Genetic and Genomic Information System (GnpIS)

Genetic and Genomic Information System (GnpIS) integrates genetic, genomic, and phenotypic data on plant and fungal pests to enable genotype–phenotype analyses, QTL and GWAS interpretation, and comparative genomics across species such as Triticeae.

Key Features:

• Data integration: Aggregates heterogeneous data types including genetic maps, quantitative trait loci (QTL), markers, single nucleotide polymorphisms (SNPs), germplasms, genotypes, genomic sequences, physical maps, genome annotations, and expression data.
• Phenotyping and G×E datasets: Integrates phenotyping experiments and genotype × environment datasets to support construction of datasets for G×E analyses.
• GWAS and genetic analysis support: Stores and links results from Genome-Wide Association Studies (GWAS) and other genetic analyses to facilitate candidate gene identification and allele discovery.
• Embedded tools: Incorporates InterMine and JBrowse for polymorphism exploration, genome browsing, and data interrogation of specific genomic regions.
• Semantic integration and data modeling: Implements advanced data modeling and semantic integration to enable cross-dataset queries and next-generation data mining.
• FAIR alignment: Adheres to findability, accessibility, interoperability, and reusability (FAIR) principles for biological data management.
• Federated data exchange: Operates within a coordinated federation of information systems (e.g., International Grapevine Genome Program) to provide integrated interfaces for distributed data integration.
• Support for complex genomes: Targets genome-scale research on complex species such as Triticeae (including bread wheat and barley) and supports integration of agronomical and oenological data for crops like grapevine.

Scientific Applications:

• QTL mapping and GWAS interpretation: Enables interpretation of QTL and GWAS results to formulate or verify hypotheses about candidate genes and significant alleles for breeding.
• Genotype–phenotype linking: Facilitates linking of genotypes to phenotypes across germplasm collections for trait discovery and selection.
• Genotype × environment studies: Supports analyses of genotype × environment interactions using integrated phenotyping and genotyping datasets.
• Comparative and complex-genome genomics: Supports decoding and comparative analysis of complex genomes such as those in the Triticeae family and research in viticulture and other crop domains.

Methodology:

Develops and uses common data formats and tools, integrates heterogeneous datasets with InterMine and JBrowse, applies semantic integration and advanced data modeling, and leverages improvements in sequencing technologies and novel analysis strategies to decipher complex genomes and enable data exchange across distributed resources.