Jujube (Ziziphus jujuba Mill.) is a fruit crop of high economic value, renowned for its distinctive flavor and wide range of phenotypic diversity. Despite major advancements in jujube genomics, the role of genetic variants in underlying agronomic trait formation is still poorly understood. Here, we used seven high-quality jujube genomes to construct a pan-TE (transposon element) map and investigated how TEs shape genome evolution and agronomic traits. We found that TEs constitute 29.05%–30.38% of the genome, predominantly long terminal repeat (LTR) retrotransposons such as Copia and Gypsy. A positive correlation (R2 = 0.76) between TE content and genome size underscores their role in genomic expansion. TE insertions within gene bodies significantly reduce gene expression, particularly for genes involved in cell wall biosynthesis and glucose metabolism. Population scale analysis of 1041 accessions identified 4176 transposable element insertion polymorphisms (TIPs) that distinguish wild and cultivated groups. Wild jujubes harbor stress-related TIPs (e.g. in peroxidase genes), whereas cultivated accessions carry TIPs linked to fruit development. Notably, a Gypsy insertion upstream of the cellulose synthase gene ZjCESA4 is associated with reduced expression and thinner pericarp in ‘Dongzao’ compared to ‘Huizao’. Similarly, a downstream LTR/Gypsy insertion near the MADS-box transcription factor gene ZjAGL18 correlates with suppressed expression, highlighting the recurrent targeting of key regulatory genes by TEs during domestication. Our findings demonstrate that TIPs are a major source of genetic variation in jujube, providing molecular markers for breeding programs that aim to balance fruit quality and stress resilience.

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