High-resolution genome and genetic map of tetraploidAllium porrumexpose pericentromeric recombination

We present the first reference genome of highly heterozygous autotetraploidAllium porrum(leek). Combining long-read sequencing with SNP-array screening of two experimental F1 populations, we generated a genetic map with 11,429 SNP markers across 8 linkage groups and a chromosome-scale assembly ofAllium porrum(leek) totaling 15.2 Gbp in size. 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 otherAlliumspecies. Comparative genomics revealing structural rearrangements betweenA. porrumand its relatives (A. fistulosum,A. sativum,A. cepa), suggests a closer genomic relationship toA. sativum. Our annotated high-quality reference genome delivers crucial insights into the leek genome structure, recombination landscape, and evolutionary relationships within theAlliumgenus, offering significant implications for breeding programs, facilitating marker-assisted selection and genetic improvement in leek.