Exploring natural genetic variation in tomato sucrose synthases on the basis of increased kinetic properties

Impact of diverse exogenous hormones on parthenocarpy, yield, and quality of pepino (Solanum muricatum) in the Qinghai-Tibet plateau's natural conditions

Pepino (Solanum muricatum), native to the Andes Mountains, requires exogenous hormones in its brief frost-free plateau environment to induce parthenocarpy and ensure yield.The effects of different plant growth regulators and application methods on pepino's growth, yield, and fruit quality were analyzed. Results showed that exogenous plant growth regulators had significant effects on various plant traits For instance, plant height decreased by 43.56% in the flower dipping treatment with 40 parts per million (ppm) 2,4-Dichlorophenoxyacetic acid (2,4-D), while stem diameter decreased by 21.6% with 40 ppm 4-Chlorophenoxyacetic acid (4-CPA) spraying, indicating a notable inhibition of vegetative growth. In contrast, reproductive growth improved, with the 20 ppm 2,4-D spray treatment boosting yield by 627.06% compared to the control. Furthermore, the 30 ppm 2,4-D spray produced the highest single fruit weight, a 69.16% increase over the control. However, exogenous hormones also caused fruit cracking, with the highest rate (55.5%) in the 20 ppm 2,4-D spray treatment. As for fruit quality, glucose content decreased, while fructose and sucrose levels significantly increased in hormone-treated fruits compared to the control. No significant differences were observed in flavonoid, total phenol, or vitamin C content. Transcriptome sequencing showed that 16,836 genes were significantly downregulated in pepino flower buds 72 h after a 30 ppm 4-CPA spray. KEGG enrichment analysis suggested that 4-CPA regulates parthenocarpy by influencing amino acid and protein synthesis pathways. Applying plant growth regulators in different concentrations and methods significantly impacts pepino's growth, yield, and fruit quality. These findings could guide other crops facing similar environmental challenges and potentially transform agricultural practices in high-altitude regions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01533-7.

Releasing a sugar brake generates sweeter tomato without yield penalty

In tomato, sugar content is highly correlated with consumer preferences, with most consumers preferring sweeter fruit1-4. However, the sugar content of commercial varieties is generally low, as it is inversely correlated with fruit size, and growers prioritize yield over flavour quality5-7. Here we identified two genes, tomato (Solanum lycopersicum) calcium-dependent protein kinase 27 (SlCDPK27; also known as SlCPK27) and its paralogue SlCDPK26, that control fruit sugar content. They act as sugar brakes by phosphorylating a sucrose synthase, which promotes degradation of the sucrose synthase. Gene-edited SlCDPK27 and SlCDPK26 knockouts increased glucose and fructose contents by up to 30%, enhancing perceived sweetness without fruit weight or yield penalty. Although there are fewer, lighter seeds in the mutants, they exhibit normal germination. Together, these findings provide insight into the regulatory mechanisms controlling fruit sugar accumulation in tomato and offer opportunities to increase sugar content in large-fruited cultivars without sacrificing size and yield.

The Sink-Source Relationship in Cucumber (Cucumis sativus L.) Is Modulated by DNA Methylation

The optimization of the sink-source relationship is of great importance for crop yield regulation. Cucumber is a typical raffinose family oligosaccharide (RFO)-transporting crop. DNA methylation is a common epigenetic modification in plants, but its role in sink-source regulation has not been demonstrated in RFO-translocating species. Here, whole-genome bisulfite sequencing (WGBS-seq) was conducted to compare the nonfruiting-node leaves (NFNLs) and leaves of fruit setting (FNLs) at the 12th node by removing all female flowers in other nodes of the two treatments. We found considerable differentially methylated genes enriched in photosynthesis and carbohydrate metabolic processes. Comparative transcriptome analysis between FNLs and NFNLs indicated that many differentially expressed genes (DEGs) with differentially methylated regions were involved in auxin, ethylene and brassinolide metabolism; sucrose metabolism; and RFO synthesis pathways related to sink-source regulation. Moreover, DNA methylation levels of six sink-source-related genes in the pathways mentioned above decreased in leaves after 5-aza-dC-2'-deoxycytidine (5-Aza-dC, a DNA methyltransferase inhibitor) treatment on FNLs, and stachyose synthase (CsSTS) gene expression, enzyme activity and stachyose content in RFO synthesis pathway were upregulated, thereby increasing fruit length and dry weight. Taken together, our findings proposed an up-to-date inference for the potential role of DNA methylation in the sink-source relationship, which will provide important references for further exploring the molecular mechanism of DNA methylation in improving the yield of RFO transport plants.

Severe but reversible impaired diaphragm function in septic mechanically ventilated patients

Background

Whether sepsis-associated diaphragm dysfunction may improve despite the exposure of mechanical ventilation in critically ill patients is unclear. This study aims at describing the diaphragm function time course of septic and non-septic mechanically ventilated patients.

Methods

Secondary analysis of two prospective observational studies of mechanically ventilated patients in whom diaphragm function was assessed twice: within the 24 h after intubation and when patients were switched to pressure support mode, by measuring the endotracheal pressure in response to bilateral anterior magnetic phrenic nerve stimulation (Ptr,stim). Change in diaphragm function was expressed as the difference between Ptr,stim measured under pressure support mode and Ptr,stim measured within the 24 h after intubation. Sepsis was defined according to the Sepsis-3 international guidelines upon inclusion. In a sub-group of patients, the right hemidiaphragm thickness was measured by ultrasound.

Results

Ninety-two patients were enrolled in the study. Sepsis upon intubation was present in 51 (55%) patients. In septic patients, primary reason for ventilation was acute respiratory failure related to pneumonia (37/51; 73%). In non-septic patients, main reasons for ventilation were acute respiratory failure not related to pneumonia (16/41; 39%), coma (13/41; 32%) and cardiac arrest (6/41; 15%). Ptr,stim within 24 h after intubation was lower in septic patients as compared to non-septic patients: 6.3 (4.9–8.7) cmH₂O vs. 9.8 (7.0–14.2) cmH₂O (p = 0.004), respectively. The median (interquartile) duration of mechanical ventilation between first and second diaphragm evaluation was 4 (2–6) days in septic patients and 3 (2–4) days in non-septic patients (p = 0.073). Between first and second measurements, the change in Ptr,stim was + 19% (− 13–61) in septic patients and − 7% (− 40–12) in non-septic patients (p = 0.005). In the sub-group of patients with ultrasound measurements, end-expiratory diaphragm thickness decreased in both, septic and non-septic patients. The 28-day mortality was higher in patients with decrease or no change in diaphragm function.

Conclusion

Septic patients were associated with a more severe but reversible impaired diaphragm function as compared to non-septic patients. Increase in diaphragm function was associated with a better survival.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13613-022-01005-9.

Tersect: a set theoretical utility for exploring sequence variant data

SUMMARY

Comparing genomic features among a large panel of individuals across the same species is considered nowadays a core part of the bioinformatics analyses. This typically involves a series of complex theoretical expressions to compare, intersect, extract symmetric differences between individuals within a large set of genotypes. Several publically available tools are capable of performing such tasks; however, due to the sheer size of variants being queried, such tasks can be computationally expensive with a runtime ranging from few minutes up to several hours depending on the dataset size. This makes existing tools unsuitable for interactive data query or as part of genomic data visualization platforms such as genome browsers. Tersect is a lightweight, high-performance command-line utility which interprets and applies flexible set theoretical expressions to sets of sequence variant data. It can be used both for interactive data exploration and as part of a larger pipeline thanks to its highly optimized storage and indexing algorithms for variant data.

AVAILABILITY AND IMPLEMENTATION

Tersect was implemented in C and released under the MIT license. Tersect is freely available at https://github.com/tomkurowski/tersect.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

High-Altitude Wild Species Solanum arcanum LA385-A Potential Source for Improvement of Plant Growth and Photosynthetic Performance at Suboptimal Temperatures

Plant growth, development, and yield of current tomato cultivars are directly affected by low temperatures. Although wild tomato species have been suggested as a potential source for low temperature tolerance, very little is known about their behavior during the reproductive phase. Here, we investigated the impact of suboptimal temperatures (SOT, 16/14°C), as compared to control temperatures (CT, 22/20°C), on plant growth, photosynthetic capacity, and carbohydrate metabolism. Under these conditions, two genotypes were analyzed: a Solanum lycopersicum cultivar Moneymaker and a high-altitude wild species Solanum arcanum LA385, from flowering onset until a later stage of fruit development. Total dry matter production in cv. Moneymaker was reduced up to 30% at SOT, whereas it was hardly affected in wild accession LA385. Specific leaf area, total leaf area, and number of fruits were also decreased at SOT in cv. Moneymaker. In contrast, wild accession LA385 showed an acclimation to SOT, in which Φ_PSII and net CO₂ assimilation rates were less affected; a similar specific leaf area; higher total leaf area; and higher number of fruits compared to those at CT. In addition, LA385 appeared to have a more distinct sucrose metabolism than cv. Moneymaker at both temperatures, in which it had higher contents of sucrose-6-phosphate, sucrose, and ratio of sucrose: starch in leaves and higher ratio of sucrose: hexose in fruits. Overall, our findings indicate that wild accession LA385 is able to acclimate well to SOT during the reproductive phase, whereas growth and development of cv. Moneymaker is reduced at SOT.