CarrotOmics

CarrotOmics provides an integrated relational database and genomic resource for carrot (Daucus carota L.) and Apiales research.

Key Features:

• Genomic Resources: Includes the carrot reference genome, gene predictions, annotations, and sequence assemblies.
• Genetic Markers and Maps: Houses 11,224 genetic markers across 73 linkage maps or genotyping-by-sequencing datasets and descriptions of 371 mapped loci.
• Species and Germplasm Collections: Records data for 1,601 Apiales species or subspecies and 9,408 accessions from 11 germplasm collections representing over 600 species.
• Phenotypic Data: Contains phenotypic data for 204 Apiales species comprising 28,517 observations from 10,041 biological samples.
• Data Access and Visualization: Provides comprehensive genomic data access and visualization tools.

Scientific Applications:

• Genomic-assisted selection: Enables genomic-assisted selection in carrot breeding by linking markers, mapped loci, and phenotypic data.
• Trait mapping and genotype–phenotype association: Supports trait mapping and phenotype–genotype association studies using linkage maps, genotyping-by-sequencing datasets, and phenotypic observations.
• Comparative genomics: Facilitates comparative genomics across Apiales using the reference genome, gene annotations, and species/germplasm datasets.
• Genetic research and cultivar development: Supports genetic research to develop improved cultivars of Daucus carota L., including adaptation to tropical climates and changing environmental conditions.

Methodology:

Implemented as a web-based relational database built with Tripal integrated with Drupal modules and developed using resources from the MainLab Bioinformatics core.