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<jats:p>Climate change is expected to increase soil salinity and heat-wave intensity, duration, and frequency. These stresses, often present in combination, threaten food security as most common crops do not tolerate them. The African eggplant (<jats:italic>Solanum aethiopicum</jats:italic> L.) is a nutritious traditional crop found in sub-Saharan Africa and adapted to local environments. Its wider use is, however, hindered by the lack of research on its tolerance. This project aimed to describe the effects of salinity (100 mM NaCl solution) combined with elevated temperatures (27/21°C, 37/31°C, and 42/36°C). High temperatures reduced leaf biomass while cell membrane stability was reduced by salinity. Chlorophyll levels were boosted by salinity only at the start of the stress with only the different temperatures significantly impacted the levels at the end of the experiment. Other fluorescence parameters such as maximum quantum yield and non-photochemical quenching were only affected by the temperature change. Total antioxidants were unchanged by either stress despite a decrease of phenols at the highest temperature. Leaf sodium concentration was highly increased by salinity but phosphorus and calcium were unchanged by this stress. These findings shed new light on the tolerance mechanisms of the African eggplant under salinity and heat. Further research on later developmental stages is needed to understand its potential in the field in areas affected by these abiotic stresses.</jats:p>

<jats:p>Compared to fluctuating soil water (FW) conditions, stable soil water (SW) can increase plant water use efficiency (WUE) and improve crop growth and aboveground yield. It is unknown, however, how stable and fluctuating soil water affect root vegetables. Here, the effects of SW and FW were studied on cherry radish in a pot experiment, using negative pressure irrigation and conventional irrigation, respectively. The assessed effects included agronomic parameters, physiological indices, yield, quality and WUE of cherry radish. Results showed that under similarly average soil water contents, compared with FW, SW increased plant photosynthetic rate, stomatal conductance and transpiration rate, decreased leaf proline content by 13.7–73.3% and malondialdehyde content by 12.5–40.0%, and increased soluble sugars content by 6.3–22.1%. Cherry radish had greater biomass accumulation and nutrient uptake in SW than in FW. Indeed, SW increased radish output by 34.6–94.1% with no influence on root/shoot ratio or root quality. In conclusion, soil water stability affected directly the water physiological indicators of cherry radish and indirectly its agronomic attributes and nutrient uptake, which in turn influenced the crop biomass and yield, as well as WUE. This study provides a new perspective for improving agronomy of root crops and WUE through managing soil water stability.</jats:p>

<jats:p>Before the commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, polymerase chain reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole-genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole-genomic sequencing coverage that meets the regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop<jats:sup>®</jats:sup> enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234, and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.</jats:p>

<jats:p>Over the past several decades, a decreasing trend in solar radiation has been observed during the wheat growing season. The effects of shade stress on grain yield formation have been extensively studied. However, little information on shade stress’s effects on protein formation warrants further investigation. Two wheat cultivars were grown under three treatments, no shade as the control group (CK), shading from the joint to the anthesis stage (S1), and shading from the joint to the mature stage (S2), to investigate the effects of shade stress on the free amino acids of the caryopsis and endosperm and protein accumulation during grain filling. The dry mass of caryopsis and endosperm was significantly decreased under shade stress, whereas Glu, Ser, Ala, and Asp and protein relative content increased during grain filling. The observed increases in total protein in S1 and S2 were attributed to the increases in the SDS-isoluble and SDS-soluble protein extracts, respectively. S1 improved polymer protein formation, but S2 delayed the conversion of albumins and globulins into monomeric and polymeric proteins. Moreover, shade stress increased the proportion of SDS-unextractable polymeric protein, which represented an increase in the degree of protein polymerization. The polymerization of protein interrelations between protein components and accumulation in caryopsis and endosperm provided novel insights into wheat quality formation under shade stress.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Precision monitoring maturity in climacteric fruits like tomato is crucial for minimising losses within the food supply chain and enhancing pre- and post-harvest production and utilisation.</jats:p></jats:sec><jats:sec><jats:title>Objectives</jats:title><jats:p>This paper introduces an approach to analyse the precision maturation of tomato using hyperspectral tomography-like.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>A novel bi-directional spectral reconstruction method is presented, leveraging visible to near-infrared (Vis-NIR) information gathered from tomato spectra and their internal tissues (skin, pulp, and seeds). The study, encompassing 118 tomatoes at various maturation stages, employs a multi-block hierarchical principal component analysis combined with partial least squares for bi-directional reconstruction. The approach involves predicting internal tissue spectra by decomposing the overall tomato spectral information, creating a superset with eight latent variables for each tissue. The reverse process also utilises eight latent variables for reconstructing skin, pulp, and seed spectral data.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The reconstruction of the tomato spectra presents a mean absolute percentage error of 30.44 % and 5.37 %, 5.25 % and 6.42 % and Pearson’s correlation coefficient of 0.85, 0.98, 0.99 and 0.99 for the skin, pulp and seed, respectively. Quality parameters, including soluble solid content (%), chlorophyll (a.u.), lycopene (a.u.), and puncture force (N), were assessed and modelled with PLS with the original and reconstructed datasets, presenting a range of R2 higher than 0.84 in the reconstructed dataset. An empirical demonstration of the tomato maturation in the internal tissues revealed the dynamic of the chlorophyll and lycopene in the different tissues during the maturation process.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>The proposed approach for inner tomato tissue spectral inference is highly reliable, provides early indications and is easy to operate. This study highlights the potential of Vis-NIR devices in precision fruit maturation assessment, surpassing conventional labour-intensive techniques in cost-effectiveness and efficiency. The implications of this advancement extend to various agronomic and food chain applications, promising substantial improvements in monitoring and enhancing fruit quality.</jats:p></jats:sec>

<jats:p>The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO<jats:sub>2</jats:sub>-concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. <jats:italic>In silico</jats:italic> approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond <jats:italic>in vivo</jats:italic> experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Hybrid poplars are industrial trees in China. An understanding of the molecular mechanism underlying wood formation in hybrid poplars is necessary for molecular breeding. Although the division and differentiation of vascular cambial cells is important for secondary growth and wood formation, the regulation of this process is largely unclear.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>In this study, <jats:italic>mPagGRF15</jats:italic> OE and <jats:italic>PagGRF15-SRDX</jats:italic> transgenic poplars were generated to investigate the function of <jats:italic>PagGRF15</jats:italic>. RNA-seq and qRT-PCR were conducted to analyze genome-wide gene expression, while ChIP‒seq and ChIP-PCR were used to identified the downstream genes regulated by <jats:italic>PagGRF15</jats:italic>.</jats:p></jats:sec><jats:sec><jats:title>Results and discussion</jats:title><jats:p>We report that <jats:italic>PagGRF15</jats:italic> from hybrid poplar (<jats:italic>Populus alba</jats:italic> × <jats:italic>P. glandulosa</jats:italic>), a growth-regulating factor, plays a critical role in the regulation of vascular cambium activity. <jats:italic>PagGRF15</jats:italic> was expressed predominantly in the cambial zone of vascular tissue. Overexpression of <jats:italic>mPagGRF15</jats:italic> (the mutated version of <jats:italic>GRF15</jats:italic> in the <jats:italic>miR396</jats:italic> target sequence) in Populus led to decreased plant height and internode number. Further stem cross sections showed that the <jats:italic>mPagGRF15</jats:italic> OE plants exhibited significant changes in vascular pattern with an increase in xylem and a reduction in phloem. In addition, cambium cell files were decreased in the <jats:italic>mPagGRF15</jats:italic> OE plants. However, dominant suppression of the downstream genes of <jats:italic>PagGRF15</jats:italic> using <jats:italic>PagGRF15-SRDX</jats:italic> showed an opposite phenotype. Based on the RNA-seq and ChIP-seq results, combining qRT-PCR and ChIP-PCR analysis, candidate genes, such as <jats:italic>WOX4b</jats:italic>, <jats:italic>PXY</jats:italic> and <jats:italic>GID1.3</jats:italic>, were obtained and found to be mainly involved in cambial activity and xylem differentiation. Accordingly, we speculated that <jats:italic>PagGRF15</jats:italic> functions as a positive regulator mediating xylem differentiation by repressing the expression of the <jats:italic>WOX4a</jats:italic> and <jats:italic>PXY</jats:italic> genes to set the pace of cambial activity. In contrast, <jats:italic>PagGRF15</jats:italic> mediated the GA signaling pathway by upregulating <jats:italic>GID1.3</jats:italic> expression to stimulate xylem differentiation. This study provides valuable information for further studies on vascular cambium differentiation mechanisms and genetic improvement of the specific gravity of wood in hybrid poplars.</jats:p></jats:sec>

<jats:p>Desiccation tolerance in vegetative tissues enables resurrection plants to remain quiescent under severe drought and rapidly recover full metabolism once water becomes available. <jats:italic>Barbacenia graminifolia</jats:italic> is a resurrection plant that occurs at high altitudes, typically growing on rock slits, exposed to high irradiance and limited water availability. We analyzed the levels of reactive oxygen species (ROS) and antioxidants, carotenoids and its cleavage products, and stress-related phytohormones in fully hydrated, dehydrated, and rehydrated leaves of <jats:italic>B. graminifolia</jats:italic>. This species exhibited a precise adjustment of its antioxidant metabolism to desiccation. Our results indicate that this adjustment is associated with enhanced carotenoid and apocarotenoids, α-tocopherol and compounds of ascorbate-glutathione cycle. While α-carotene and lutein increased in dried-leaves suggesting effective protection of the light-harvesting complexes, the decrease in β-carotene was accompanied of 10.2-fold increase in the content of β-cyclocitral, an apocarotenoid implicated in the regulation of abiotic stresses, compared to hydrated plants. The principal component analysis showed that dehydrated plants at 30 days formed a separate cluster from both hydrated and dehydrated plants for up to 15 days. This regulation might be part of the protective metabolic strategies employed by this resurrection plant to survive water scarcity in its inhospitable habitat.</jats:p>

<jats:p>Microspore embryogenesis (ME) is the most powerful tool for creating homozygous lines in plant breeding and molecular biology research. It is still based mainly on the reprogramming of microspores by temperature, osmotic and/or nutrient stress. New compounds are being sought that could increase the efficiency of microspore embryogenesis or even induce the formation of haploid embryos from recalcitrant genotypes. Among these, the mitogenic factor phytosulfokine alpha (PSK-α) is promising due to its broad spectrum of activity <jats:italic>in vivo</jats:italic> and <jats:italic>in vitro</jats:italic>. The aim of our study was to investigate the effect of PSK-α on haploid embryogenesis from microspores of oilseed rape (<jats:italic>Brassica napus</jats:italic> L., DH4079), one of the most important oil crops and a model plant for studying the molecular mechanisms controlling embryo formation. We tested different concentrations (0, 0.01, 0.1 and 1 µM) of the peptide and evaluated its effect on microspore viability and embryo regeneration after four weeks of culture. Our results showed a positive correlation between addition of PSK-α and cultured microspore viability and a positive effect also on the number of developed embryos. The analysis of transcriptomes across three time points (day 0, 2 and 4) with or without PSK-α supplementation (15 RNA libraries in total) unveiled differentially expressed genes pivotal in cell division, microspore embryogenesis, and subsequent regeneration. PCA grouped transcriptomes by RNA sampling time, with the first two principal components explaining 56.8% variability. On day 2 with PSK, 45 genes (15 up- and 30 down-regulated) were differentially expressed when PSK-α was added and their number increased to 304 by day 4 (30 up- and 274 down-regulated). <jats:italic>PSK</jats:italic>, <jats:italic>PSKR</jats:italic>, and <jats:italic>PSI</jats:italic> gene expression analysis revealed dynamic patterns, with <jats:italic>PSK2</jats:italic> displaying the highest increase and overall expression during microspore culture at days 2 and 4. Despite some variations, only <jats:italic>PSK1</jats:italic> showed significant differential expression upon PSK-α addition. Of 16 ME-related molecular markers, 3 and 15 exhibited significant differential expression in PSK-supplemented cultures at days 2 and 4, respectively. Embryo-specific markers predominantly expressed after 4 days of culture, with higher expression in medium without PSK, while on day 0, numerous sporophyte-specific markers were highly expressed.</jats:p>