Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding.

In contrast, we identified a major QTL for isochlorogenic acids content in both fruit peel and flesh on chromosome 4 (4.88–5.55 Mb), with highly significant marker-trait associations ( p -values from 1.2 × 10−19 to 1.15 × 10−76; PVE up to 74%; Fig. 9a, b , Supplementary Figs. 13c, d , and 14c, d , Supplementary Data 15 and 16 ).

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