Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in ‘D’Anjou’ and ‘Bartlett’ Pear Fruit

AbstractEuropean pear (Pyrus communis L.) cultivars require a genetically pre-determined duration of cold-temperature exposure to induce autocatalytic system 2 ethylene biosynthesis and subsequent fruit ripening. The physiological responses of pear to cold-temperature-induced ripening have been well characterized, but the molecular mechanisms underlying this phenomenon continue to be elucidated. This study employed established cold temperature conditioning treatments for ripening of two pear cultivars, ‘D’Anjou’ and ‘Bartlett’. Using a time-course transcriptomics approach, global gene expression responses of each cultivar were assessed at four different developmental stages during the cold conditioning process. Differential expression, functional annotation, and gene ontology enrichment analyses were performed. Interestingly, evidence for the involvement of cold-induced, vernalization-related genes and repressors of endodormancy release was found. These genes have not previously been described to play a role in fruit during the ripening transition. The resulting data provide insight into cultivar-specific mechanisms of cold-induced transcriptional regulation of ripening in European pear, as well as a unique comparative analysis of the two cultivars with very different cold conditioning requirements.

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Evidence for pre-climacteric activation of AOX transcription during cold-induced conditioning to ripen in European pear (Pyrus communis L.)

10.1101/755686 ◽

2019 ◽

Cited By ~ 1

Author(s):

Christopher Hendrickson ◽

Seanna Hewitt ◽

Mark E. Swanson ◽

Todd Einhorn ◽

Amit Dhingra

Keyword(s):

Time Course ◽

Transcript Abundance ◽

Ethylene Biosynthesis ◽

Pyrus Communis ◽

Cold Temperature ◽

Fruit Peel ◽

Physiological Indicators ◽

Conditioning Model ◽

Time Course Experiment ◽

Temperature Exposure

AbstractEuropean pears (Pyrus communis L.) require a range of cold-temperature exposure to induce ethylene biosynthesis and fruit ripening. Physiological and hormonal responses to cold temperature storage in pear have been well characterized, but the molecular underpinnings of these phenomena remain unclear. An established low-temperature conditioning model was used to induce ripening of ‘D’Anjou’ and ‘Bartlett’ pear cultivars and quantify the expression of key genes representing ripening-related metabolic pathways in comparison to non-conditioned fruit. Physiological indicators of pear ripening were recorded, and fruit peel tissue sampled in parallel, during the cold-conditioning and ripening time-course experiment to correlate gene expression to ontogeny. Two complementary approaches, Nonparametric Multi-Dimensional Scaling and efficiency-corrected 2-(ΔΔCt), were used to identify genes exhibiting the most variability in expression. Interestingly, the enhanced alternative oxidase (AOX) transcript abundance at the pre-climacteric stage in ‘Bartlett’ and ‘D’Anjou’ at the peak of the conditioning treatments suggests that AOX may play a key and a novel role in the achievement of ripening competency. There were indications that cold-sensing and signaling elements from ABA and auxin pathways modulate the S1-S2 ethylene transition in European pears, and that the S1-S2 ethylene biosynthesis transition is more pronounced in ‘Bartlett’ as compared to ‘D’Anjou’ pear. This information has implications in preventing post-harvest losses of this important crop.

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Identification of Transcription Factors Involved in the Regulation of Flowering in Adonis Amurensis Through Combined RNA-seq Transcriptomics and iTRAQ Proteomics

Genes ◽

10.3390/genes10040305 ◽

2019 ◽

Vol 10 (4) ◽

pp. 305 ◽

Cited By ~ 1

Author(s):

Zhou ◽

Sun ◽

Dai ◽

Feng ◽

Zhang ◽

...

Keyword(s):

Transcription Factors ◽

Low Temperatures ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Global Gene Expression ◽

Early Spring ◽

Rna Seq ◽

Itraq Proteomics

Temperature is one of the most important environmental factors affecting flowering in plants. Adonis amurensis, a perennial herbaceous flower that blooms in early spring in northeast China where the temperature can drop to −15 °C, is an ideal model for studying the molecular mechanisms of flowering at extremely low temperatures. This study first investigated global gene expression profiles at different developmental stages of flowering in A. amurensis by RNA-seq transcriptome and iTRAQ proteomics. Finally, 123 transcription factors (TFs) were detected in both the transcriptome and the proteome. Of these, 66 TFs belonging to 14 families may play a key role in multiple signaling pathways of flowering in A. amurensis. The TFs FAR1, PHD, and B3 may be involved in responses to light and temperature, while SCL, SWI/SNF, ARF, and ERF may be involved in the regulation of hormone balance. SPL may regulate the age pathway. Some members of the TCP, ZFP, MYB, WRKY, and bHLH families may be involved in the transcriptional regulation of flowering genes. The MADS-box TFs are the key regulators of flowering in A. amurensis. Our results provide a direction for understanding the molecular mechanisms of flowering in A. amurensis at low temperatures.

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Integrated transcriptomic and proteomic analysis reveals the complex molecular mechanisms underlying stone cell formation in Korla pear

Scientific Reports ◽

10.1038/s41598-021-87262-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Aisajan Mamat ◽

Kuerban Tusong ◽

Juan Xu ◽

Peng Yan ◽

Chuang Mei ◽

...

Keyword(s):

Cell Differentiation ◽

Proteomic Analysis ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Cell Formation ◽

Parenchyma Cell ◽

Lignin Biosynthesis ◽

Cell Content ◽

Stone Cell ◽

Fruit Samples

AbstractKorla pear (Pyrus sinkiangensis Yü) is a landrace selected from a hybrid pear species in the Xinjiang Autonomous Region in China. In recent years, pericarp roughening has been one of the major factors that adversely affects fruit quality. Compared with regular fruits, rough-skin fruits have a greater stone cell content. Stone cells compose sclerenchyma tissue that is formed by secondary thickening of parenchyma cell walls. In this work, we determined the main components of stone cells by isolating them from the pulp of rough-skin fruits at the ripening stage. Stone cell staining and apoptosis detection were then performed on fruit samples that were collected at three different developmental stages (20, 50 and 80 days after flowering (DAF)) representing the prime, late and stationary stages of stone cell differentiation, respectively. The same batches of samples were used for parallel transcriptomic and proteomic analysis to identify candidate genes and proteins that are related to SCW biogenesis in Korla pear fruits. The results showed that stone cells are mainly composed of cellulose (52%), hemicellulose (23%), lignin (20%) and a small amount of polysaccharides (3%). The periods of stone cell differentiation and cell apoptosis were synchronous and primarily occurred from 0 to 50 DAF. The stone cell components increased abundantly at 20 DAF but then decreased gradually. A total of 24,268 differentially expressed genes (DEGs) and 1011 differentially accumulated proteins (DAPs) were identified from the transcriptomic and proteomic data, respectively. We screened the DEGs and DAPs that were enriched in SCW-related pathways, including those associated with lignin biosynthesis (94 DEGs and 31 DAPs), cellulose and xylan biosynthesis (46 DEGs and 18 DAPs), S-adenosylmethionine (SAM) metabolic processes (10 DEGs and 3 DAPs), apoplastic ROS production (16 DEGs and 2 DAPs), and cell death (14 DEGs and 6 DAPs). Among the identified DEGs and DAPs, 63 significantly changed at both the transcript and protein levels during the experimental periods. In addition, the majority of these identified genes and proteins were expressed the most at the prime stage of stone cell differentiation, but their levels gradually decreased at the later stages.

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Integrative Modelling of Gene Expression and Digital Phenotypes to Describe Senescence in Wheat

Genes ◽

10.3390/genes12060909 ◽

2021 ◽

Vol 12 (6) ◽

pp. 909

Author(s):

Anyela Valentina Camargo Rodriguez

Keyword(s):

Gene Expression ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Computational Modelling ◽

Plant Morphology ◽

Reproductive Organs ◽

Biological Trait ◽

Cereal Grain ◽

Plant Level

Senescence is the final stage of leaf development and is critical for plants’ fitness as nutrient relocation from leaves to reproductive organs takes place. Although senescence is key in nutrient relocation and yield determination in cereal grain production, there is limited understanding of the genetic and molecular mechanisms that control it in major staple crops such as wheat. Senescence is a highly orchestrated continuum of interacting pathways throughout the lifecycle of a plant. Levels of gene expression, morphogenesis, and phenotypic development all play key roles. Yet, most studies focus on a short window immediately after anthesis. This approach clearly leaves out key components controlling the activation, development, and modulation of the senescence pathway before anthesis, as well as during the later developmental stages, during which grain development continues. Here, a computational multiscale modelling approach integrates multi-omics developmental data to attempt to simulate senescence at the molecular and plant level. To recreate the senescence process in wheat, core principles were borrowed from Arabidopsis Thaliana, a more widely researched plant model. The resulted model describes temporal gene regulatory networks and their effect on plant morphology leading to senescence. Digital phenotypes generated from images using a phenomics platform were used to capture the dynamics of plant development. This work provides the basis for the application of computational modelling to advance understanding of the complex biological trait senescence. This supports the development of a predictive framework enabling its prediction in changing or extreme environmental conditions, with a view to targeted selection for optimal lifecycle duration for improving resilience to climate change.

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Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (Rubus idaeus L.)

Agronomy ◽

10.3390/agronomy11040794 ◽

2021 ◽

Vol 11 (4) ◽

pp. 794

Author(s):

Luca M. Scolari ◽

Robert D. Hancock ◽

Pete E. Hedley ◽

Jenny Morris ◽

Kay Smith ◽

...

Keyword(s):

Genetic Control ◽

Developmental Disorder ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Microarray Experiment ◽

Rubus Idaeus ◽

Red Raspberry ◽

Genotype By Sequencing ◽

First Time ◽

Selection Of

‘Crumbly’ fruit is a developmental disorder in raspberry that results in malformed and unsaleable fruits. For the first time, we define two distinct crumbly phenotypes as part of this work. A consistent crumbly fruit phenotype affecting the majority of fruits every season, which we refer to as crumbly fruit disorder (CFD) and a second phenotype where symptoms vary across seasons as malformed fruit disorder (MFD). Here, segregation of crumbly fruit of the MFD phenotype was examined in a full-sib family and three QTL (Quantitative Trait Loci) were identified on a high density GbS (Genotype by Sequencing) linkage map. This included a new QTL and more accurate location of two previously identified QTLs. A microarray experiment using normal and crumbly fruit at three different developmental stages identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within the three QTL. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of crumbly fruit. These candidate genes provided insights regarding the molecular mechanisms involved in the genetic control of crumbly fruit in red raspberry. This study will contribute to new breeding strategies and diagnostics through the selection of molecular markers associated with the crumbly trait.

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Decoding the temporal nature of brain GR activity in the NFκB signal transition leading to depressive-like behavior

Molecular Psychiatry ◽

10.1038/s41380-021-01016-1 ◽

2021 ◽

Author(s):

Young-Min Han ◽

Min Sun Kim ◽

Juyeong Jo ◽

Daiha Shin ◽

Seung-Hae Kwon ◽

...

Keyword(s):

Inhibitory Action ◽

Time Course ◽

Molecular Mechanisms ◽

Late Phase ◽

Fine Tuning ◽

Dependent Manner ◽

Middle Phase ◽

Temporal Shift

AbstractThe fine-tuning of neuroinflammation is crucial for brain homeostasis as well as its immune response. The transcription factor, nuclear factor-κ-B (NFκB) is a key inflammatory player that is antagonized via anti-inflammatory actions exerted by the glucocorticoid receptor (GR). However, technical limitations have restricted our understanding of how GR is involved in the dynamics of NFκB in vivo. In this study, we used an improved lentiviral-based reporter to elucidate the time course of NFκB and GR activities during behavioral changes from sickness to depression induced by a systemic lipopolysaccharide challenge. The trajectory of NFκB activity established a behavioral basis for the NFκB signal transition involved in three phases, sickness-early-phase, normal-middle-phase, and depressive-like-late-phase. The temporal shift in brain GR activity was differentially involved in the transition of NFκB signals during the normal and depressive-like phases. The middle-phase GR effectively inhibited NFκB in a glucocorticoid-dependent manner, but the late-phase GR had no inhibitory action. Furthermore, we revealed the cryptic role of basal GR activity in the early NFκB signal transition, as evidenced by the fact that blocking GR activity with RU486 led to early depressive-like episodes through the emergence of the brain NFκB activity. These results highlight the inhibitory action of GR on NFκB by the basal and activated hypothalamic-pituitary-adrenal (HPA)-axis during body-to-brain inflammatory spread, providing clues about molecular mechanisms underlying systemic inflammation caused by such as COVID-19 infection, leading to depression.

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Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages

Insects ◽

10.3390/insects12030226 ◽

2021 ◽

Vol 12 (3) ◽

pp. 226

Author(s):

Siying Fu ◽

Yujie Duan ◽

Siqi Wang ◽

Yipeng Ren ◽

Wenjun Bu

Keyword(s):

Molecular Mechanisms ◽

Developmental Stages ◽

Average Length ◽

Transcriptome Assembly ◽

Expression Profiles ◽

Economic Losses ◽

Future Research ◽

Economic Damage ◽

Wing Formation ◽

Riptortus Pedestris

Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.

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Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process

International Journal of Molecular Sciences ◽

10.3390/ijms22137029 ◽

2021 ◽

Vol 22 (13) ◽

pp. 7029

Author(s):

Cai-Yun Xiong ◽

Qing-You Gong ◽

Hu Pei ◽

Chang-Jian Liao ◽

Rui-Chun Yang ◽

...

Keyword(s):

Regulatory Networks ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Rna Seq ◽

Short Branch ◽

Transcriptional Dynamics ◽

New Varieties ◽

Elongation Process ◽

Temporal Expression Pattern ◽

Maize Ear

In maize, the ear shank is a short branch that connects the ear to the stalk. The length of the ear shank mainly affects the transportation of photosynthetic products to the ear, and also influences the dehydration of the grain by adjusting the tightness of the husks. However, the molecular mechanisms of maize shank elongation have rarely been described. It has been reported that the maize ear shank length is a quantitative trait, but its genetic basis is still unclear. In this study, RNA-seq was performed to explore the transcriptional dynamics and determine the key genes involved in maize shank elongation at four different developmental stages. A total of 8145 differentially expressed genes (DEGs) were identified, including 729 transcription factors (TFs). Some important genes which participate in shank elongation were detected via function annotation and temporal expression pattern analyses, including genes related to signal transduction hormones (auxin, brassinosteroids, gibberellin, etc.), xyloglucan and xyloglucan xyloglucosyl transferase, and transcription factor families. The results provide insights into the genetic architecture of maize ear shanks and developing new varieties with ideal ear shank lengths, enabling adjustments for mechanized harvesting in the future.

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Gene expression profiling identifies pathways involved in seeds maturation of Jatropha curcas

10.21203/rs.2.12916/v1 ◽

2019 ◽

Author(s):

Fatemeh Maghuly ◽

Tamas Deak ◽

Klemens Vierlinger ◽

Stephan Pabinger ◽

Hakim Tafer ◽

...

Keyword(s):

Fatty Acid ◽

Seed Development ◽

Jatropha Curcas ◽

Molecular Mechanisms ◽

Seed Quality ◽

Developmental Stages ◽

Seed Maturation ◽

Nutrient Mobilization ◽

Starting Point ◽

Maturation Stages

Abstract Background: Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with a high content of oil and protein. To better understand the development of its seeds to improve Jatropha`s agronomic performance, a two-step approach was performed: 1) generation of the entire transcriptome of six different maturation stages of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels in six different developmental stages of seeds using a custom Agilent 8x60K oligonucleotide microarray. Results: A total of 793,875 high-quality reads were assembled into 19,841 unique full-length contigs, of which 13,705 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9,111 probes (out of 57,842 probes), which were differentially expressed between the six developmental stages. The expression results were validated for 70 randomly selected putative genes. Result from cluster analyses showed that transcripts related to sucrose, fatty acid, flavonoid, phenylpropanoid, lignin, hormone biosynthesis were over-represented in the early stage, while lipid storage, seed dormancy and maturation in the late stage. Generally, the expression of the most over-represented transcripts decrease in the last stage of seed maturation. Further, expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas is in late stages. The co-expression result showed a high degree of connectivity between genes that play essential role in fatty acid biosynthesis and nutrient mobilization. Furthermore, seed development and hormone pathways are significantly well connected. Conclusion: The obtained results revealed DESs regulating important pathways related to seed maturation, which could contribute to understanding the complex regulatory network during seed development. This study provides detailed information on transcription changes during J. curcas seed development and provides a starting point for a genomic survey of seed quality traits. The current results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed development, and it is anticipated that this data can be delivered to other Euphorbiaceae species of economic value.

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Using naturalistic incubation temperatures to demonstrate how variation in the timing and continuity of heat wave exposure influences phenotype

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.0992 ◽

2020 ◽

Vol 287 (1932) ◽

pp. 20200992 ◽

Cited By ~ 1

Author(s):

Anthony T. Breitenbach ◽

Amanda W. Carter ◽

Ryan T. Paitz ◽

Rachel M. Bowden

Keyword(s):

Heat Wave ◽

Time Course ◽

Heat Waves ◽

Heat Exposure ◽

Effect Of Temperature ◽

Similar Time ◽

Expression Of Genes ◽

Short Period ◽

The Face ◽

Temperature Exposure

Most organisms are exposed to bouts of warm temperatures during development, yet we know little about how variation in the timing and continuity of heat exposure influences biological processes. If heat waves increase in frequency and duration as predicted, it is necessary to understand how these bouts could affect thermally sensitive species, including reptiles with temperature-dependent sex determination (TSD). In a multi-year study using fluctuating temperatures, we exposed Trachemys scripta embryos to cooler, male-producing temperatures interspersed with warmer, female-producing temperatures (heat waves) that varied in either timing during development or continuity and then analysed resulting sex ratios. We also quantified the expression of genes involved in testis differentiation ( Dmrt1 ) and ovary differentiation ( Cyp19A1 ) to determine how heat wave continuity affects the expression of genes involved in sexual differentiation. Heat waves applied during the middle of development produced significantly more females compared to heat waves that occurred just 7 days before or after this window, and even short gaps in the continuity of a heat wave decreased the production of females. Continuous heat exposure resulted in increased Cyp19A1 expression while discontinuous heat exposure failed to increase expression in either gene over a similar time course. We report that even small differences in the timing and continuity of heat waves can result in drastically different phenotypic outcomes. This strong effect of temperature occurred despite the fact that embryos were exposed to the same number of warm days during a short period of time, which highlights the need to study temperature effects under more ecologically relevant conditions where temperatures may be elevated for only a few days at a time. In the face of a changing climate, the finding that subtle shifts in temperature exposure result in substantial effects on embryonic development becomes even more critical.

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