Alignment of a Salix linkage map to the Populus genomic sequence reveals macrosynteny between willow and poplar genomes

Abstract

Poplars (genus Populus) and willows (genus Salix) are members of the Salicaceae, a family of catkin-bearing trees, shrubs and sub-shrubs. Poplar is considered the model system for biological studies in trees and considerable genetic and genomic resources have become available in recent years. The transfer of information to research studies in willow, for which fewer resources are currently available, would be highly beneficial. However, the extent of conservation between poplar and willow genomes has not yet been extensively studied. To address this, we have constructed a linkage map of willow based on a large mapping population derived from a cross between two Salix viminalis × (S. viminalis × S. schwerinii) hybrid sibs, and aligned this to the publicly available poplar genome sequence. A set of genome-wide, expressed poplar sequences was selected and used to design primer sets that efficiently amplified homeologous regions in willow. Direct sequencing of the willow products confirmed homology with the poplar target in the majority of instances and allowed identification of single nucleotide polymorphisms (SNPs) that were used to map these loci. In total, 202 amplified fragment length polymorphisms (AFLPs), 75 microsatellites and 79 SNPs were used to construct a willow consensus map that spanned 1,856.7 cM with an average interval between markers of 6.3 cM. Poplar sequences homologous to those of the mapped willow microsatellite loci were identified and used in addition to the SNP markers to putatively align all but two minor linkage groups to the poplar genome sequence. A high degree of macrosynteny was revealed.