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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic and Genomic Basis of Vegetable and Fruit Biology, Quality and Nutrient Content

Location: Plant, Soil and Nutrition Research

Title: Catalyzing plant science research with RNA-seq

Authors
item Martin, Laetitia -
item Giovannoni, James
item Rose, Jocelyn -

Submitted to: Frontiers in Plant Systems Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 10, 2013
Publication Date: April 1, 2013
Citation: Martin, L., Giovannoni, J.J., Rose, J. 2013. Catalyzing plant science research with RNA-seq. Frontiers in Plant Systems Biology. 4(66):1-10.

Interpretive Summary: Next generation sequencing (NGS) is revolutionizing the life sciences and it is difficult to think of many areas of biology that will not be profoundly affected by increasingly cheap and rapid access to massive amounts of DNA sequence information. Plant biology is naturally no exception and plant scientists are moving on from a decade where the first genome sequence of a plant, that of Arabidopsis thaliana provided the major impetus for large swathes of plant molecular biology, to the present day where the growing number of sequenced plant genomes including many crop plants is driving biological discovery across the dinner table. Here we describe a low-cost high-output gene expression profiling technology termed RNA-seq and its application to tomato fruit development and ripening. We identify previously known and novel genes associated with ripening and fruit quality. Some may prove useful as markers for selection and additional breeding pathways to improved fruit crop species.

Technical Abstract: Next generation DNA sequencing technologies are driving increasingly rapid, affordable and high resolution analyses of plant transcriptomes through sequencing of the associated cDNA populations; an analytical platform commonly referred to as RNA-sequencing (RNA-seq). Since its first adoption only a few years ago, RNA-seq has proven itself to be a powerful tool in a remarkably diverse range of fields and disciplines, from detailed studies of biological processes at the cell type specific level, to providing insights into fundamental questions in plant biology on an evolutionary time scale. Applications include generating genomic data for unsequenced species, changing forever what can be considered as ‘model organism’, elucidating structural and regulatory gene networks, revealing how plants respond to developmental cues and environmental conditions, and allowing a better understanding of the relationships between genes and their products, uniting the ‘omics’ fields of transcriptomics, proteomics and metabolomics into a systems biology paradigm. We provide an overview of the breadth of such studies and summarize the range of RNA-seq protocols that have been developed address questions such as cell-type specific based transcriptomics, transcript secondary structure and gene mapping.

Last Modified: 7/23/2014
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