Museomics platform for assessing crop wild relative genetic diversity in seed banks

Overview

Seed banks are the primary source of germplasm for introducing new traits such as disease resistance into crops, yet it remains unclear whether they adequately capture the full genomic diversity of crop wild relatives (CWRs). This solution applies a museomics approach—leveraging targeted enrichment-sequencing of historical herbaria specimens—to assess genetic diversity and disease resistance gene (R-gene) content in CWRs. By comparing results across stock centres and herbaria for important vegetable CWRs, the platform can advise conservation policies and identify where new wild collections are needed. The approach avoids the cost and labor of fresh field expeditions while delivering actionable insights for breeding programs targeting stress resistance.

Technical specifications

Key features:

• Targeted enrichment sequencing (myBaits, AnArbor Biosciences) of R-genes and genetic diversity markers from herbaria and seed bank samples
• Sequencing performed on a PacBio Sequel II platform for high-resolution data
• Novel Markov clustering-based comparative genomics pipeline for reliable assessment of overall genetic diversity and R-gene capture
• Application to Solanum chilense, a well-studied tomato CWR and source of virus resistance
• Expert-curated sampling strategy based on SolanaceaeSource.org data, targeting specific populations and geographic locations
• Comparative analysis framework evaluating whether seed banks capture the genomic diversity present in wild herbaria specimens

Technology readiness level

The methodology has been validated through prior work demonstrating that tomato populations from seed banks can be used to assess evolutionary history, and that targeted enrichment sequencing for R-genes effectively captures diversity across different populations. Earlier studies confirmed that R-genes are highly diverse in a tomato CWR. The next validation phase focuses on S. chilense, with planned enrichment and sequencing of samples from two populations across both herbaria and seed banks at a budget of USD 15,000. This work represents an early-to-mid stage technology validation, moving from proof-of-concept toward practical deployment for conservation policy guidance and breeding program support.