Crop genome evolution and polyploidy
Comparative genomics reconstructs chromosome, subgenome, and species histories, especially in crops shaped by hybridization, polyploidization, and domestication.
PolyploidyDomesticationSynteny
Research across genome scales.
We connect genome structure, inherited variation, and gene regulation to explain how complex crop genomes evolve and how useful traits arise.
Core themes / 01
Four connected questions.
Each theme addresses a different layer of crop diversity. Together, they form a route from genome representation to biological mechanism.
Graph pangenomics
Graph models represent sequence and structural diversity beyond a single reference genome, including dosage-aware variation in mixed-ploidy populations.
Genome graphsStructural variationDosage
Population genetics and complex traits
Population-scale data reveal selection, introgression, and adaptation, while graph-based association connects diverse alleles to agronomic traits.
Population genomicsGWASSelection
Chromatin and regulatory genomics
Chromatin accessibility, expression, and sequence variation are integrated to study cis-regulatory evolution and the molecular basis of hybrid performance.
Chromatin accessibilityCis-regulationHeterosis
Research program / 02
Represent. Map. Explain. Test.
The aim is an analytical chain in which each result creates a stronger, testable question for the next stage.
Represent diversity
Build references and pangenome graphs that retain haplotype, structural, and dosage information across diverse genomes.
Map evolutionary forces
Use comparative and population genomics to identify the signatures of domestication, selection, introgression, and polyploidization.
Explain trait variation
Link graph-derived alleles and regulatory states to phenotypes with models appropriate for diploid and polyploid populations.
Prioritize testable targets
Turn genomic evidence into candidate genes, regulatory elements, and alleles suitable for functional validation and crop improvement.
Study systems / 03
Grasses with informative complexity.
Sugarcane and maize provide complementary systems for understanding genome complexity, crop evolution, and regulatory variation.
SACCHARUM
Sugarcane and wild relatives
Mixed ploidy, extensive hybridization, and high allele dosage make Saccharum a stringent test of genome representation and association methods.
- Multiscale pangenome graphs
- Allo-autopolyploid genome evolution
- Dosage-aware trait mapping
ZEA & ANDROPOGONEAE
Maize and related grasses
Rich genetic resources and diverse genomes support studies of structural variation, domestication, chromatin accessibility, and hybrid performance.
- Presence–absence and structural variation
- Chromatin accessibility in hybrids
- Comparative evolution across Andropogoneae