Synteny‐based comparative pan‐genome reveals a male‐specific FT gene underlying flowering time dimorphism in kiwifruit

Actinidia spp. (kiwifruit) are functionally dioecious with separate male and female individuals that exhibit a subtle difference in flowering time. However, this sexually dimorphic trait, along with its evolutionary history and the role of sexually antagonistic selection, remains to be fully understood. To investigate the underlying causes of this dimorphism at the genus level, we conducted a comparative pan-genome analysis of two representative kiwifruit species, Actinidia chinensis and Actinidia eriantha, using 10 chromosome-scale genome assemblies from six distinct male and female genotypes. The construction of the pan-genome revealed a total of 52 774 non-redundant pan-gene orthogroups comprising 42 370 gene clusters and 10 404 unassigned genes. Building on this, the comparative analysis further identified 657 syntenic gene sets belonging to 595 pan-gene orthogroups that exhibit significant inter-sexual divergence. It is plausible that they are drivers of the antagonistic selection responsible for conserved sexually dimorphic traits across the extant kiwifruit species. One of these genes is Y-linked FT (YFT), a male-specific variant of FLOWERING LOCUS T that originated following the recent whole-genome duplication event. We demonstrate that A. eriantha YFT is able to promote flowering, suggesting that it may contribute to the sexual dimorphism in kiwifruit flowering time. Notably, YFT is located in the sex-determining region (SDR), with linkage to the sex-determining genes, facilitating its spread in natural populations and SDR's expansion on the Y chromosome. For ease of use and analysis, the entire comparative pan-genome workflow was integrated into a custom Perl script, SynPanScan. This approach helps decipher the genetic basis of flowering sexual dimorphism in kiwifruit and establishes a synteny-based comparative pan-genomic framework for investigating the heritable architecture of natural phenotypic variation.