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Multi-Omics Strategies for Decoding Smoke-Assisted Germination Pathways and Seed Vigour.

ABSTRACT: The success of seed germination and the successful establishment of seedlings across diverse environmental conditions depends on seed vigour, which is of both economic and ecologic importance. The smoke-derived exogenous compound karrikins (KARs) and the endogenous plant hormone strigolactone (SL) are two classes of butanolide-containing molecules that follow highly similar signalling pathways to control diverse biological activities in plants. Unravelling the precise mode-of-action of these two classes of molecules in model species has been a key research objective. However, the specific and dynamic expression of biomolecules upon stimulation by these signalling molecules remains largely unknown. Genomic and post-genomic profiling approaches have enabled mining and association studies across the vast genetic diversity and phenotypic plasticity. Here, we review the background of smoke-assisted germination and vigour and the current knowledge of how plants perceive KAR and SL signalling and initiate the crosstalk with the germination-associated hormone pathways. The recent advancement of 'multi-omics' applications are discussed in the context of KAR signalling and with relevance to their adoption for superior agronomic trait development. The remaining challenges and future opportunities for integrating multi-omics datasets associated with their application in KAR-dependent seed germination and abiotic stress tolerance are also discussed.

SUBMITTER: Bose U

PROVIDER: S-EPMC7593932 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Multi-Omics Strategies for Decoding Smoke-Assisted Germination Pathways and Seed Vigour.

Bose Utpal U Juhász Angéla A Broadbent James A JA Komatsu Setsuko S Colgrave Michelle L ML

International journal of molecular sciences 20201012 20

The success of seed germination and the successful establishment of seedlings across diverse environmental conditions depends on seed vigour, which is of both economic and ecologic importance. The smoke-derived exogenous compound karrikins (KARs) and the endogenous plant hormone strigolactone (SL) are two classes of butanolide-containing molecules that follow highly similar signalling pathways to control diverse biological activities in plants. Unravelling the precise mode-of-action of these two ...[more]

PMID: 33053786

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Project description:Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.

Project description:BackgroundHeat treatment is widely used to break dormancy for seed germination and phytohormones could be deeply involved. However, effect of heat treatment on phytohormone related genes/proteins/metabolites and possible relationship with dormancy release remains unclear in oil palm. In this study, oil palm seeds were heat-treated at 39 °C for 60 days according to the method for commercial production. The embryos of seeds during heat treatment (0 d, 15 d, 30 d, 45 d and 60 d) and of germinated seeds (70 d and 75 d) were selected to discover the mechanisms involved in oil palm seed germination. RNA-seq and iTRAQ were applied to investigate DEGs and DEPs related to seed germination; qPCR and western blot were used as validation accordingly; endogenous phytohormones were determined by LC-MS/MS and exogenous phytohormones were also applied to validate their effects on seed germination.ResultsRNA-seq results showed that plant hormone signal transduction was one of the most important pathways and eight phytohormones involved, while six of them (ABA, GA, ET, CTK, IAA and JA) were also identified by iTRAQ. Both RNA-seq and iTRAQ results showed that the expression of ABA decreased after heat treatment, which was further validated by qPCR and western blot. Furthermore, changes in endogenous phytohormones showed that ABA decreased rapidly to about 9% of the control at 30 d and then stayed at very low levels until germination; GA and CTK increased while IAA was not affected by heat treatment. Besides, exogenous ABA treatments (10, 100, 1000 mg/L) showed that the germination rate decreased to 63, 42 and 16% of the control, respectively, suggesting that ABA suppress seed germination and the inhibition effect increase with higher concentration; while the germination rates of exogenous GA and IAA treatments barely changed among different concentrations.ConclusionsPhytohormones are deeply involved in oil palm seed germination and ABA acts as an inhibitor. Heat treatment can eliminate endogenous ABA and break dormancy, while GA and CTK may also involve in dormancy release. At least 30 days of heat treatment might be necessary. This study provided informative perspectives on oil palm seed germination, which could be also applicable in other palm species.

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Multi-Omics Strategies for Decoding Smoke-Assisted Germination Pathways and Seed Vigour.

Publications

Multi-Omics Strategies for Decoding Smoke-Assisted Germination Pathways and Seed Vigour.

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