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<jats:p>To sustain normal growth and allow rapid responses to environmental cues, plants alter the plasma membrane protein composition under different conditions presumably by regulation of delivery, stability, and internalization. Exocytosis is a conserved cellular process that delivers proteins and lipids to the plasma membrane or extracellular space in eukaryotes. The octameric exocyst complex contributes to exocytosis by tethering secretory vesicles to the correct site for membrane fusion; however, whether the exocyst complex acts universally for all secretory vesicle cargo or just for specialized subsets used during polarized growth and trafficking is currently unknown. In addition to its role in exocytosis, the exocyst complex is also known to participate in membrane recycling and autophagy. Using a previously identified small molecule inhibitor of the plant exocyst complex subunit EXO70A1, Endosidin2 (ES2), combined with a plasma membrane enrichment method and quantitative proteomic analysis, we examined the composition of plasma membrane proteins in the root of Arabidopsis seedlings, after inhibition of the ES2-targetted exocyst complex, and verified our findings by live imaging of GFP-tagged plasma membrane proteins in root epidermal cells. The abundance of 145 plasma membrane proteins was significantly reduced following short-term ES2 treatments and these likely represent candidate cargo proteins of exocyst-mediated trafficking. Gene Ontology analysis showed that these proteins play diverse functions in cell growth, cell wall biosynthesis, hormone signaling, stress response, membrane transport, and nutrient uptake. Additionally, we quantified the effect of ES2 on the spatial distribution of EXO70A1 with live-cell imaging. Our results indicate that the plant exocyst complex mediates constitutive dynamic transport of subsets of plasma membrane proteins during normal root growth.</jats:p>

<jats:p>Water plays a very important role in the growth of tomato (<jats:italic>Solanum lycopersicum</jats:italic> L.), and how to detect the water status of tomato is the key to precise irrigation. The objective of this study is to detect the water status of tomato by fusing RGB, NIR and depth image information through deep learning. Five irrigation levels were set to cultivate tomatoes in different water states, with irrigation amounts of 150%, 125%, 100%, 75%, and 50% of reference evapotranspiration calculated by a modified Penman-Monteith equation, respectively. The water status of tomatoes was divided into five categories: severely irrigated deficit, slightly irrigated deficit, moderately irrigated, slightly over-irrigated, and severely over-irrigated. RGB images, depth images and NIR images of the upper part of the tomato plant were taken as data sets. The data sets were used to train and test the tomato water status detection models built with single-mode and multimodal deep learning networks, respectively. In the single-mode deep learning network, two CNNs, VGG-16 and Resnet-50, were trained on a single RGB image, a depth image, or a NIR image for a total of six cases. In the multimodal deep learning network, two or more of the RGB images, depth images and NIR images were trained with VGG-16 or Resnet-50, respectively, for a total of 20 combinations. Results showed that the accuracy of tomato water status detection based on single-mode deep learning ranged from 88.97% to 93.09%, while the accuracy of tomato water status detection based on multimodal deep learning ranged from 93.09% to 99.18%. The multimodal deep learning significantly outperformed the single-modal deep learning. The tomato water status detection model built using a multimodal deep learning network with ResNet-50 for RGB images and VGG-16 for depth and NIR images was optimal. This study provides a novel method for non-destructive detection of water status of tomato and gives a reference for precise irrigation management.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Strawberry fruit are highly valued for their aroma which develops during ripening. However, they have a short shelf-life. Low temperature storage is routinely used to extend shelf-life for transport and storage in the supply chain, however cold storage can also affect fruit aroma. Some fruit continue to ripen during chilled storage; however, strawberries are a non-climacteric fruit and hence ripening postharvest is limited. Although most strawberry fruit is sold whole, halved fruit is also used in ready to eat fresh fruit salads which are of increasing consumer demand and pose additional challenges to fresh fruit storage.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>To better understand the effects of cold storage, volatilomic and transcriptomic analyses were applied to halved <jats:italic>Fragaria x ananassa</jats:italic> cv. Elsanta fruit stored at 4 or 8°C for up to 12 days over two growing seasons.</jats:p></jats:sec><jats:sec><jats:title>Results and discussion</jats:title><jats:p>The volatile organic compound (VOC) profile differed between 4 or 8°C on most days of storage. Major differences were detected between the two different years of harvest indicating that aroma change at harvest and during storage is highly dependent on environmental factors during growth. The major component of the aroma profile in both years was esters. Over 3000 genes changed in expression over 5 days of storage at 8°C in transcriptome analysis. Overall, phenylpropanoid metabolism, which may also affect VOCs, and starch metabolism were the most significantly affected pathways. Genes involved in autophagy were also differentially expressed. Expression of genes from 43 different transcription factor (TF) families changed in expression: mostly they were down-regulated but NAC and WRKY family genes were mainly up-regulated. Given the high ester representation amongst VOCs, the down-regulation of an alcohol acyl transferase (AAT) during storage is significant. A total of 113 differentially expressed genes were co-regulated with the AAT gene, including seven TFs. These may be potential AAT regulators.</jats:p></jats:sec>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Blood orange (<jats:italic>Citrus sinensis</jats:italic> L.) is a valuable source of nutrition because it is enriched in anthocyanins and has high organoleptic properties. Grafting is commonly used in citriculture and has crucial effects on various phenotypes of the blood orange, including its coloration, phenology, and biotic and abiotic resistance. Still, the underlying genetics and regulatory mechanisms are largely unexplored.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>In this study, we investigated the phenotypic, metabolomic, and transcriptomic profiles at eight developmental stages of the lido blood orange cultivar (<jats:italic>Citrus sinensis</jats:italic> L. Osbeck cv. Lido) grafted onto two rootstocks.</jats:p></jats:sec><jats:sec><jats:title>Results and discussion</jats:title><jats:p>The Trifoliate orange “Zhiyang Xingcheng” rootstock provided the best fruit quality and flesh color for Lido blood orange. Comparative metabolomics suggested significant differences in accumulation patterns of metabolites and we identified 295 differentially accumulated metabolites. The major contributors were flavonoids, phenolic acids, lignans and coumarins, and terpenoids. Moreover, transcriptome profiling resulted in the identification of 4179 differentially expressed genes (DEGs), and 54 DEGs were associated with flavonoids and anthocyanins. Weighted gene co-expression network analysis identified major genes associated to 16 anthocyanins. Furthermore, seven transcription factors (<jats:italic>C2H2</jats:italic>, <jats:italic>GANT</jats:italic>, <jats:italic>MYB-related</jats:italic>, <jats:italic>AP2/ERF</jats:italic>, <jats:italic>NAC</jats:italic>, <jats:italic>bZIP</jats:italic>, and <jats:italic>MYB</jats:italic>) and five genes associated with anthocyanin synthesis pathway (<jats:italic>CHS</jats:italic>, <jats:italic>F3H</jats:italic>, <jats:italic>UFGT</jats:italic>, and <jats:italic>ANS</jats:italic>) were identified as key modulators of the anthocyanin content in lido blood orange. Overall, our results revealed the impact of rootstock on the global transcriptome and metabolome in relation to fruit quality in lido blood orange. The identified key genes and metabolites can be further utilized for the quality improvement of blood orange varieties.</jats:p></jats:sec>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential key enzyme in the glycolytic pathway and plays an important role in stress responses. Although GAPDH family genes have been found in different plant species, the determination of their gene family analysis and their functional roles in soybean are still unknown. </jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>In this study, gene sequence and expression data were obtained using online tools, and systematic evolution, expression profile analysis, and qRT-PCR analysis were conducted.</jats:p></jats:sec><jats:sec><jats:title>Results and Discussion</jats:title><jats:p>Here a total of 16 GmGAPDH genes were identified on nine chromosomes, which were classified into three clusters. Additionally, all GmGAPDH genes harbor two highly conserved domains, including Gp_dh_N (PF00044) and Gp_dh_C (PF02800). The qRTPCR analysis also showed that most GmGAPDH genes significantly responded to multiple abiotic stresses, including NaHCO3, polyethylene glycol, cold, and salt. Among them, GmGAPDH14 was extraordinarily induced by salt stress. The GmGAPDH14 gene was cloned and overexpressed through soybean hair roots. The overexpressed transgenic soybean plants of the GmGAPDH14 gene have also shown better growth than that of control plants. Moreover, the overexpressed transgenic plants of GmGAPDH14 gene had higher activities of superoxide dismutase but lower malonaldehyde (MDA) content than those of control plants under salt stress. Meanwhile, a total of four haplotypes were found for the GmGAPDH14 gene, and haplotypes 2, 3, and 4 were beneficial for the tolerance of soybean to salt stress. These results suggest that the GmGAPDH14 gene might be involved in the process of soybean tolerance to salt stress. The results of this study will be valuable in understanding the role of GAPDH genes in the abiotic stress response of soybean.</jats:p></jats:sec>

<jats:p>Soybean seed protein content (PC) and oil content (OC) have important economic value. Detecting the loci/gene related to PC and OC is important for the marker-assisted selection (MAS) breeding of soybean. To detect the stable and new loci for PC and OC, a total of 320 soybean accessions collected from the major soybean-growing countries were used to conduct a genome-wide association study (GWAS) by resequencing. The PC ranged from 37.8% to 46.5% with an average of 41.1% and the OC ranged from 16.7% to 22.6% with an average of 21.0%. In total, 23 and 29 loci were identified, explaining 3.4%–15.4% and 5.1%–16.3% of the phenotypic variations for PC and OC, respectively. Of these, eight and five loci for PC and OC, respectively, overlapped previously reported loci and the other 15 and 24 loci were newly identified. In addition, nine candidate genes were identified, which are known to be involved in protein and oil biosynthesis/metabolism, including lipid transport and metabolism, signal transduction, and plant development pathway. These results uncover the genetic basis of soybean protein and oil biosynthesis and could be used to accelerate the progress in enhancing soybean PC and OC.</jats:p>

<jats:p>Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determine cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA) that relies on the patterns of isotope labeling of metabolites in the network. For metabolic systems, typical for plants, where all potentially labeled atoms effectively have only one source atom pool, only isotopically nonstationary MFA can provide information about intracellular fluxes. There are several global approaches that implement MFA for an entire metabolic network and estimate, at once, a steady-state flux distribution for all reactions with identifiable fluxes in the network. In contrast, local approaches deal with estimation of fluxes for a subset of reactions, with smaller data demand for flux estimation. Here we present a systematic comparative review and benchmarking of the existing local approaches for isotopically nonstationary MFA. The comparison is conducted with respect to the required data and underlying computational problems solved on a synthetic network example. Furthermore, we benchmark the performance of these approaches in estimating fluxes for a subset of reactions using data obtained from the simulation of nitrogen fluxes in the <jats:italic>Arabidopsis thaliana</jats:italic> core metabolism. The findings pinpoint practical aspects that need to be considered when applying local approaches for flux estimation in large-scale plant metabolic networks.</jats:p>