Littérature scientifique sur le sujet « Berry development transcriptomic route »

The progress of the grapevine genomics and the development of high-throughput technologies for gene expression analysis stimulated the investigation of the physical, biochemical and physiological changes of grape berry growth and maturation at transcriptomic level. The molecular information generated in the last decade is however still fragmented since it relies upon detailed analysis of few stages and thus lacks continuity over grape development. To identify the molecular events associated with berry development at a higher temporal resolution and define a transcriptomic map, we performed RNA-seq analysis of berry samples collected every week from fruit-set to maturity in Pinot noir and Cabernet Sauvignon for three consecutive years, resulting in 219 samples. Using the most variable portion of the transcriptome, we built a preliminary transcriptomic model of berry development based on the Cabernet Sauvignon samples. The Pinot noir samples were then aligned onto this preliminary ripening map to investigate its performance in describing the development of another grape variety. A further step for testing the model was the projection of RNA-seq samples of fruit development of five red-skin Italian cultivars. For all these surveys, the transcriptomic route allowed a precise definition of the progression of berry development during both formation and ripening phases.

<p style="text-align: justify;"><strong>Aims</strong>: The aim of this paper was to use recent transcriptomic tools available for grape in order to understand berry softening.</p><p style="text-align: justify;"><strong>Methods and results</strong>: A microarray bearing specific 50 mer oligonucleotide for 3,200 genes was used to study gene expression along 8 stages of berry development in Chardonnay and Shiraz berries. Transcripts corresponding to aquaporin genes and to genes involved in cell wall metabolism were studied in detail and ranked according to their pattern of expression.</p><p style="text-align: justify;"><strong>Conclusion</strong>: Several structural and regulatory genes whose expression pattern correlated with the late phases of ripening were identified. Significance and impact of study: This study provides a preliminary molecular basis to identify molecular markers of berry ripening.</p>

Root restriction (RR) has been reported to enhance grape berry quality in diverse aspects of grape life. In this study, RR-induced increases in the main primary metabolites in the grape berry and the expression of their related genes were studied at different developmental stages. Mainly the transcriptomic and metabolomic level were analyzed using ‘Summer Black’ grape berry as a material. The main results were as follows: A total of 11 transcripts involved in the primary metabolic pathways were significantly changed by the RR treatment. Metabolites such as sugars, organic acids, amino acids, starch, pectin, and cellulose were qualitatively and quantitatively analyzed along with their metabolic pathways. Sucrose synthase (VIT_07s0005g00750, VIT_11s0016g00470) and sucrose phosphate synthase (VIT_18s0089g00410) were inferred to play critical roles in the accumulation of starch, sucrose, glucose, and fructose, which was induced by the RR treatment. RR treatment also promoted the malic acid and tartaric acid accumulation in the young berry. In addition, the grape berries after the RR treatment tended to have lower pectin and cellulose content.

Heat stress has a strong and detrimental effect on plant growth and yield. Goji berry or wolfberry (Lycium barbarum L.) is a dual-purpose medicinal and food plant but an increase in high temperatures has caused a serious decline in wolfberry yield and quality. In this study, we first explored the heat stress responses of Goji berry, and found that heat stress adaptation mechanisms fluctuated over 48 h. Moreover, L.barbarum 1402 was more heat resistant while L.barbarum Ningqi No. 7 (N7) was sensitive to high temperatures, in which amino acids and alkaloids played key roles; expression and accumulation timing was also crucial. That is, 1402 responded to heat stress rapidly starting at 1 h under high temperature, activated related genes, and accumulated metabolites earlier in the amino acid metabolic pathway compared to N7, which responded to heat stress starting at 3 h under high temperature. Thus, 1402 resisted high temperatures much earlier and better compared to N7. Furthermore, joint transcriptome and metabolome analysis results showed that L-phenylalanine, L-tyrosine, N-benzylformamide, N-benzylmethylene isomethylamine, lysoPC 19:1, and N-acetyl-D-glucosamine-1-phosthate, as well as their related genes, were higher in content, or earlier in expression, in 1402 compared to N7 under heat treatment. This study initially elucidates that Goji berry 1402 has a better tolerance to heat stress than N7 for earlier and higher expression or accumulation of amino acids and alkaloids when related to high temperatures.

Abstract Drought events are a major challenge for many horticultural crops, including grapes, which are often cultivated in dry and warm climates. It is not understood how the cuticle contributes to the grape berry response to water deficit (WD); furthermore, the cuticular waxes and the related biosynthetic pathways are poorly characterized in this fruit. In this study, we identified candidate wax-related genes from the grapevine genome by phylogenetic and transcriptomic analyses. Developmental and stress response expression patterns of these candidates were characterized across pre-existing RNA sequencing data sets and confirmed a high responsiveness of the pathway to environmental stresses. We then characterized the developmental and WD-induced changes in berry cuticular wax composition, and quantified differences in berry transpiration. Cuticular aliphatic wax content was modulated during development and an increase was observed under WD, with wax esters being strongly up-regulated. These compositional changes were related to up-regulated candidate genes of the aliphatic wax biosynthetic pathway, including CER10, CER2, CER3, CER1, CER4, and WSD1. The effect of WD on berry transpiration was not significant. This study indicates that changes in cuticular wax amount and composition are part of the metabolic response of the grape berry to WD, but these changes do not reduce berry transpiration.

Grapevine cultivation, such as the whole horticulture, is currently challenged by several factors, among which the extreme weather events occurring under the climate change scenario are the most relevant. Within this context, the present study aims at characterizing at the berry level the physiological response of Vitis vinifera cv. Sauvignon Blanc to sequential stresses simulated under a semi-controlled environment: flooding at bud-break followed by multiple summer stress (drought plus heatwave) occurring at pre-vèraison. Transcriptomic and metabolomic assessments were performed through RNASeq and NMR, respectively. A comprehensive hormone profiling was also carried out. Results pointed out a different response to the heatwave in the two situations. Flooding caused a developmental advance, determining a different physiological background in the berry, thus affecting its response to the summer stress at both transcriptional levels, with the upregulation of genes involved in oxidative stress responses, and metabolic level, with the increase in osmoprotectants, such as proline and other amino acids. In conclusion, sequential stress, including a flooding event at bud-break followed by a summer heatwave, may impact phenological development and berry ripening, with possible consequences on berry and wine quality. A berry physiological model is presented that may support the development of sustainable vineyard management solutions to improve the water use efficiency and adaptation capacity of actual viticultural systems to future scenarios.

Lo sviluppo della bacca di vite può essere descritto come una successione di cambiamenti fisiologici e biochimici che riflettono la modulazione trascrizionale di molti geni. Nello scorso decennio molti studi trascrittomici sono stati eseguiti per descrivere in modo più approfondito questo processo di sviluppo dinamico e complesso. Tuttavia, la maggior parte di questi studi trascrittomici si sono focalizzati solo su un’unica varietà per volta e quindi vi è ancora una mancanza di risorse per poter effettuare comparazioni sullo sviluppo della bacca in differenti varietà di vite. Questa tesi riguarda la prima comparazione del trascrittoma della bacca di vite effettuato attraverso RNA sequencing di 120 campioni di RNA, corrispondenti alle bacche di dieci varietà raccolte a quattro stadi fenologici, due precedenti e due successivi all’invaiatura, in triplicato biologico. Quest’analisi RNA-seq ha mostrato un’evidente e profonda transizione del trascrittoma dalla fase verde alla maturazione che avviene all’invaiatura indipendentemente da colore della buccia e varietà, che coinvolge la soppressione di diversi processi metabolici relativi alla crescita vegetativa, e l’induzione di solo poche vie, come processi di metabolismo secondario e di risposta a stimoli biotici. Questo importante riprogramma del trascrittoma durante la maturazione è stato evidenziato da diversi approcci: correlazione con distanza di Pearson, analisi a componenti principali (PCA), O2PLS-DA, ricerca di biomarcatori, analisi clustering e network di correlazione. La creazione della prima via trascrittomica di sviluppo della bacca di vite, corrispondente a geni aventi un profilo di espressione simile durante tutto lo sviluppo indipendentemente dalla varietà, ha permesso di identificare geni coinvolti nei maggiori processi biologici che avvengono durante la maturazione del frutto. Infine, l’espressione dei geni appartenenti alla via biosintetica dei fenilpropanoidi/flavonoidi si sono mostrati insufficienti da soli nello spiegare le differenze trascrittomiche tra varietà rosse e bianche; tuttavia si presuppone che questi – probabilmente per effetto dell’accumulo di antociani nella buccia della bacca dall’inizio della maturazione – influenzino comunque il programma della fase di maturazione, determinando il coinvolgimento e reclutamento di geni appartenenti ad altri processi biologici.
Grape berry development can be described as a succession of physiological and biochemical changes reflecting the transcriptional modulation of many genes. In the last decade, many transcriptomic studies have been carried out to deeper describe this dynamic and complex development. Nonetheless, most of those transcriptomic studies focused on one single variety at a time and then there is still a lack of resources for comparing berry development in different grape varieties. This thesis describes the first berry transcriptome comparison carried out by RNA sequencing of 120 RNA samples, corresponding to 10-variety berries collected at four phenological growth stages, two pre- and two post-véraison, in biological triplication. This RNA-Seq analysis showed an evident deep green-to-maturation transcriptome shift occurring at véraison independently on skin colour and variety, which involves the suppression of diverse metabolic processes related to vegetative growth, and the induction of only a few pathways, such as secondary metabolic processes and responses to biotic stimuli. This fundamental transcriptome reprogramming during ripening was highlighted by distinct approaches: Pearson’s correlation distance, PCA, O2PLS-DA, biomarker discovery, clustering analysis and correlation network method. The establishment of the first grape berry development transcriptomic route, corresponding to the genes having similar patterns of expression during whole development independently on the variety, allowed identifying genes involved in the main biological processes occurring during berry development. Finally, the expression of phenylpropanoid/flavonoid biosynthetic pathway-related genes was found to be insufficient by itself to explain the differences between red- and white-grape transcriptomes, however it was supposed to influence – supposedly by the effect of anthocyanins accumulation in berry skin since the onset of ripening – maturation-phase transcriptional program, determining the recruitment of genes belonging to other biological processes.

Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that interfere with whitefly-mediated begomovirus transmission. The project objectives were to: 1) Perform gene expression analyses using microarrays to study the response of whiteflies (B, Q and A biotypes) to the acquisition of begomoviruses (Tomato yellow leaf curl (TYLCV) and Squash leaf curl (SLCV). 2) Construct a whitefly proteome from whole whiteflies and dissected organs after begomovirus acquisition. 3) Validate gene expression by q-RTPCR and sub-cellular localization of candidate ESTs identified in microarray and proteomic analyses. 4) Verify functionality of candidate ESTs using an RNAi approach, and to link these datasets to overall functional whitefly anatomical studies. During the first and second years biological experiments with TYLCV and SLCV acquisition and transmission were completed to verify the suitable parameters for sample collection for microarray experiments. The parameters were generally found to be similar to previously published results by our groups and others. Samples from whole whiteflies and midguts of the B, A and Q biotypes that acquired TYLCV and SLCV were collected in both the US and Israel and hybridized to B. tabaci microarray. The data we analyzed, candidate genes that respond to both viruses in the three tested biotypes were identified and their expression that included quantitative real-time PCR and co-localization was verified for HSP70 by the Israeli group. In addition, experiments were undertaken to employ in situ hybridization to localize several candidate genes (in progress) using an oligonucleotide probe to the primary endosymbiont as a positive control. A proteome and corresponding transcriptome to enable more effective protein identification of adult whiteflies was constructed by the US group. Further validation of the transmission route of begomoviruses, mainly SLCV and the involvement of the digestive and salivary systems was investigated (Cicero and Brown). Due to time and budget constraints the RNAi-mediated silencing objective to verify gene function was not accomplished as anticipated. HSP70, a strong candidate protein that showed over-expression after TYLCV and SLCV acquisition and retention by B. tabaci, and co-localization with TYLCV in the midgut, was further studies. Besides this protein, our joint research resulted in the identification of many intriguing candidate genes and proteins that will be followed up by additional experiments during our future research. To identify these proteins it was necessary to increase the number and breadth of whitefly ESTs substantially and so whitefly cDNAs from various libraries made during the project were sequenced (Sanger, 454). As a result, the proteome annotation (ID) was far more successful than in the initial attempt to identify proteins using Uniprot or translated insect ESTs from public databases. The extent of homology shared by insects in different orders was surprisingly low, underscoring the imperative need for genome and transcriptome sequencing of homopteran insects. Having increased the number of EST from the original usable 5500 generated several years ago to >600,000 (this project+NCBI data mining), we have identified about one fifth of the whitefly proteome using these new resources. Also we have created a database that links all identified whitefly proteins to the PAVEdb-ESTs in the database, resulting in a useful dataset to which additional ESTS will be added. We are optimistic about the prospect of linking the proteome ID results to the transcriptome database to enable our own and other labs the opportunity to functionally annotate not only genes and proteins involved in our area of interest (whitefly mediated transmission) but for the plethora of other functionalities that will emerge from mining and functionally annotating other key genes and gene families in whitefly metabolism, development, among others. This joint grant has resulted in the identification of numerous candidate proteins involved in begomovirus transmission by B. tabaci. A next major step will be to capitalize on validated genes/proteins to develop approaches to interfere with the virus transmission.

Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.