Whole-genome resequencing reveals the evolutionary history and molecular basis of flavor formation in Zanthoxylum germplasm

Zanthoxylum (Prickly Ash) is a plant with significant medicinal and spice value, and its aroma and pungency are critical characteristics for agricultural production and industrial uses. However, the trade-off between the unique aroma of Red Prickly Ash ( Zanthoxylum bungeanum ) and the superior pungency of Green Prickly Ash ( Zanthoxylum armatum ) restricts breeding progress. Therefore, elucidating the genetic basis and evolutionary status of the Zunyi landrace, which exhibits a unique intermediate phenotype, is crucial for increasing its economic value. Whole-genome resequencing and transcriptomic analyses were performed on 35 accessions of Zunyi landraces and mainstream cultivars. Population genomic analyses revealed that the Zunyi landrace acts as an evolutionary “transitional ecotype” linking Green and Red lineages, retaining high genetic diversity. Notably, the elite cultivar “Yinhongjiao” (YHJ) presents a fascinating “genetic paradox,” possessing a Z. bungeanum genomic background yet exhibiting distinct quality traits typical of the Zunyi landrace. Integrating selective sweep and transcriptomic analyses, and targeted qRT-PCR validation, we uncovered the genetic basis of key quality traits. Specifically, the differential expression of key monoterpene synthase genes maintains aroma accumulation during late maturity, while the high expression level of the rate-limiting enzyme ZaBAHD1 ensures robust pungency, avoiding the trait degeneration observed in typical red cultivars. Additionally, ZaHCT expression reflects a metabolic trade-off between anthocyanin biosynthesis and stress resistance. Ultimately, the identified core loci (e.g., ZaBAHD1 and ZaLIMS1 ) can serve as molecular markers to facilitate genomic-assisted breeding. These resources lay the foundation for cultivating superior varieties that combine high yield with the dual premium traits of aroma and pungency, meeting industrial demands. • Zunyi landrace is identified as an evolutionary “transitional ecotype”. • “Yinhongjiao” combines red pericarp background with high flavor quality. • Heterochronic expression of ZaLIMS1 maintains aroma in mature fruit. • Dosage-dependent expression of ZaBAHD1 ensures robust pungency. • Genomic insights aid breeding for balanced aroma and pungency traits.