CottonMD

CottonMD integrates multi-omics datasets for cotton (Gossypium spp.) to enable analysis of genetic and phenotypic variation and to support identification of candidate genes and variants.

Key Features:

• Data integration: Consolidates 25 genomic sequences, transcriptomic profiles from 76 tissue samples across cotton species, epigenomic data from five species, metabolomic data of 768 metabolites from four tissues, and genetic variation and trait datasets from 4180 cotton accessions.
• Centralized repository: Provides a single resource for exploration and analysis of genetic and phenotypic variation in cotton (Gossypium spp.).
• Statistical association analysis: Employs multiple statistical methodologies to elucidate associations between genetic variations and phenotypes.
• Candidate/causal gene and variant identification: Supports pinpointing candidate or causal genes and variants involved in trait formation and regulation.
• Multi-omics analysis: Facilitates cross-layer analysis across genomic, transcriptomic, epigenomic, metabolomic, genetic variation, and trait datasets.
• Case-study validation: Includes example case studies demonstrating identification and analysis of candidate genes.

Scientific Applications:

• Trait genetics: Identification of candidate genes and variants underlying agronomic traits in cotton.
• Breeding support: Informing cotton genetic breeding through integrated genomic and phenotypic evidence.
• Functional genomics: Exploring molecular underpinnings of phenotypic diversity across cotton species using multi-omics data.

Methodology:

Consolidation and integration of diverse omics datasets (genomic, transcriptomic, epigenomic, metabolomic, genetic variation, and trait data) and application of multiple statistical methodologies to elucidate associations between genetic variations and phenotypes and to identify candidate or causal genes/variants.