Advances in sequencing technologies have enabled the construction of pangenomes and super-pangenomes that capture the full spectrum of genetic diversity within species and across related taxa. Here, we report a comprehensive study of Solanum melongena (eggplant) and its wild relatives based on a core collection of 368 accessions representing global diversity. These accessions were extensively phenotyped across multiple environments for agronomic performance, disease resistance, and fruit metabolic composition. We generated resequencing data for the core collection and produced chromosome-scale genome assemblies for 40 accessions, including S. melongena, its wild progenitor S. insanum, and its closest sister species S. incanum. These genomic resources enabled the construction of two graph-based pangenomes. The first graph, including 33 S. melongena, 3 S. insanum, and 4 S. incanum accessions, was used to investigate genetic diversity, population structure, and domestication history within the eggplant core collection. The second graph, focused on S. melongena, supported a comprehensive pangenome-wide association (Pan-GWA) analyses across the pan-phenome, identifying a total of 3192 significant marker-trait associations. We demonstrate the power of these resources through specific examples. Structural variants affecting the LONELY GUY (LOG) 3 gene and a cluster of resistance genes were identified as key determinants of prickliness and resistance to Fusarium oxysporum f. sp. melongenae, respectively. In addition, a mutation in a GDSL-like esterase/lipase gene was linked to variation in the levels of isochlorogenic acids, important metabolites involved in fruit browning and antioxidant activity. Overall, our results demonstrate the potential of graph-based pangenomes to dissect the genetic architecture of complex traits, providing a keystone for pangenome-informed breeding and genetic improvement in eggplant. Acknowledgments: This work was supported by the European Commission, Horizon 2020 G2P-SOL project (grant agreement no. 677379) and by the “Promoting a Plant Genetic Resource Community for Europe (PRO-GRACE)” project (grant agreement no. 101094738).
Graph-based pangenomes enable pan-phenome dissection and breeding insights in eggplant.
Gaccione L.;Portis E.;Lanteri S.;Barchi L
2026-01-01
Abstract
Advances in sequencing technologies have enabled the construction of pangenomes and super-pangenomes that capture the full spectrum of genetic diversity within species and across related taxa. Here, we report a comprehensive study of Solanum melongena (eggplant) and its wild relatives based on a core collection of 368 accessions representing global diversity. These accessions were extensively phenotyped across multiple environments for agronomic performance, disease resistance, and fruit metabolic composition. We generated resequencing data for the core collection and produced chromosome-scale genome assemblies for 40 accessions, including S. melongena, its wild progenitor S. insanum, and its closest sister species S. incanum. These genomic resources enabled the construction of two graph-based pangenomes. The first graph, including 33 S. melongena, 3 S. insanum, and 4 S. incanum accessions, was used to investigate genetic diversity, population structure, and domestication history within the eggplant core collection. The second graph, focused on S. melongena, supported a comprehensive pangenome-wide association (Pan-GWA) analyses across the pan-phenome, identifying a total of 3192 significant marker-trait associations. We demonstrate the power of these resources through specific examples. Structural variants affecting the LONELY GUY (LOG) 3 gene and a cluster of resistance genes were identified as key determinants of prickliness and resistance to Fusarium oxysporum f. sp. melongenae, respectively. In addition, a mutation in a GDSL-like esterase/lipase gene was linked to variation in the levels of isochlorogenic acids, important metabolites involved in fruit browning and antioxidant activity. Overall, our results demonstrate the potential of graph-based pangenomes to dissect the genetic architecture of complex traits, providing a keystone for pangenome-informed breeding and genetic improvement in eggplant. Acknowledgments: This work was supported by the European Commission, Horizon 2020 G2P-SOL project (grant agreement no. 677379) and by the “Promoting a Plant Genetic Resource Community for Europe (PRO-GRACE)” project (grant agreement no. 101094738).
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