Eggplant (Solanum melongena L.) is one of the key Solanaceous crops. Contrary to potato, tomato and pepper, whose wild ancestors and domestication centers are in the Americas, eggplant derives from the Asian species S.insanum, was domesticated in two separate locations (Indian subcontinent and South-East Asia), and arrived to Europe around the 10th century AD (Barchi et al, 2023). An eggplant core collection of 368 domesticated and wild accessions was constructed from a starting collection of >3,400 genotyped, georeferenced worldwide accessions (Barchi et al, 2023). The collection was resequenced using DNBseq short reads and phenotyped in three different locations (Italy, Spain and Türkiye) for traits related to yield, disease resistance, plant and fruit morphology, and fruit metabolic composition. Additionally, 40 accessions were sequenced using ONT long reads, and the resulting assemblies were used to construct a pangenome graph of the eggplant species (Gaccione et al, 2025). Genome-wide association studies were carried out using the phenotypic and metabolic data, as well as SNPs, small and large structural variants. Hundreds of quantitative trait loci (QTLs) for the above traits, robustly expressed in multiple locations, were identified and mapped. Analysis of the variants and selective sweeps associated with specific traits, and of their prevalence in accessions of different origin, shed light on the key genomic events underlying the domestication and breeding of this cosmopolitan crop. Acknowledgments: This work was supported by the European Commission, projects G2P-SOL (grant agreement no. 677379) and PRO-GRACE (grant agreement no. 101094738).
Pangenome-Assisted Genome-Wide Association Analysis of a Worldwide Eggplant Core Collection Reveals Major Selective Events during Domestication and Breeding
Barchi L.
;Gaccione L.;Portis E.;Lanteri S.;
2025-01-01
Abstract
Eggplant (Solanum melongena L.) is one of the key Solanaceous crops. Contrary to potato, tomato and pepper, whose wild ancestors and domestication centers are in the Americas, eggplant derives from the Asian species S.insanum, was domesticated in two separate locations (Indian subcontinent and South-East Asia), and arrived to Europe around the 10th century AD (Barchi et al, 2023). An eggplant core collection of 368 domesticated and wild accessions was constructed from a starting collection of >3,400 genotyped, georeferenced worldwide accessions (Barchi et al, 2023). The collection was resequenced using DNBseq short reads and phenotyped in three different locations (Italy, Spain and Türkiye) for traits related to yield, disease resistance, plant and fruit morphology, and fruit metabolic composition. Additionally, 40 accessions were sequenced using ONT long reads, and the resulting assemblies were used to construct a pangenome graph of the eggplant species (Gaccione et al, 2025). Genome-wide association studies were carried out using the phenotypic and metabolic data, as well as SNPs, small and large structural variants. Hundreds of quantitative trait loci (QTLs) for the above traits, robustly expressed in multiple locations, were identified and mapped. Analysis of the variants and selective sweeps associated with specific traits, and of their prevalence in accessions of different origin, shed light on the key genomic events underlying the domestication and breeding of this cosmopolitan crop. Acknowledgments: This work was supported by the European Commission, projects G2P-SOL (grant agreement no. 677379) and PRO-GRACE (grant agreement no. 101094738).
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