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Effect of TIF on gene expression under inductive and non-inductive photoperiods

ABSTRACT: The primary objective of this project is to determine the physiological and developmental differences between photoperiod and root induced tuberization responses in potato using genomic techniques. These experiments will establish baseline genomic and proteomic response associated with a partially characterized root-produced compound (TIF) that either substitutes for, or over-rides, the primary leaf perceived photoperiod induction signal in potato. The proposed work will answer the following questions. Are photoperiod and root induced tuberization responses the same? Do photoperiod and root induced tuberization trigger the same developmental processes in the stolon? How are photoperiod and root induced signals expressed in the genome of the leaf, stolon and roots? The data from the proposed experiments will prove invaluable in identifying key pathways in specific tissues to target in subsequent experiments in order to determine identify of, and establish the mode of action of the TIF compound. Keywords: Direct comparison

ORGANISM(S): Solanum tuberosum

PROVIDER: GSE8280 | GEO | 2007/09/01

SECONDARY ACCESSION(S): PRJNA101237

REPOSITORIES: GEO

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Project description:Purpose: MicroRNAs (miRNAs) are ubiquitous components of endogenous plant transcriptome. miRNAs are small, single-stranded and ~21 nt long RNAs which regulate gene expression at the post-transcriptional level and are known to play essential roles in various aspects of plant development and growth. Previously, a number of miRNAs have been identified in potato through in silico analysis and deep sequencing approach. However, identification of miRNAs through deep sequencing approach was limited to a few tissue types and developmental stages. This study reports the identification and characterization of potato miRNAs in three different vegetative tissues and four stages of tuber development by high throughput sequencing. Results: Small RNA libraries were constructed from leaf, stem, root and four early developmental stages of tuberization and subjected to deep sequencing, followed by bioinformatics analysis. A total of 89 conserved miRNAs (belonging to 33 families), 147 potato-specific miRNAs (with star sequence) and 112 candidate potato-specific miRNAs (without star sequence) were identified. The digital expression profiling based on TPM (Transcripts Per Million) and qRT-PCR analysis of conserved and potato-specific miRNAs revealed that some of the miRNAs showed tissue specific expression (leaf, stem and root) while a few demonstrated tuberization stage-specific expressions. Targets were predicted for identified conserved and potato-specific miRNAs, and predicted targets of four conserved miRNAs, miR160, miR164, miR172 and miR171, which are ARF16 (Auxin Response Factor 16), NAM (NO APICAL MERISTEM), RAP1 (Relative to APETALA2 1) and HAIRY MERISTEM (HAM) respectively, were experimentally validated using 5M-bM-^@M-2RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). Gene ontology (GO) analysis for potato-specific miRNAs was also performed to predict their potential biological functions. Conclusions: We report a comprehensive study of potato miRNAs at genome-wide level by high-throughput sequencing and demonstrate that these miRNAs have tissue and/or developmental stage specific expression profile. Also, predicted targets of conserved miRNAs were experimentally confirmed for the first time in potato. Our findings indicate the existence of extensive and complex small RNA population in this crop and suggest their important role in pathways involved in diverse biological processes, including tuber developmental process. Total seven (Leaf, Root, Stem, Potato Tuber stage 0(PT0),Potato Tuber stage 1(PT1),Potato Tuber stage 2(PT2),Potato Tuber stage 3(PT3) ) small RNA libraries were consctructed and sequenced by deep sequencing using Illumina GAIIx.

Project description:Purpose: MicroRNAs (miRNAs) are ubiquitous components of endogenous plant transcriptome. miRNAs are small, single-stranded and ~21 nt long RNAs which regulate gene expression at the post-transcriptional level and are known to play essential roles in various aspects of plant development and growth. Previously, a number of miRNAs have been identified in potato through in silico analysis and deep sequencing approach. However, identification of miRNAs through deep sequencing approach was limited to a few tissue types and developmental stages. This study reports the identification and characterization of potato miRNAs in three different vegetative tissues and four stages of tuber development by high throughput sequencing. Results: Small RNA libraries were constructed from leaf, stem, root and four early developmental stages of tuberization and subjected to deep sequencing, followed by bioinformatics analysis. A total of 89 conserved miRNAs (belonging to 33 families), 147 potato-specific miRNAs (with star sequence) and 112 candidate potato-specific miRNAs (without star sequence) were identified. The digital expression profiling based on TPM (Transcripts Per Million) and qRT-PCR analysis of conserved and potato-specific miRNAs revealed that some of the miRNAs showed tissue specific expression (leaf, stem and root) while a few demonstrated tuberization stage-specific expressions. Targets were predicted for identified conserved and potato-specific miRNAs, and predicted targets of four conserved miRNAs, miR160, miR164, miR172 and miR171, which are ARF16 (Auxin Response Factor 16), NAM (NO APICAL MERISTEM), RAP1 (Relative to APETALA2 1) and HAIRY MERISTEM (HAM) respectively, were experimentally validated using 5′RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). Gene ontology (GO) analysis for potato-specific miRNAs was also performed to predict their potential biological functions. Conclusions: We report a comprehensive study of potato miRNAs at genome-wide level by high-throughput sequencing and demonstrate that these miRNAs have tissue and/or developmental stage specific expression profile. Also, predicted targets of conserved miRNAs were experimentally confirmed for the first time in potato. Our findings indicate the existence of extensive and complex small RNA population in this crop and suggest their important role in pathways involved in diverse biological processes, including tuber developmental process.

Project description:Nelumbo, a perennial aquatic herbage that belongs to the family of Nelumbonaceae, comprises two extant species: N. nucifera Gaertn. and N. lutea (Wild.) Pers. Based on a previous study, N. nucifera is distributed in over Asia and Northern Australia while N. lutea is found in North America and northern of South America (1). N. nucifera can be divided into two cultivars including temperate lotus and tropical lotus based on its rhizome phenotype. The temperate lotus rhizome is expanded at the end of growth while tropical lotus root is of no significant enlargement during development (2). Normally, the temperate lotus root buds germinate in April, thereafter it takes several days from sowing to long roots and leaves. In mid-to-late may, vertical leaves rise out of the water, following July and August are the blooming period. Secondarily the first half of September is the final flowering period. The fruit ripening period is from late July to mid September, which is also the period of stem expansion and enrichment. After mid-October, it’s the dormant period, which is the lotus storage organ’s substance accumulation period. Thus the storage organ, mainly lotus rhizome, provides the energy for the lifecycle (Fig.1). Lotus rhizome, which is called metamorphic storage organ, is a kind of modified subterraneous stem, like potato (Solanum tuberosum) tuber and onion (Allium cepa L.) bulb (3). Most parts of lotus like rhizome, leaf, lotus seed and germ are used for traditional medicine (4). Rhizome especially is a kind of popular vegetable in Asia for its richness in nutrients including starch, proteins, vitamins (5). Nowadays it is a worldwide product in the form of the processed and semi-finished form like tea and vegetables. In general, the development of lotus rhizome can be classified into four stages: stolon stage, initial swelling, middle swelling, and later swelling stage (6, 7). The first three stages mainly focus on cell division and synthesis of some important carbohydrates, like starch, which play a critical part in the quantity and quality of rhizome, while accumulation of starch greatly increases at the last stage. Numerous studies have done in lotus to shed light on the environmental factors and morphometric indexes relevant to rhizome formation (8, 9). Short day light and low temperature promote tuber formation (10, 11). Also genes and proteins related to hormone, photoperiod (12, 13), starch synthesis (14, 15) and flowering time locus family genes were involved in the lotus rhizome formation (16). Previous studies include transcriptomics (6), genomics (17) and certain physiological researches, revealing numerous genes involved in photoperiod pathway, starch metabolism and hormone signal transduction, trying to make lotus a model plant of rhizome growth, while there is a lack of protein-level dynamic analysis and protein phosphorylation information, which is a strong proof for the dynamic processes in lotus rhizome. Proteomics is an indispensable method in storage organs research findings (18, 19), 2-DE and MALDI-TOF-TOF was employed to find some different protein profiles in fresh-cut lotus tuber before and after browning (20). And comparative proteomic was employed to analyze the Horsetail (Equisetum hyemale) underground stem to throw light upon the related proteins of developing rhizomes in ancient vascular plant Equisetum hyemale and different monocot species (21). Proteomics can also assist us in getting the changes of proteins in differently treated samples of potato tuber by using a LC-MS spectral-counting proteomics strategy (1), and shed light on the molecular basis of tuberization in potato to monitor differentially expressed proteins at different development stages (22). But the proteomic study of lotus rhizome enlargement hasn’t been reported now. Here, we employed comparative proteomics and phosphoproteomics to get proteins and its phosphorylation changes in the course of different rhizome development stages. Our data highlights some pathways, proteins and phosphorylated proteins during the development, and the difference between proteome and phosphoproteome in rhizome formation process.

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Effect of TIF on gene expression under inductive and non-inductive photoperiods

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