Transcriptome Analysis Reveals that Red and Blue Light Regulate Growth and Phytohormone Metabolism in Norway Spruce [Picea abies (L.) Karst.]

PLoS ONE, Год журнала: 2015, Номер 10(8), С. e0127896 - e0127896

Опубликована: Авг. 3, 2015

The mechanisms by which different light spectra regulate plant shoot elongation vary, and phytohormones respond differently to such spectrum-associated regulatory effects. Light supplementation can effectively control seedling growth in Norway spruce. However, knowledge of the effective spectrum for promoting phytohormone metabolism this species is lacking. In study, 3-year-old spruce clones were illuminated 12 h after sunset under blue or red light-emitting diode (LED) 90 d, stem increments other traits determined. Endogenous hormone levels transcriptome differences current needles assessed identify genes related responses. results showed that increment gibberellin (GA) seedlings 8.6% 29.0% higher, respectively, than those light. indoleacetic acid (IAA) level was 54.6% lower light, there no significant abscisic (ABA) zeatin riboside [ZR] between two groups seedlings. revealed 58,736,166 60,555,192 clean reads blue-light- red-light-illuminated samples, respectively. Illumina sequencing 21,923 unigenes, 2744 (approximately 93.8%) out 2926 differentially expressed (DEGs) found be upregulated main KEGG classifications DEGs metabolic pathway (29%), biosynthesis secondary metabolites (20.49%) signal transduction (8.39%). With regard transduction, AUXIN-RESISTANT1 (AUX1), AUX/IAA genes, auxin-inducible early auxin-responsive [(auxin response factor (ARF) small auxin-up RNA (SAUR)] all compared with might have yielded higher IAA level. DELLA phytochrome-interacting 3 (PIF3), involved negative GA signaling, also may quality affects endogenous hormones influencing metabolism. Blue promoted phenylpropanoid biosynthesis, phenylalanine metabolism, flavonoid flavone flavonol accompanied upregulation most their pathways. conclusion, promote regulating GAs, flavonoid, lignin, some (such as jasmonic acid) defense spruce, reduce primary available growth.

Язык: Английский

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Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus

Frontiers in Plant Science, Год журнала: 2015, Номер 6

Опубликована: Дек. 17, 2015

To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. understand vegetative bud endodormancy, we collected paradormant, and ecodormant axillary buds from Populus trees under natural conditions. Of 44,441 gene models analyzed using NimbleGen microarrays, found that 1,362 (3.1%) were differentially expressed among the three dormancy states, another 429 (1.0%) during only one two transitions (false discovery rate p-value < 0.05). all genes, 69% down-regulated paradormancy to which was expected given lower metabolic activity associated with endodormancy. Dormancy accompanied by changes multiple genes DNA methylation (via RNA-directed methylation) histone modifications Polycomb Repressive Complex 2), confirming extending knowledge chromatin modification as major features transitions. Among chromatin-associated similar SPT (SUPPRESSOR OF TY) strongly up-regulated Transcription factor sets atypically endodormancy include seems encode trihelix transcription proteins involved responses ethylene, cold, other abiotic stresses. These latter factors ETHYLENE INSENSITIVE 3 (EIN3), ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN (EBP), RESPONSE FACTOR (ERF), ZINC FINGER 10 (ZAT10), ZAT12, WRKY DNA-binding domain proteins. Analyses phytohormone-associated suggest important auxin, brassinosteroids occur We weaker evidence for salicylic acid jasmonic acid, little gibberellins, abscisic cytokinin. identified 315 upstream sequence motifs eight patterns expression, including novel previously circadian clock photoperiod, dehydration, ABA. Analogies between regulation flowering roles SQUAMOSA-PROMOTER PROTEIN-LIKE (SPL), DORMANCY ASSOCIATED MADS-BOX (DAM), SUPPRESSOR OVEREXPRESSION CONSTANS 1 (SOC1).

Язык: Английский

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Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

BMC Plant Biology, Год журнала: 2017, Номер 17(1)

Опубликована: Янв. 19, 2017

Bud dormancy is an important biological phenomenon of perennial plants that enables them to survive under harsh environmental circumstances. Grape (Vitis vinifera) one the most grown fruit crop worldwide; however, underlying mechanisms involved in grape bud are not yet clear. This work was aimed explore molecular mechanism regulating grape.We have performed transcriptome and differential transcript expression analyses "Shine Muscat" buds using Illumina RNA-seq system. Comparisons levels among three stages dormancy, paradormancy (PD) vs endodormancy (ED), summer (SB) ED SB PD, resulted detection 8949, 9780 3938 differentially expressed transcripts, respectively. Out approximately 78 million high-quality generated reads, 6096 transcripts were (log2 ratio ≥ 1, FDR ≤ 0.001). reference genome used for alignment sequence reads measure level transcripts. Furthermore, findings obtained then compared two different databases; Gene Ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG), annotate descriptions assign a pathway each transcript. KEGG analysis revealed secondary metabolites biosynthesis plant hormone signaling found enriched out 127 total pathways. In comparisons PD buds, gibberellin (GA) abscisic acid (ABA) pathways be enriched. The ABA GA further analyzed observe pattern Transcripts related PP2C family (ABA pathway) up-regulated comparison down-regulated comparisons. GID1 (GA while DELLA during stages. Differentially (DEGs) redox activity abundant GO process category. RT-qPCR assay results 12 selected validated data by RNA-seq.At this stage, taking into account so far, it possible put forward hypothesis which may pave way ultimate improvements industry.

Язык: Английский

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Epigenetic stress memory in gymnosperms

PLANT PHYSIOLOGY, Год журнала: 2024, Номер 195(2), С. 1117 - 1133

Опубликована: Янв. 31, 2024

Abstract Gymnosperms are long-lived, cone-bearing seed plants that include some of the most ancient extant plant species. These relict land have evolved to survive in habitats marked by chronic or episodic stress. Their ability thrive these environments is partly due their phenotypic flexibility, and epigenetic regulation likely plays a crucial part this plasticity. We review current knowledge on abiotic biotic stress memory gymnosperms possible mechanisms underlying long-term adaptations. also discuss recent technological improvements new experimental possibilities will advance our understanding hard-to-study plants.

Язык: Английский

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Climate change affects the suitability of Chinese cherry (Prunus pseudocerasus Lindl.) in China

Molecular Horticulture, Год журнала: 2025, Номер 5(1)

Опубликована: Март 6, 2025

The rapid development of Prunus pseudocerasus related industry has increasingly contributed to rural vitalization in China. This study employed a biomod2 ensemble model, utilizing environmental and species occurrence data from 151 P. germplasm wild/local samples, predict potential geographical distribution, suitability changes, climate dependence, ecological niche dynamics. optimized maximum entropy (MaxEnt) model yielded the most accurate predictions. variables with greatest impact on were precipitation warmest quarter mean diurnal temperature range. total suitable area for was approximately 2.78 × 106 km2, increasing CO2 concentration. highly primarily concentrated basin terrains, plateaus, plains Sichuan Province. current centroid Lichuan exhibited gradual latitudinal longitudinal movement. predicted (2090s) trends varied under different pathways periods, higher concentration associated lower overlap. emission SSP246 scenario emerged as model. Climate change is driving both expansion distribution contraction overlapping areas pseudocerasus. These findings provide theoretical basis wild resource conservation, site selection production, introduction allopatry

Язык: Английский

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Transcriptome variation along bud development in grapevine (Vitis viniferaL.)

BMC Plant Biology, Год журнала: 2012, Номер 12(1)

Опубликована: Окт. 5, 2012

Vegetative buds provide plants in temperate environments the possibility for growth and reproduction when environmental conditions are favorable. In grapevine, crucial developmental events take place within during two growing seasons consecutive years. The first season, shoot apical meristem bud differentiates all basic elements of including flowering transition lateral primordia development inflorescence primordia. These practically end with dormancy. second resume associated to flower formation development. Gene expression has been previously monitored at specific stages but never followed along seasons.Gene changes were analyzed annual cycle eight different time points. Principal Components Analysis (PCA) revealed that main factors explaining global gene differences processes dormancy active as well stress responses. Accordingly, non dormant showed an enrichment functional categories typical actively proliferating cells together over abundance transcripts belonging response pathways. Differential analyses performed between points indicated major transcriptional para/endodormancy, endo/ecodormancy ecodormancy/bud break transitions. Transcripts encoding key regulators reproductive grouped three clusters corresponding to: (i) induction, (ii) specification initiation (iii) putatively involved Within this cluster, a MADS-box (VvFLC2) other similar patterns could participate regulation.This work provides view taking highlighting those molecular biological functions As reported woody species, results suggest genes regulating also be regulatory pathways grapevine.

Язык: Английский

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An adaptive epigenetic memory in conifers with important implications for seed production

Seed Science Research, Год журнала: 2012, Номер 22(2), С. 63 - 76

Опубликована: Янв. 24, 2012

Abstract Conifers are evolutionarily more ancient than their angiosperm counterparts, and thus some adaptive mechanisms features influenced by epigenetic appear highly displayed in these woody gymnosperms. such as Norway spruce have very long generation times life spans, well large genome sizes. This seemingly excessive amount of genomic DNA without apparent duplications could be a rich source sites for regulation modifications. In spruce, an important mechanism has been identified, called memory. affects the growth cycle trees living environments with mild summers cold winters, allowing them to adapt rapidly new and/or changing environments. The temperature during post-meiotic megagametogenesis seed maturation epigenetically shifts programme embryos. results significant long-lasting phenotypic change progeny, advance or delay vital phenological processes high value, like bud break set. phenomenon is not only evolutionary significance but clear practical implications forest production conservation genetic resources. underlying molecular that causes ‘memory’ long-lived species currently under investigation. Here we summarize information related memory gymnosperms, special emphasis on conifers. behind this still unknown transcriptional changes clearly involved. Epigenetic may realized through several mechanisms, including methylation, histone modification, chromatin remodelling, small non-coding RNAs transposable element regulation, which might one most determinants.

Язык: Английский

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RNA-Seq-based transcriptome analysis of dormant flower buds of Chinese cherry (Prunus pseudocerasus)

Gene, Год журнала: 2014, Номер 555(2), С. 362 - 376

Опубликована: Ноя. 17, 2014

Язык: Английский

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Comprehensive Transcriptome Analyses Reveal Differential Gene Expression Profiles of Camellia sinensis Axillary Buds at Para-, Endo-, Ecodormancy, and Bud Flush Stages

Frontiers in Plant Science, Год журнала: 2017, Номер 8

Опубликована: Апрель 18, 2017

Winter dormancy is an important biological feature for tea plant to survive cold winters, and it also affects the economic output of plant, one few woody plants in world whose leaves are harvested non-conifer evergreen species with characterized dormancies. To discover bud regulation mechanism winter, we analyzed global gene expression profiles axillary buds at paradormancy, endodormancy, ecodormancy, flush stages by RNA-Seq analysis. In total, 16,125 differentially expressed genes (DEGs) were identified among different measured conditions. Gene set enrichment analysis was performed on DEGs from each transition. Enriched ontology terms, sets transcription factors mainly associated epigenetic mechanisms, phytohormone signaling pathways, callose-related cellular communication regulation. Furthermore, as well chromatin- phytohormone-associated identified. GI-, CAL-, SVP-, PHYB-, SFR6-, LHY-, ZTL-, PIF4/6-, ABI4-, EIN3-, ETR1-, CCA1-, PIN3-, CDK-, CO-related enriched. Based sequence homology analysis, summarized key significant differences poplar plant. The major molecular pathways involved consistent those a certain extent; however, patterns varied. This study provides transcriptome overwintering meaningful improving understanding

Язык: Английский

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Temperature-dependent differential transcriptomes during formation of an epigenetic memory in Norway spruce embryogenesis

Tree Genetics & Genomes, Год журнала: 2014, Номер 10(2), С. 355 - 366

Опубликована: Янв. 10, 2014

Язык: Английский

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