A dense linkage map of hybrid cottonwood (Populus fremontii x P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree

Cottonwoods are foundation riparian species, and hybridization among species is known to produce ecological effects at levels higher than the population, including effects on dependent species, communities and ecosystems. Because these patterns result from increased genetic variation in key cottonwood traits, novel applications of genetic tools (for example, QTL mapping) could be used to place broad-scale ecological research into a genomic perspective. In addition, linkage maps have been produced for numerous species within the genus, and, coupled with the recent publication of the Populus genome sequence, these maps present a unique opportunity for genome comparisons in a model system. Here, we conducted linkage analyses in order to (1) create a platform for QTL and candidate gene studies of ecologically important traits, (2) create a framework for chromosomal-scale perspectives of introgression in a natural population, and (3) enhance genome-wide comparisons using two previously unmapped species. We produced 246 backcross mapping (BC₁) progeny by crossing a naturally occurring F₁ hybrid (Populus fremontii × P. angustifolia) to a pure P. angustifolia from the same population. Linkage analysis resulted in a dense linkage map of 541 AFLP and 111 SSR markers distributed across 19 linkage groups. These results compared favorably with other Populus linkage studies, and addition of SSR loci from the poplar genome project provided coarse alignment with the genome sequence. Preliminary applications of the data suggest that our map represents a useful framework for applying genomic research to ecological questions in a well-studied system, and has enhanced genome-wide comparisons in a model tree.