High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination

We present the first reference genome of the highly heterozygous autotetraploid Allium porrum (leek). Combining long-read sequencing with single-nucleotide polymorphism (SNP)-array screening of two experimental F1 populations, we generated a genetic map with 11,429 SNP markers across eight linkage groups and a chromosome-scale assembly of A. porrum (leek) totaling 15.2 Gbp in size. The high quality of the reference genome is substantiated by 97.2% BUSCO completeness and a mapping rate of 96% for full-length transcripts. The linkage map exposes the recombination landscape of leek and confirms that crossovers are predominantly proximal, located to the centromeres, contrasting with distal recombination landscapes observed in other Allium species. Comparative genomics reveals structural rearrangements between A. porrum and its relatives (Allium fistulosum, Allium sativum, and Allium cepa), suggesting a closer genomic relationship to A. sativum. Our annotated high-quality reference genome delivers crucial insights into the leek genome structure, recombination landscape, and evolutionary relationships within the Allium genus, with implications for species compatibility in breeding programs, facilitating marker-assisted selection and genetic improvement in leek.