Unknown,Transcriptomics,Genomics,Proteomics

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Comprehensive transcriptome analysis of phytohormone pathway genes and miRNAs in ABA initiated strawberry receptacle ripening

ABSTRACT: We used Illumina sequencing to investigate the global transcriptomic expression of hormonal pathway genes in ABA initiated strawberry receptacle ripening. Expression profiles of hormone synthetic and signaling genes further demonstrated the positive roles of ABA and GA, and the negative role of auxin in receptacle ripening. We also evaluated the transcript profiling of ethylene and JA pathway genes, and the results suggested that both ethylene and JA participated in receptacle ripening. Furthermore, two novel miRNAs and three conserved miRNAs were identified and validated to target genes in ABA and auxin pathways, respectively. Our analyses reveal the molecular mechanism of hormonal regulation during strawberry receptacle ripening. The data also provide an abundant of genetic information for molecular manipulation on non-climacteric fruit ripening. Sample 1: CK0 (Strawberry fruit two weeks after athesis treated with water, set as day 0); Sample 2: CK5 (fruit treated with water on day 5); Sample 3: CK8 (fruit treated with water on day 8); Sample 4: ABA5 (fruit treated with ABA on day 5); Sample 5: ABA8 (fruit treated with ABA on day 5); Sample 6: NDGA5 (fruit treated with water on day 5); Sample 7: NDGA8 (fruit treated with NDGA on day 8).

ORGANISM(S): Fragaria x ananassa

SUBMITTER: Dongdong Li

PROVIDER: E-GEOD-63224 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Tomato fruit ripening is under the control of ethylene as well as a group of ethylene-independent transcription factors, including NON-RIPENING (NOR) and RIPENING INHIBITOR (RIN). During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) under the control of the PHYTOENE DESATURASE (PDS) promoter resulted in increased levels of β-carotene and ABA and in decreased ethylene levels. Genes regulated by ABA, or involved in its synthesis and signaling, were overexpressed, while those associated with ethylene and cell wall remodeling were repressed. In agreement with the transcriptional data, LCYb-overexpressing fruits exhibited increased density of cell wall material containing linear, under-methylated pectins and displayed an array of additional ripening phenotypes, including delayed softening, increased turgor, enhanced shelf life and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoids also changed in the transgenics, which could be attributed to delayed fruit ripening and to ABA respectively. Network correlation analysis suggests that ABA, acting through NOR and RIN, is responsible for many of the above phenotypes. These data reinforce suggestions that ABA plays an important role in tomato fruit ripening and provide clues that fruit b-carotene, acting as a precursor for ABA, actively participates in controlling the ripening process rather than merely being an output thereof. Overexpression of a LCYb gene from Arabidopsis under the control of the ripening-associated PDS promoter leads to ripe tomato fruits accumulating high β-carotene levels. Using several independent transgenic lines, we conducted a system-wide study of the effect of increased β-carotene levels on tomato fruit ripening and shelf life. Our data suggest that β-carotene, acting through ABA, is involved in a regulatory loop within the network controlling tomato fruit ripening.

Project description:Purpose: The goals of this study was to provide genome-wide data to investigate the molecular mechanism of the interaction between ABA and ethylene during tomato fruit ripening Methods: Regarding the fruits sampled at the 9th day as a well-characterized stage, we used RNA-seq to conducted a comparative analysis of exogenous ABA and NDGA effects on all components involved in biosynthesis and signaling of ethylene and ABA.The identified crucial genes in response to ABA were further performed a ripening time-course analysis by RT-PCR. In addition, we also detected how ethylene affected ABA action at the onset of ripening by treating the fruits with 1-MCP immediately after ABA application. Results: Our study not only illustrated how ABA regulated itself at the transcription level, but also elucidated that ABA can facilitate ethylene production and response by regulating some crucial genes such as LeACS4, LeACO1 and LeETR6 etc. In addition, investigation on the fruits treated with 1-MCP immediately after ABA exposure revealed that ethylene might be essential for the induction of ABA biosynthesis and signaling at the onset of fruit ripening. Furthermore, some specific transcription factors (TFs) known as regulators of ethylene synthesis and sensibility (e.g. MADS-RIN, TAGL1, CNR and NOR etc.) were also observed to be ABA responsive, which implied that ABA influenced ethylene action possibly through the regulation of these TFs expression. Conclusions: Our data suggested that ABA may act as an upstream regulator to modulate ethylene synthesis and signal transduction, which consequently influenced the ripening process. This comprehensive survey not only demonstrated how ABA regulated itself at the molecular level, but also indicated that ABA had a positive impact on ethylene production and action by regulating key genes such as LeACS2, LeACS4, LeACO1 and LeETR6. Besides, our results also revealed that ethylene might be of great importance to induce ABA accumulation and response at the onset of ripening. Moreover, many ripening related TFs, such as MADS-RIN, TAGL1, CNR and NOR, were observed to be affected by ABA, implying that a TF-mediated manner may be involved in the interaction between ABA and ethylene. This study extends our understanding of the mechanism that how ABA-triggered tomato fruit ripening, and illustrates the complex mechanism of reciprocity between ABA and ethylene at the transcription level.

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Comprehensive transcriptome analysis of phytohormone pathway genes and miRNAs in ABA initiated strawberry receptacle ripening

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