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Mining Plant Genomic and Genetic Data Using the GnpIS Information System.

A-F Adam-Blondon1, M Alaux2, S Durand2

  • 1Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France. afadam@versailles.inra.fr.

Methods in Molecular Biology (Clifton, N.J.)
|December 18, 2016
PubMed
Summary
This summary is machine-generated.

The GnpIS information system aids plant and fungi scientists in understanding trait variations by integrating genetic and phenotypic data. It facilitates exploring genotype-environment interactions and identifying key genes for breeding programs.

Keywords:
GMOD genome browserGWASGenetic resourcesGnpISInterMineMarkersPhenotypesPolymorphism

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Area of Science:

  • Plant and Fungal Genetics
  • Bioinformatics
  • Genomics

Background:

  • Understanding the genetic basis of trait variation in plants and fungi is crucial for agricultural and ecological research.
  • Integrating diverse data types (genetic, genomic, phenotypic) presents a significant challenge for researchers.
  • Existing information systems may not adequately support the complex analyses required for trait variation studies.

Purpose of the Study:

  • To introduce the GnpIS (Genetic and Phenotypic Information System) as a tool for deciphering the molecular and genetic architecture of trait variations.
  • To demonstrate how GnpIS facilitates the exploration of phenotyping, genetic analysis, and genomic polymorphism data.
  • To highlight the utility of GnpIS in studying genotype × environment interactions and supporting breeding programs.

Main Methods:

  • Utilizing the GnpIS information system to navigate and explore integrated genetic, genomic, and phenotypic datasets.
  • Leveraging embedded tools such as InterMine and JBrowse for detailed genomic analysis.
  • Building new datasets from phenotyping experiments for genotype × environment interaction studies.

Main Results:

  • GnpIS enables users to explore phenotyping data to create datasets for genotype × environment interaction studies.
  • Users can browse genetic analysis results, including Genome-Wide Association Studies (GWAS), to hypothesize candidate genes and identify important alleles.
  • The system allows for in-depth exploration of genomic polymorphism in specific regions.

Conclusions:

  • GnpIS provides a comprehensive platform for researchers to investigate the genetic underpinnings of trait variations in plants and fungi.
  • The system enhances the discovery of candidate genes and alleles crucial for crop improvement and breeding programs.
  • GnpIS empowers scientists to conduct advanced analyses of genotype-environment interactions and genomic diversity.