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Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding
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Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding
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Journal Article
Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding
2025
Overview
Eggplant (
Solanum melongena
L.) is a major Solanaceous crop of Asian origin, but genomic resources remain limited compared to related species. Here, a core collection of 368 accessions spanning global diversity of
S. melongena
and wild relatives is phenotyped for agronomic, disease resistance and fruit metabolomic traits and resequenced. Additionally, 40 chromosome-level assemblies of
S. melongena
, its progenitor
S. insanum
and the allied species
S. incanum
enable the construction of two graph-based pangenomes, capturing broad genetic variation. We demonstrate the power of these datasets by identifying major loci controlling prickliness and resistance to
Fusarium oxysporum
f. sp.
melongenae
, driven by SVs affecting the
LONELY GUY 3
gene and a resistance gene cluster, respectively, as well as a mutation in a
GDSL-like esterase/lipase
gene altering the levels of dicaffeoyl-quinic acids. These findings provide a cornerstone for pangenome-assisted breeding, enabling detailed analyses of genetic diversity, domestication history, and trait evolution in eggplant.
Eggplants are important vegetables worldwide. Here, the authors report 40 genome assemblies of
Solanum melongena
, its progenitor
S. insanum
and the allied species
S. incanum
to construct two pangenomes, and identify loci associated with multiple traits via pangenome-wide association analysis.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
