Population genomics of a rare and endangered semi-wild cucumber ( Cucumis sativus var. xishuangbannanensis ) reveals genetic architecture of seasonal flowering, fruit morphology, and carotenoid accumulation

The Xishuangbanna cucumber (Cucumis sativus var. xishuangbannanensis, XIS) is a rare and endangered semi-wild variety endemic to Yunnan Province, China. It possesses orange-fleshed fruits, large fruit mass, excellent storage tolerance, and disease resistance, making it a valuable resource for cucumber genetic improvement. However, genetic basis underlying its key agronomic traits remains largely unexplored. Here, we present a telomere-to-telomere gapless genome assembly of the XIS (322.9 Mb). Whole-genome resequencing of 342 XIS accessions identified 1,482,096 SNPs, 267,632 INDELs, 19,475 SVs, and 5,739 CNVs. Comparative population genomics between stable and unstable seasonal flowering accessions identified 248 selected genes commonly detected by XP-CLR, FST, and πSFF/πUSFF, revealing an integrated regulatory network converging on photoperiod and circadian clock (e.g., CONSTANS-like), flowering time (FY, SPL4), and multiple hormone signaling pathways (ARF9, MYC2, AOS1, GSK3). Genome-wide association study identified 4,109 variants significantly associated with flower and fruit traits, yielding 2,709 candidate genes. Two major hotspots on chromosome 1 harboring FT and COP1 were associated with multiple flower traits. Additionally, a distinct auxin-related cluster comprising TMK4 and HDA8 was identified as a key regulator of fruit morphology. Quantification of 68 carotenoid compounds revealed high inter-accession variation, with β-carotene, β-cryptoxanthin, and (E/Z)-phytoene being predominant. These carotenoid compounds were associated with a set of candidate genes including core carotenoids pathway genes BCH1, DXS, PDS, PSY, and LCYB, multiple transcription factors, etc. This work provides insights into seasonal flowering, fruit morphology, and carotenoid accumulation, establishing foundation for conservation and utilization of XIS, enabling genomics-assisted breeding of cucumber varieties.