Traditional crop breeding relies heavily on reference genomes, yet a single genome cannot capture the full genetic diversity within a species. This limitation is especially pronounced in crops like eggplant, whose genome is large, repetitive, and shaped by complex domestication histories across Africa, Southeast Asia, Europe, and China. Previous eggplant genomes contained unresolved gaps and overlooked many structural variants, leaving critical genes related to yield, stress tolerance, and fruit traits undiscovered. Meanwhile, modern breeding demands precise genetic targets to overcome narrowing diversity and environmental challenges. Based on these challenges, it became necessary to conduct an in-depth investigation of eggplant genomic diversity using complete genomes and a pan-genome framework.
Researchers from the Vegetable Research Institute, Guangxi Academy of Agricultural Sciences reported these findings in Horticulture Research, published (DOI: 10.1093/hr/uhaf248) in 2025. Using advanced long-read sequencing technologies, the team assembled two near telomere-to-telomere eggplant genomes—one from a wild African relative and one from a cultivated variety—and integrated them with resequencing data from 238 global accessions. This approach enabled a comprehensive pan-genome analysis that links hidden genetic variation to domestication history and key agronomic traits, offering new insights into how eggplant yield and fruit characteristics are genetically controlled.
The study achieved a major technical milestone by assembling two ultra-high-quality eggplant genomes with nearly complete chromosome continuity. These genomes revealed thousands of genes and structural regions that were missing from earlier references. Building on this foundation, the researchers constructed an Asian-representative eggplant pan-genome containing over 84,000 genes, including a substantial proportion of dispensable and unique genes that vary among populations.
Population genomic analysis of 238 eggplant accessions uncovered clear genetic differentiation linked to geography, showing that eggplants were domesticated earlier in Southeast Asia and later independently in Europe and China. Within China, northern and southern eggplants followed distinct evolutionary paths with limited gene flow.
Crucially, genome-wide association studies identified hundreds of genetic loci associated with ten key agronomic traits, including fruit size, shape, seed weight, and surface characteristics. Many of these trait-associated genes were located in pan-genome-specific regions rather than the standard reference genome, highlighting the importance of using a pan-genome approach. Pathway analyses further revealed that hormone-related pathways—such as zeatin biosynthesis and circadian rhythm regulation—play central roles in determining yield-related traits, directly linking genetic variation to practical breeding outcomes.
“This work fundamentally changes how we understand eggplant genetics,” said the study’s corresponding author. “By moving beyond a single reference genome, we were able to uncover hidden genes and structural variations that directly influence yield, fruit morphology, and stress resistance. These genomic resources allow breeders to precisely target beneficial traits that were previously invisible, especially those derived from wild relatives. Our findings demonstrate that pan-genomes are essential for unlocking the full genetic potential of complex crop species.”
The comprehensive eggplant pan-genome provides a powerful roadmap for future breeding strategies. By identifying trait-associated genes beyond traditional reference genomes, breeders can more effectively introduce yield-enhancing and stress-resilient traits into cultivated varieties. The discovery of hormone- and metabolism-related pathways linked to fruit development offers clear molecular targets for marker-assisted and genomic selection. Beyond eggplant, this study serves as a model for applying telomere-to-telomere genomes and pan-genome frameworks to other crops with complex domestication histories. Ultimately, these advances support more efficient breeding, improved food security, and the development of resilient vegetable crops suited to changing environmental conditions.
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References
DOI
10.1093/hr/uhaf248
Original Source URL
https://doi.org/10.1093/hr/uhaf248
Funding information
This work was supported by the Guangxi Key Research and Development Program Project (GuikeAB 25069493), the National Natural Science Foundation of China (32360764), Guangxi Innovation Team of National Modern Agricultural Technology System (nycytxgxcxtd-2023-10-1), Nanning Science Research and Technology Development Program Project (NNKJ202402), Thanks to Shaofang He and Xinxin Yi for guiding the data analysis of this article.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.