Multi-omics integration platform for plant functional genomics and crop improvement

Overview

This project adapts the MORF multi-omics research factory, a browser-based data integration platform, for use with complex plant genomes. Originally developed to create digital twins of microbial systems, MORF will be extended to handle large eukaryotic genomes for the first time, using Amaranthus as the inaugural plant model. The platform integrates genome, transcriptome, metabolome, and phenome data into a single explorable resource, enabling researchers to map metabolites to metabolic pathways and connect gene function to plant phenotypes. By applying MORF to Amaranthus, a drought-tolerant and nutritious leafy vegetable important for food security in Sub-Saharan Africa, the project aims to accelerate breeding of improved varieties with enhanced agronomic and nutritional traits.

Technical specifications

Core platform capabilities:

• Browser-based multi-omics data integration and exploration interface
• Supports genome, transcriptome, metabolome, and phenome data layers in a unified resource
• Published MOBpsi method for multi-omics integration applied to metabolic engineering
• Orthologue matching methods for cross-species gene annotation
• Integration with KEGG and GO term mapping frameworks

Amaranthus project specifics:

• Eight varieties from two Amaranthus species forming the primary dataset
• Complete pseudochromosomal-level genomes combined with RNAseq and untargeted metabolomics data from glasshouse-grown leaf tissue
• Funannotate pipeline for genome annotation
• Additional annotation layers including protein localisation prediction, natural product pathway prediction, and structural function inference
• Metabolic pathway construction by mapping onto related plant models
• Candidate gene, protein, and reaction relationship mapping for RNAseq interpretation
• Gene and interactome network analysis for deeper biological insight

Technology readiness level

The MORF platform has over five years of development history and has been successfully validated in bacterial systems for stress response analysis and systems metabolic engineering. It has been implemented in a simple eukaryotic system but never for a large complex eukaryote prior to this project. The Amaranthus dataset is already collected and ready for import. The proposed project is scoped at six to twelve months, using MORF staff and seconded personnel from the collaborating research group. Upon completion, the adapted platform will provide a data architecture applicable to other plant genomes, enabling broader multi-omics research across crop species.