scholarly journals Genetic regulation of shoot architecture in cucumber

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaofeng Liu ◽  
Jiacai Chen ◽  
Xiaolan Zhang
Keyword(s):  
Leaf Shape ◽  
Economic Value ◽  
Genetic Regulation ◽  
Strong Impact ◽  
Crop Species ◽  
Visual Appearance ◽  
Regulatory Pathways ◽  
Architectural Features ◽  
Shoot Architecture ◽  
Plant Form

AbstractCucumber (Cucumis sativus L.) is an important vegetable crop species with great economic value. Shoot architecture determines the visual appearance of plants and has a strong impact on crop management and yield. Unlike most model plant species, cucumber undergoes vegetative growth and reproductive growth simultaneously, in which leaves are produced from the shoot apical meristem and flowers are generated from leaf axils, during the majority of its life, a feature representative of the Cucurbitaceae family. Despite substantial advances achieved in understanding the regulation of plant form in Arabidopsis thaliana, rice, and maize, our understanding of the mechanisms controlling shoot architecture in Cucurbitaceae crop species is still limited. In this review, we focus on recent progress on elucidating the genetic regulatory pathways underlying the determinant/indeterminant growth habit, leaf shape, branch outgrowth, tendril identity, and vine length determination in cucumber. We also discuss the potential of applying biotechnology tools and resources for the generation of ideal plant types with desired architectural features to improve cucumber productivity and cultivation efficiency.

scholarly journals MFCIS: an automatic leaf-based identification pipeline for plant cultivars using deep learning and persistent homology

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yanping Zhang ◽  
Jing Peng ◽  
Xiaohui Yuan ◽  
Lisi Zhang ◽  
Dongzi Zhu ◽  
...  
Keyword(s):  
Prunus Avium ◽  
Cultivar Identification ◽  
Leaf Shape ◽  
Persistent Homology ◽  
Growth Period ◽  
Image Features ◽  
Crop Species ◽  
Score Level Fusion ◽  
Level Fusion ◽  
Leaf Image

AbstractRecognizing plant cultivars reliably and efficiently can benefit plant breeders in terms of property rights protection and innovation of germplasm resources. Although leaf image-based methods have been widely adopted in plant species identification, they seldom have been applied in cultivar identification due to the high similarity of leaves among cultivars. Here, we propose an automatic leaf image-based cultivar identification pipeline called MFCIS (Multi-feature Combined Cultivar Identification System), which combines multiple leaf morphological features collected by persistent homology and a convolutional neural network (CNN). Persistent homology, a multiscale and robust method, was employed to extract the topological signatures of leaf shape, texture, and venation details. A CNN-based algorithm, the Xception network, was fine-tuned for extracting high-level leaf image features. For fruit species, we benchmarked the MFCIS pipeline on a sweet cherry (Prunus avium L.) leaf dataset with >5000 leaf images from 88 varieties or unreleased selections and achieved a mean accuracy of 83.52%. For annual crop species, we applied the MFCIS pipeline to a soybean (Glycine max L. Merr.) leaf dataset with 5000 leaf images of 100 cultivars or elite breeding lines collected at five growth periods. The identification models for each growth period were trained independently, and their results were combined using a score-level fusion strategy. The classification accuracy after score-level fusion was 91.4%, which is much higher than the accuracy when utilizing each growth period independently or mixing all growth periods. To facilitate the adoption of the proposed pipelines, we constructed a user-friendly web service, which is freely available at http://www.mfcis.online.

Genetic regulation of entry into meiosis in Caenorhabditis elegans

Development ◽  
1998 ◽  
Vol 125 (10) ◽  
pp. 1803-1813 ◽  
Author(s):  
L.C. Kadyk ◽  
J. Kimble
Keyword(s):  
Signal Transduction ◽  
Caenorhabditis Elegans ◽  
Germ Cells ◽  
Genetic Regulation ◽  
Signal Transduction Pathway ◽  
Mitotic Cell ◽  
Transduction Pathway ◽  
Germline Development ◽  
Large Tumor ◽  
Regulatory Pathways

The Caenorhabditis elegans germline is composed of mitotically dividing cells at the distal end that give rise to meiotic cells more proximally. Specification of the distal region as mitotic relies on induction by the somatic distal tip cell and the glp-1 signal transduction pathway. However, the genetic control over the transition from mitosis to meiosis is not understood. In this paper, we report the identification of a gene, gld-2, that has at least two functions in germline development. First, gld-2 is required for normal progression through meiotic prophase. Second, gld-2 promotes entry into meiosis from the mitotic cell cycle. With respect to this second function, gld-2 appears to be functionally redundant with a previously described gene, gld-1 (Francis, R., Barton, M. K., Kimble, J. and Schedl, T. (1995) Genetics 139, 579–606). Germ cells in gld-1(o) and gld-2 single mutants enter meiosis at the normal time, but germ cells in gld-2 gld-1(o) double mutants do not enter meiosis. Instead, the double mutant germline is mitotic throughout and forms a large tumor. We suggest that gld-1 and gld-2 define two independent regulatory pathways, each of which can be sufficient for entry into meiosis. Epistasis analyses show that gld-1 and gld-2 work downstream of the glp-1 signal transduction pathway. Therefore, we hypothesize that glp-1 promotes proliferation by inhibiting the meiosis-promoting functions of gld-1 and gld-2.

scholarly journals Key Regulatory Pathways, MicroRNAs, and Target Genes Participate in Adventitious Root Formation of Acer Rubrum L

2021 ◽  
Author(s):  
Wenpeng Zhu ◽  
Manyu Zhang ◽  
Jianyi Li ◽  
Hewen Zhao ◽  
Kezhong Zhang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Seedling Survival ◽  
Expression Patterns ◽  
Economic Value ◽  
Acer Rubrum ◽  
Pcr Analysis ◽  
Asexual Propagation ◽  
Regulatory Pathways

Abstract BackgroundAcer rubrum L. is a colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the survival of asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms in the formation of ARs of A. ruburm. To address this knowledge gap, we sequenced the transcriptome and sRNA of the A. rubrum variety ‘Autumn Fantasy’ using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. ResultsWe identified 82,468 differentially expressed genes between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene ArARF10 were shown to be involved in the auxin response. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. ConclusionsDifferential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.

VP74 Orphan Black Box: Explanatory Principles

2019 ◽  
Vol 35 (S1) ◽  
pp. 92-93
Author(s):  
George Wang ◽  
Richard Macaulay
Keyword(s):  
Market Access ◽  
Economic Value ◽  
Orphan Drugs ◽  
Regulatory Approval ◽  
Marketing Authorization ◽  
European Medicines Agency ◽  
Reimbursement Mechanisms ◽  
Regulatory Pathways ◽  
Small Patient ◽  
Pricing And Reimbursement

IntroductionOrphan legislations over the past thirty years have successfully increased the number of drugs receiving marketing authorization for rare diseases. However, for a therapy to be accessible to most patients, it requires not only marketing authorization, but market access via public reimbursement. In many major markets, the pricing and reimbursement of new therapies is based on an assessment by a national Health Technology Assessment (HTA) body, for which economic value is typically a key consideration. This research evaluates the outcome of HTAs of orphan drugs in Europe.MethodsHTA decision data (to 31/08/2017) was extracted from Gemeinsame Bundesausschuss (G-BA), Haute Autorité de Santé (HAS), National Institute for Health and Care Excellence (NICE), Pharmaceutical Benefits Advisory Committee (PBAC), and Scottish Medicines Consortium (SMC) websites. EC-approval data was extracted from the European Medicines Agency (to 31/08/2017).ResultsOnly a small minority of drugs for orphan diseases received full recommendations for their licensed indication(s) by NICE (3/35, 9%), SMC (8/66, 12%) and PBAC (1/44, 2%). 37% (26/70) of drugs assessed received positive HTA outcome by HAS (ASMR I-III). In Germany, all approved orphan drugs (100/100) received automatic additional benefit post regulatory approval by G-BA.ConclusionsThere have been significant challenges for manufacturers in converting regulatory approval of orphan drugs into commercial success and optimised market access. Attaining positive HTA appraisals for these drugs, which have been approved under expedited regulatory pathways on a less than fully mature dataset, whilst also having high prices, due to small patient populations, limiting commercial returns, may necessitate increased utilisation of alternative reimbursement mechanisms.

scholarly journals Key Regulatory Pathways, microRNAs, and Target Genes Participate in Adventitious Root Formation of Acer Rubrum L.

2021 ◽  
Author(s):  
Wenpeng Zhu ◽  
Manyu Zhang ◽  
Jianyi Li ◽  
Hewen Zhao ◽  
Kezhong Zhang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Seedling Survival ◽  
Expression Patterns ◽  
Economic Value ◽  
Acer Rubrum ◽  
Pcr Analysis ◽  
Asexual Propagation ◽  
Regulatory Pathways

Abstract BackgroundAcer rubrum L. is a colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the survival of asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms in the formation of ARs of A. ruburm. To address this knowledge gap, we sequenced the transcriptome and sRNA of the A. rubrum variety ‘Autumn Fantasy’ using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. ResultsWe identified 82,468 differentially expressed genes between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene ArARF10 were shown to be involved in the auxin response. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. ConclusionsDifferential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.

scholarly journals O-glycosylation of SPL transcription factors regulates plant developmental transitions downstream of miR156

2019 ◽  
Author(s):  
Krishna Vasant Mutanwad ◽  
Nicole Neumayer ◽  
Claudia Freitag ◽  
Isabella Zangl ◽  
Doris Lucyshyn
Keyword(s):  
Transcription Factors ◽  
Leaf Growth ◽  
Leaf Shape ◽  
Fine Tuning ◽  
Post Translational Modifications ◽  
Developmental Transitions ◽  
Environmental Signals ◽  
Regulatory Pathways ◽  
Trichome Formation ◽  
High Degree

SUMMARYThe timing of plant developmental transitions is decisive for reproductive success and thus tightly regulated by a number of pathways with a high degree of crosstalk between them. Such complex regulatory pathways often involve post-translational modifications (PTMs), integrating internal and environmental signals. O-glycosylation, the attachment of a single monosaccharide to serine or threonine of nuclear and cytosolic proteins, is one of these PTMs, affecting a number of very diverse proteins. Here we show that mutants in the O-fucosyltransferase SPINDLY (SPY) show accelerated developmental transitions. In plants, the transition from juvenile to adult and later to reproductive phase is controlled by an endogenous pathway regulated by miR156, targeting the SQUAMOSA PROMOTER BINDING PROTEIN (SBP/SPL) family of transcription factors. SPLs regulate a number of developmental processes, such as trichome formation, leaf shape, leaf growth rate and floral transition. We present genetic analysis showing that O-glycosylation regulates transitions independently of miR156 levels, but depending on functional SPLs. Moreover, SPLs interact directly with SPY and are O-glycosylated. Our results suggest a model where O-glycosylation is involved at several steps in the regulation of developmental transitions, and plays an important role in fine-tuning different regulatory pathways.

scholarly journals Overexpression of BpCUC2 Influences Leaf Shape and Internode Development in Betula pendula

2019 ◽  
Vol 20 (19) ◽  
pp. 4722
Author(s):  
Liu ◽  
Xu ◽  
Han ◽  
Wang ◽  
Liu ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Woody Plants ◽  
Growth And Development ◽  
Functional Role ◽  
Betula Pendula ◽  
Leaf Shape ◽  
Genetic Regulation ◽  
Leaf Margin ◽  
Transgenic Lines ◽  
Short Internodes

The CUP-SHAPED COTYLEDON 2 (CUC2) gene, which is negatively regulated by microRNA164 (miR164), has been specifically linked to the regulation of leaf margin serration and the maintenance of phyllotaxy in model plants. However, few studies have investigated these effects in woody plants. In this study, we integrated genomic, transcriptomic, and physiology approaches to explore the function of BpCUC2 gene in Betula pendula growth and development. Our results showed that Betula pendula plants overexpressing BpCUC2, which is targeted by BpmiR164, exhibit shortened internodes and abnormal leaf shapes. Subsequent analysis indicated that the short internodes of BpCUC2 overexpressed transgenic lines and were due to decreased epidermal cell size. Moreover, transcriptome analysis, yeast one-hybrid assays, and ChIP-PCR suggested that BpCUC2 directly binds to the LTRECOREATCOR15 (CCGAC), CAREOSREP1 (CAACTC), and BIHD1OS (TGTCA) motifs of a series of IAA-related and cyclin-related genes to regulate expression. These results may be useful to our understanding of the functional role and genetic regulation of BpCUC2.

scholarly journals Citizen science to enhance evaluation of local wastewater treatment – a case study from Oslo

2019 ◽  
Vol 79 (10) ◽  
pp. 1887-1896 ◽  
Author(s):  
S. Damman ◽  
H. Helness ◽  
I. L. Tyholt Grindvoll ◽  
C. Sun
Keyword(s):  
Citizen Science ◽  
Local Treatment ◽  
Cross Flow ◽  
Monitoring And Evaluation ◽  
High Rate ◽  
Alternative Measure ◽  
Strong Impact ◽  
Combined Sewer Overflows ◽  
Visual Appearance ◽  
Local Water

Abstract The paper discusses how citizen science within an ecosystem services (ESS) framework may enhance evaluation of de-centralized water solutions. In a demonstration case in Oslo, citizens were engaged in long-term monitoring and evaluation of two solutions for treatment of combined sewer overflows. The citizens participated in the design of the study, systematic observations, and final evaluation, via interviews and workshops. A wealth of real-time information was collected, supplementing simulation data and water sampling results. The concept of ESS drew attention to benefits that tend to be ignored in standard evaluations. It is, however, most elaborate for ecological services, and less developed for social aspects. Involving the citizens complemented the framework in these areas, while providing new insights into the contextual interactions influencing ESS and benefits of local treatment. Both solutions, a cross-flow lamella settler and a high-rate filtration system, were quite efficient in removing suspended solids, with a strong impact on visual appearance. A range of wider benefits were identified. These were difficult to monetize, but the citizens' evaluation provided an alternative measure. The study highlights the benefits of citizen science in local water management and suggests the need for more research on beneficiaries in ESS evaluation.

scholarly journals A Snap-Shot of Domatial Mite Diversity of Coffea arabica in Comparison to the Adjacent Umtamvuna Forest in South Africa

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 79
Author(s):  
Sivuyisiwe Situngu ◽  
Nigel P. Barker ◽  
Susanne Vetter
Keyword(s):  
South Africa ◽  
Economic Value ◽  
Sampling Period ◽  
Mite Species ◽  
Plant Host ◽  
Crop Species ◽  
Coffee Plantations ◽  
Commercial Crop ◽  
Indigenous Forest

Some plant species possess structures known as leaf domatia, which house mites. The association between domatia-bearing plants and mites has been proposed to be mutualistic, and has been found to be important in species of economic value, such as grapes, cotton, avocado and coffee. This is because leaf domatia affect the distribution, diversity and abundance of predatory and mycophagous mites found on the leaf surface. As a result, plants are thought to benefit from increased defence against pathogens and small arthropod herbivores. This study assesses the relative diversity and composition of mites on an economically important plant host (Coffea aribica) in comparison to mites found in a neighbouring indigenous forest in South Africa. Our results showed that the coffee plantations were associated with only predatory mites, some of which are indigenous to South Africa. This indicates that coffee plantations are able to be successfully colonised by indigenous beneficial mites. We also found an “edge effect”, in that coffee trees at the edge of the plantation hosted fewer mite species. These results are a snap-shot from a single sampling period. Nonetheless, they highlight the potential importance of this mutualism in commercial crop species and the possible role of faunal exchanges between indigenous and exotic crop species. This study expands our understanding of the mite–plant mutualism in Southern Africa, a region where acarological studies are sparse.

scholarly journals A high-quality Actinidia chinensis (kiwifruit) genome

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Haolin Wu ◽  
Tao Ma ◽  
Minghui Kang ◽  
Fandi Ai ◽  
Junlin Zhang ◽  
...  
Keyword(s):  
Reference Genome ◽  
Gene Annotation ◽  
Repetitive Sequences ◽  
Economic Value ◽  
Actinidia Chinensis ◽  
Long Terminal Repeats ◽  
High Quality ◽  
Horticultural Crop ◽  
Crop Species ◽  
Protein Coding

Abstract Actinidia chinensis (kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. Two versions of the A. chinensis genomes have been previously assembled, based mainly on relatively short reads. Here, we report an improved chromosome-level reference genome of A. chinensis (v3.0), based mainly on PacBio long reads and Hi-C data. The high-quality assembled genome is 653 Mb long, with 0.76% heterozygosity. At least 43% of the genome consists of repetitive sequences, and the most abundant long terminal repeats were further identified and account for 23.38% of our novel genome. It has clear improvements in contiguity, accuracy, and gene annotation over the two previous versions and contains 40,464 annotated protein-coding genes, of which 94.41% are functionally annotated. Moreover, further analyses of genetic collinearity revealed that the kiwifruit genome has undergone two whole-genome duplications: one affecting all Ericales families near the K-T extinction event and a recent genus-specific duplication. The reference genome presented here will be highly useful for further molecular elucidation of diverse traits and for the breeding of this horticultural crop, as well as evolutionary studies with related taxa.

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