# Sub-pangenome analysis reveals structural variants associated with fruit color and bacterial wilt resistance in eggplant

## TL;DR

Researchers studied eggplant genomes to find genetic variations linked to fruit color and disease resistance, creating a valuable pangenome resource for breeding.

## Contribution

The study identifies structural variants associated with fruit color and bacterial wilt resistance in eggplant using a newly constructed pangenome.

## Key findings

- A 12.4 Mb inversion on chromosome 10 is strongly associated with fruit color, likely due to hitchhiking with SmMYB1.
- Variants linked to bacterial wilt resistance include a premature stop codon in SmCYP82D47 and copy number variations in SmEPS1 and SmRoq1 homologs.
- Population genomic analyses show that genetic relationships in eggplant closely track geographic origin.

## Abstract

Eggplant (Solanum melongena L.) is a globally important Solanaceae crop, yet trait-relevant genomic variants remain poorly characterized. Here, we perform population genomic analyses of 226 eggplant accessions sampled mainly from a major domestication center spanning Southeast Asia and South China, and find that genetic relationships closely track geographic origin. We generate chromosome-scale assemblies for 11 representative accessions using long-read sequencing and integrate six published genomes to build a pangenome resource. Using this resource, association scans identify a 12.4 Mb inversion on chromosome 10 segregating at 50.44% frequency that is strongly associated with fruit color, likely through hitchhiking with SmMYB1. We also detect variants associated with bacterial wilt resistance, including a premature stop codon in SmCYP82D47 and copy number variations in SmEPS1 and SmRoq1 homologs. Together, our results illuminate the evolution and phenotypic impact of large structural variants and provide genomic resources for eggplant genetics and breeding.

Eggplant is a globally widely cultivated vegetable. Here, the authors report the construction of pangenome based on 11 new and six existing chromosome-scale genomes assemblies, perform population genomic analyses of 226 accessions, and reveal structural variations associated with fruit color and bacterial wilt resistance.