Small RNA-mediated regulation during Zea mays (maize) Somatic Embryogenesis [smRNA-Seq]
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE120436 | GEO | 2019/10/21
REPOSITORIES: GEO
Similar Datasets
Project description:We report the role of sRNAs populations during the induction of callus tissues from VS-535 maize embryos displaying contrasting in vitro embryogenic potential; characterized through Next-generation sequencing (NGS). We conclude that the Embryogenic Response during Maize Somatic Embryogenesis induction is closely related to sRNAs regulation and depends on the developmental stage of the explant.
2019-10-21 | GSE120435 | GEO
Project description:Purpose: Maize somatic embryogenesis is usually required to achieve genetic transformation and represents an important alternative in plant development. Although many embryogenesis-related genes have been studied in this model, the molecular mechanisms underlying cell dedifferentiation and further plant regeneration are not completely understood. Methods: Immature embryos smRNA profiles of 15-day-after-pollination (IE) and Embryogenic Callus from one (C1), four (C4), and ten months (C10) were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed with two methods: Bowtie 1.1.2 and ShortStack 3.4. qRT–PCR validation for selected miRNAs was performed using SYBR Green assays. Results: We used high throughput sequencing to explore the sRNA populations during maize embryogenic callus induction and established subcultures from the Mexican cultivar VS-535, Tuxpeño landrace. We detected readjustments in 24 nt and 21-22 nt sRNA populations during the embryogenic callus establishment and maintenance. miRNAs related to stress response substantially increased upon callus proliferation establishment, correlating with a reduction in some of their target levels. On the other hand, while 24 nt-long hc-siRNAs derived from transposable retroelements transiently decreased in abundance during the embryogenic callus establishment, a population of 22 nt- hc-siRNAs increased. This was accompanied by reduction in transposon expression in the established callus subcultures. Conclusions: Stress- and development-related miRNAs are highly expressed upon maize EC callus induction and during maintenance subcultures, while miRNAs involved in hormone response only transiently increase during induction. The establishment of proliferative maize embryogenic callus is accompanied by important readjustments in the length of hc-siRNAs mapping to LTR retrotransposons, and their expression regulation.
2020-04-21 | GSE98055 | GEO
Project description:Differential small RNA expression upon induction and establishment of Tuxpeño maize embryogenic callus cultures
| PRJNA383829 | ENA
Project description:The cost of Carica papaya production through seed-based propagation is increased by sex segregation, making in vitro techniques a more appealing option for clonal propagation. Inducing embryogenic callus with 2,4-dichlorophenoxyacetic acid (2,4-D) hold the potential to large-scale cloning, although the molecular mechanisms underlying this process are still not well understood. In this study, we performed a temporal analysis in the proteome of C. papaya callus to identify the key players involved in embryogenic differentiation. Mature zygotic embryos were used as explants and treated with 20 μM 2,4-D to induce embryogenic callus. Total proteins were extracted at 0, 7, 14, and 21 days (T0, T7, T14, and T21), and 1407 proteins were identified using bottom-up proteomic approach. Comparative proteomics revealed 957 differentially accumulated proteins (DAPs) (p<0.05 and log2FC >0.585 or <-0.585) in at least one comparison between the analyzed induction times points. The clustering analysis revealed four clusters with distinct patterns of protein accumulation throughout the embryogenic callus induction treatment. The cluster 1 contains 386 DAPs that accumulated at all analyzed times after treatment with 2,4-D. In contrast, cluster 2 contains 165 DAPs that decrease in abundance during the induction. The cluster 3 contains 251 proteins that are most abundant just after the start of incubation in 2,4-D (T7) and cluster 4 grouped 155 proteins that accumulate after callus formation. Functional analysis revealed that proteins involved with reserve storage and seed maturation were more abundant in the explant at T0 and decreased as callus formation progressed. Biological processes involving carbohydrate and amino acid metabolism, aerobic respiration, and protein catabolic processes were enriched after induction treatment. Regulatory proteins, including histone deacetylase (HDT3) and argonaute 1, were more abundant after the start of induction treatment with 2,4-D, suggesting their role in acquisition of embryogenic competence. Predicted protein-protein networks revealed the regulatory role of proteins 14.3.3 accumulated during callus induction and the association of proteins involved in oxidative phosphorylation, hormone response, and SAM metabolism. Our findings emphasize the modulation of the proteome at different stages during embryogenic callus initiation and identify regulatory proteins that might be involved with the activation of this process.
2024-01-26 | PXD046521 | Pride
Project description:Papain-like cysteine proteases (PLCPs) play important roles in plant defense mechanisms. Previous work identified a set of five apoplastic PLCPs (CP1A, CP1B, CP2, XCP2 and CatB) which are crucial for the orchestration of SA-dependent defense signaling and vice versa in maize (Zea mays). One central question from these findings is which mechanism is triggered by apoplastic PLCPs to induce SA-dependent defenses. By a mass spectrometry approach we discovered a novel peptide (Zip1 = Zea mays immune signaling peptide) to be enriched in apoplastic fluid upon SA treatment. Zip1 induces PR-gene expression when applied to naїve maize leaves. Moreover, it activates apoplastic PLCPs similar as SA does, suggesting Zip1 to play an important role in SA-mediated defense signaling. In vitro studies using recombinant protein showed that CP1A and CP2, but not XCP2 and CatB, release Zip1 from its pro-peptide (PROZIP1) in vitro. Strikingly, metabolite analysis showed direct induction of SA de novo synthesis by Zip1 in maize leaves. In line with this, RNA sequencing revealed that Zip1-mediated changes in maize gene expression largely resemble SA-induced responses. Consequently, Zip1 increases maize susceptibility to the necrotrophic fungal pathogen Botrytis cinerea. In summary, this study identifies the PLCP-released peptide signal Zip1, which triggers SA signaling in maize.
2019-02-15 | PXD006751 | Pride
Project description:Through hierarchical clustering of transcript abundance data across a diverse set of tissues and developmental stages in maize, we have identified a number of coexpression modules which describe the transcriptional circuits of maize development.
2013-03-01 | GSE44743 | GEO
Project description:Transcriptional profiling of 4 maize varieties comparing genetic root response under control temperature conditions with genetic root response under low temperature conditions
2016-05-24 | GSE72508 | GEO
Project description:Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. For maize RNA-seq analysis, pooled tissues from three, eight-day-old maize seedlings were collected from transgenic and wild-type plants, prior to or after 2-hour dehydration, to conduct the RNA-seq analysis.
2015-03-29 | E-MTAB-4246 | biostudies-arrayexpress
Project description:To investigate the roles of sRNAs in keeping embryo dormancy or germination in Larix leptolepis, we deciphered the endogenous "sRNAome" in dormant and germinated embryos. High-throughput sequencing of the sRNA libraries showed that dormant embryos exhibited a length bias towards 24-nt, while germinated embryos showed a bias towards a 21-nt and/or 22-nt length. Both of proportions for miRNAs to the non-redundant and redundant sRNAs were higher in germinated embryos than those in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. The proportion of 21-nt and 22-nt sRNAs increased in germinated embryos, which might attribute to the higher expression level of miRNAs. We identified a total of 160 conserved miRNAs from 39 families, 16 novel miRNAs, and 14 plausible miRNA candidates, of which novel and non-conserved known miRNAs might be the main contributors. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during embryo dormancy and germination. One embryogenic cell line of Japanese larch (Larix leptolepis), designated as D878, with a high embryo maturation capacity was used in this study. Embryogenic callus were induced from immature embryos of larch on induction medium, followed by sub-culture, and culture on ABA-containing mature medium in a dark environment at 25 2 C. After cultured 45 days in mature medium, embryogenic calli developed into mature somatic embryos. In our study, the samples were harvested at day 57, one sample was collected after mature embryos continued to stay for 12 days on ABA-containing medium, and the other one was harvested after cultured for 12 days on ABA-removing medium. All samples were snap-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.
2014-07-19 | E-GEOD-49059 | biostudies-arrayexpress
Project description:Profiling transcription levels across many parental inbreds from the maize nested association mapping population.
2013-01-30 | E-MTAB-4328 | biostudies-arrayexpress