Systems biology of seeds: deciphering the molecular mechanisms of seed storage, dormancy and onset of germination

Sreenivasulu, Nese

doi:10.1007/s00299-017-2135-y

Cited by 11 publications

(8 citation statements)

References 24 publications

(23 reference statements)

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“…The advanced stages of ripening have been deeply studied, and their control mechanisms are mediated by phytohormones ( Kumar et al, 2014 ; Robert, 2019 ). In particular, fruit ripening is regulated by ethylene, while seeds dormancy, which is essential for the embryonic differentiation, is regulated by a fine balance between ABA and gibberellins, or/and auxins ( Kucera et al, 2005 ; Weiss and Ori, 2007 ; Sreenivasulu, 2017 ; Figueiredo and Köhler, 2018 ). Contrary to the ripening and its heterotrophic aspects, the first stages of fruit development and its autotrophic phase are less described.…”

Section: Discussionmentioning

confidence: 99%

The Impact of Fruit Etiolation on Quality of Seeds in Tobacco

et al. 2020

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Seed’s maturity and integrity are essential requirements for germination, and they rely on nutrients availability and a correct phytohormones’ balance. These aspects are prerequisites for prompt germination at the end of the dormancy period and strictly depend on chloroplast metabolism and photosynthesis. In the present work, capsules of Nicotiana tabacum were grown in dark during the whole post-anthesis period. Among others, photosynthetic rates, dormancy, and phytohormones levels in seeds were found to be significantly different with respect to controls. In particular, etiolated capsules had expectedly reduced photosynthetic rates and, when compared to controls, their seeds had an increased mass and volume, an alteration in hormones level, and a consequently reduced dormancy. The present findings show how, during fruit development, the presence of light and the related fruit’s photosynthetic activity play an indirect but essential role for reaching seeds maturity and dormancy. Results highlight how unripe fruits are versatile organs that, depending on the environmental conditions, may facultatively behave as sink or source/sink with associated variation in seed’s reserves and phytohormone levels.

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Section: Discussionmentioning

confidence: 99%

The Impact of Fruit Etiolation on Quality of Seeds in Tobacco

et al. 2020

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“…In addition, it is more cost effective, especially if dealing with large sample numbers. In our laboratory, we routinely use transcriptomic analyses using the microarray technology to determine the role of central regulatory hubs that govern the molecular networks and pathways involved in the growth, development and metabolism of cereal grains 5,6,7,8,9 . We also routinely use it to conduct of genome-wide gene expression profiling studies to obtain a mechanistic understanding of the response of cereal grains to abiotic stresses 10 , as well as in the conduct of transcriptome-wide association (TWAS) and linkage mapping studies to identify genes responsible for cereal grain quality and nutrition 11,12 .…”

Section: Introductionmentioning

confidence: 99%

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Butardo

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Sreeenivasulu

et al. 2020

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The characterization of gene expression is dependent on RNA quality. In germinating, developing and mature cereal seeds, the extraction of high-quality RNA is often hindered by high starch and sugar content. These compounds can reduce both the yield and the quality of the extracted total RNA. The deterioration in quantity and quality of total RNA can subsequently have a significant impact on the downstream transcriptomic analyses, which may not accurately reflect the spatial and/or temporal variation in the gene expression profile of the samples being tested. In this protocol, we describe an optimized method for extraction of total RNA with sufficient quantity and quality to be used for whole transcriptome analysis of cereal grains. The described method is suitable for several downstream applications used for transcriptomic profiling of developing, germinating, and mature cereal seeds. The method of transcriptome profiling using a microarray platform is shown. This method is specifically designed for gene expression profiling of cereals with described genome sequences. The detailed procedure from microarray handling to final quality control is described. This includes cDNA synthesis, cRNA labelling, microarray hybridization, slide scanning, feature extraction, and data quality validation. The data generated by this method can be used to characterize the transcriptome of cereals during germination, in various stages of grain development, or at different biotic or abiotic stress conditions. The results presented here exemplify high-quality transcriptome data amenable for downstream bioinformatics analyses, such as the determination of differentially expressed genes (DEGs), characterisation of gene regulatory networks, and conducting transcriptome-wide association study (TWAS).

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“…Very recently this technology was used to knock out EPLF9 which is a positive regulator of stomatal development (Hunt et al 2010). Thus, the future scope of seed biology would be to characterize functional mutants of rate-limiting enzymes and key regulatory targets of seed storage components, as well as to revalidate the models for engineering seed sink for translational nutritional and health benefits (Sreenivasulu 2017).…”

Section: Loss and Gain Of Gene Functionmentioning

confidence: 99%

“…Apart from this, they also function as an important delivery system of genetic information from generations to generation. These stored seed reserves comprise 70% of total caloric intake in the form of food and animal feed produced through sustainable agriculture (Sreenivasulu 2017). Therefore, seeds of appropriate characteristics are required to meet the demand of diverse agro-climatic conditions and intensive cropping systems.…”

Section: Introductionmentioning

confidence: 99%

Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security

et al. 2018

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Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.

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Systems biology of seeds: deciphering the molecular mechanisms of seed storage, dormancy and onset of germination

Cited by 11 publications

References 24 publications

The Impact of Fruit Etiolation on Quality of Seeds in Tobacco

The Impact of Fruit Etiolation on Quality of Seeds in Tobacco

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security

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