Plant functional genomics

  title={Plant functional genomics},
  author={Hauke Holtorf and M C Guitton and Ralf Reski},
Abstract. Functional genome analysis of plants has entered the high-throughput stage. The complete genome information from key species such as Arabidopsis thaliana and rice is now available and will further boost the application of a range of new technologies to functional plant gene analysis. To broadly assign functions to unknown genes, different fast and multiparallel approaches are currently used and developed. These new technologies are based on known methods but are adapted and improved… 


A gene by gene approach has been normally used to understand function. Functional genomics allows large-scale gene function analysis with high throughput technology and incorporates interaction of

Natural and artificial mutants as valuable resources for functional genomics and molecular breeding

This study has proposed a new strategy to generate gene-silencing mutants at the genome-wide level and evaluated the utilization of these mutants as valuable resources for molecular breeding.

Moss (Physcomitrella patens) functional genomics--Gene discovery and tool development, with implications for crop plants and human health.

Recently, the moss Physcomitrella patens was established as a versatile tool in plant functional genomics, allowing reverse genetics approaches in plants at high-throughput levels for the first time and giving new insights into the levels of diversity in land plants.

Technical aspects of functional proteomics in plants.

Physcomitrella patens as a Novel Tool for Plant Functional Genomics

Physcomitrella is developed as a novel tool in plant functional genomics, where the targeted disruption of a specific ORF leads to a loss-of-function mutation, which in turn establishes the biological role of this specific gene.

Metabolomics in Plant Stress Physiology.

Insight is provided into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics, and the workflow of measuring metabolites in plants.

Genomic and Transcriptomic Profiling: Tools for the Quality Production of Plant-Based Medicines

Next-generation sequencing (NGS) technology is rapidly becoming the method of choice for the characterization of genetic markers and can be used for transcriptomic and epigenetic studies, including genetic markers used for marker assisted breeding and quality assessment.

Plant developmental genetics: Integrating data from different experiments in databases

This review presents classification and analysis of existing databases, in which the user can find various data on plant developmental genetics, and discusses problems of these data integration both within informational resources and among them.

Reski An improved and highly standardised transformation procedure allows efficient production of single and multiple targeted gene-knockouts in a moss , Physcomitrella patens

The moss Physcomitrella patens is the only land plant known to date with highly efficient homologous recombination in its nuclear DNA, making it a unique model for plant functional genomics approaches, and a robust transformation system based on polyethylene glycol-mediated transfection of protoplasts was developed and optimised.



Metabolite profiling for plant functional genomics

The use of metabolite profiling is described as a new tool for a comparative display of gene function and has the potential not only to provide deeper insight into complex regulatory processes but also to determine phenotype directly.

Proteomics for genetic and physiological studies in plants

This review focuses on the various, mainly genetic, applications of the proteomic tools that have been developed in recent years: characterization of individuals or lines, estimation of genetic variability within and between populations, establishment of genetic distances that can be used in phylogenetic studies, characterization of mutants and localization of the genes encoding the revealed proteins.

Growth Stage–Based Phenotypic Analysis of Arabidopsis

Analysis of the development of wild-type Columbia (Col-0) plants and selected mutants are presented to illustrate a framework methodology that can be used to identify and interpret phenotypic differences in plants resulting from genetic variation and/or environmental stress.

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

Efficient screening of Arabidopsis T-DNA insertion lines using degenerate primers.

Preliminary screening results from an ordered population of nearly 60,470 independently derived T-DNA lines show the identification and isolation of isoform-specific mutants in almost all members of the Arabidopsis H(+)-proton ATPase gene family.

Genome-wide expression analysis of plant cell cycle modulated genes.

Functional genomics: probing plant gene function and expression with transposons.

  • R. Martienssen
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
Two strategies for using transposons to assess gene function are outlined here; the PCR can be used to identify plants that carry insertions into specific genes from among pools of heavily mutagenized individuals (site-selected transposon mutagenesis).

Arabidopsis gene knockout: phenotypes wanted.