas mAb COK mainly showed an oligo-mannose N-glycan structure without the plant specific glycan residues. In this study, the reduction of plant growth and biomass induced by ER retention signal peptide might be only in in vitro conditions, and thus should be carefully considered for the initial screening for transgenic lines on culture media. Taken together, nevertheless the fusion of ER retention signal peptide is an effective approach for enhancing the yields of recombinant proteins in vivo.

To modulate the soluble sugar content of strawberry fruits, we generated transgenic plants that incorporated an antisense cDNA of ADP-glucose pyrophosphorylase (AGPase) small subunit ( FagpS) under the control of the strawberry fruit-dominant ascorbate peroxidase (APX) promoter (cv. Anther). Several independent transgenic lines were obtained and grown in the greenhouse for analysis of agronomic traits. Most transgenic fruit did not show significant differences in weight and hardness compared to control fruit. However, the starch content in fruit was decreased to 27–47% and the total soluble sugar content was increased to 16–37% in transgenic plants (analyzed by the HPLC of sugar composition at four different stages of fruit development). The sugar contents of fruits in transgenic lines were particularly higher than control fruits at the red stage. The results were consistent with northern analysis, which showed that the levels of AGPase mRNA drastically were reduced in the red stage of fruits in all the transgenic plants. In other tissues of transgenic plants, the FagpS mRNA expression level was similar to control plants. Our studies indicate that fruit-specific down-regulation of the AGPase gene might be an effective strategy for increasing sugar and decreasing starch content in strawberry. [ABSTRACT FROM AUTHOR]

A negative selectable marker gene,codA, was successfully co-transformed with a GUS reporter gene to develop selectable marker gene-free transgenic plants. The pNC binary vector contained a T-DNA harboring thecodAgene next to thenptIIgene, while a second binary vector, pHG, contained a GUS reporter gene. Tobacco plants (Nicotiana tabacumcv. Samsun NN) were co-transformed via the mixture method withAgrobacterium tumefaciensLBA4404 strains harboring pNC and pHG, respectively. Seeds harvested from the co-transformants were sown on germination media containing 5-fluorocytosine (5-FC). Analysis of the progeny by GUS staining and PCR amplification revealed that all of the 5-FC-resistant R1 plants werecodAfree, and that thecodAgene segregated independently of the GUS gene. BecausecodA-free seedlings developed normally on 5-FC-containing medium, we suggest that co-transformation with negatively selectable markers is a viable method for the production of easily distinguished, selectable marker gene-free transgenic plants. [ABSTRACT FROM AUTHOR]

Plants have diversified their leaf morphologies to adapt to diverse ecological niches. The molecular components responsible for regulating leaf morphology, however, have not been fully elucidated. By screening Arabidopsis activation-tagging lines, we identified a dominant mutant, which we designated longifolia1-1D (lng1-1D). lng1-1D plants were characterized by long petioles, narrow but extremely long leaf blades with serrated margins, elongated floral organs, and elongated siliques. The elongated leaves of the mutant were due to increased polar cell elongation rather than increased cell proliferation. Molecular characterization revealed that this phenotype was caused by overexpression of the novel gene LNG1, which was found to have a homolog, LNG2,in Arabidopsis. To further examine the role of the LNG genes, we characterized lng1 and lng2 loss-of-function mutant lines. In contrast to the elongated leaves of lng1-1D plants, the lng1 and lng2 mutants showed slightly decreased leaf length. Furthermore, the lng1-3 lng2-1 double mutant showed further decreased leaf length associated with less longitudinal polar cell elongation. The leaf widths in lng1-3 lng2-1 mutant plants were similar to those in wild type, implying that the role of LNG1 and LNG2 on polar cell elongation is similar to that of ROTUNDIFOLIA3 (ROT3). However, analysis of a lng1-3 lng2-1 rot3-1 triple mutant and of a lng1-1D rot3-1 double mutant indicated that LNG1 and LNG2 promote longitudinal cell elongation independently of ROT3. Taken together, these findings indicate that LNG1 and LNG2 are new components that regulate leaf morphology by positively promoting longitudinal polar cell elongation independently of ROT3 in Arabidopsis. [ABSTRACT FROM AUTHOR]