An international team of 24 researchers from seven countries — including representatives from CREA, ENEA, CNR, and the University of Turin — has produced the first complete catalogue of eggplant (Solanum melongena) genes (the pan-genome) and phenotypic traits (the pan-phenome). The study, published in Nature Communications, reconstructs the evolutionary history of eggplant and opens new avenues for future breeding efforts.
The researchers began with a global collection of 3,400 cultivated eggplant varieties and their wild relatives. Using this resource, they traced the crop’s domestication origins to India and Southeast Asia, followed by its spread through the Middle East, Europe, and East Asia (China and Japan), likely via Arab and Chinese trade routes, according to a press release. The team then examined traits shaped by human and environmental selection, noting, for example, that varieties from India and Southeast Asia have retained non-purple skin colours and thorny leaves — features inherited from wild ancestors — while these traits have largely disappeared elsewhere.
A deeper genomic analysis was then carried out on 368 accessions representing the full global diversity of cultivated eggplants and their wild progenitors, Solanum incanum and Solanum insanum. Researchers evaluated 218 traits — covering agronomy, resistance to abiotic and biotic stresses, and fruit metabolic composition — across three field trials in Valencia (Spain), Montanaso Lombardo (Italy), and Antalya (Türkiye). Advanced bioinformatics analysis revealed that the eggplant “core” genome comprises roughly 16,300 gene families shared by all varieties, while around 4,000 gene families were deemed “dispensable,” appearing only in one or a few accessions.
CREA’s Contribution
CREA played a central role in coordinating the exchange of plant material among partners and led phenotypic and pathogen-resistance evaluations conducted in Italy. It also coordinated all characterisation activities across participating environments through the development and adoption of a shared “phenotyping kit,” ensuring harmonised data collection. Leveraging its extensive expertise in S. melongena and the physiological mechanisms underlying key agronomic traits — particularly disease resistance — CREA contributed significantly to identifying candidate genes within major QTLs and to their subsequent functional characterisation.
The results constitute a real milestone: not only do they rewrite the history of the genetic evolution of this important vegetable, but “open new perspectives for the use of precise genetic improvement techniques for the selection of innovative eggplant cultivars” says Giuseppe L. Rotino of CREA-GB. In addition, it highlights the crucial role of the maintenance and utilisation of genetic resources as a key element to support and advance research in the field of plant genetics.
“Our work has revealed over 3,000 associations between characters and chromosomal regions and, for many of them, we have identified the exact mutation of the DNA at the base of the character,” Laura Toppino of CREA-GB explains. “In this article we present three examples: the formation of thorns, resistance to Fusarium — a serious fungal disease that greatly reduces the productivity of eggplants — and the content of isochlorogenic acid in fruits, powerful antioxidants associated with the browning of the pulp. The other 215 characters studied will be the subject of further publications.”
The genomic data and associated accessions are publicly available. CREA, together with AVRDC (Taiwan), has been designated to maintain the collection of 368 accessions, which will be distributed under a standard material transfer agreement in accordance with the FAO International Treaty. By sharing both data and genetic resources, this publicly funded research ensures that all stakeholders — germplasm banks, researchers, seed companies, and consumers — can benefit from its outcomes.
