Large effect quantitative trait loci for salicinoid phenolic glycosides in : Implications for gene discovery.

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)-ecologically important compounds with significant commercial, cultural, and medicinal applications-remain largely undescribed. We used a linkage map derived from a full-sib population of hybrid cottonwoods ( spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH-salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 genome. We discovered 21 QTL for the two traits, including a major QTL for HCH-salicortin ( = .52) that colocated with a QTL for salicortin on chr12. Using the V3.0 genome sequence, we identified 2,983 annotated genes and 1,480 genes of unknown function within our QTL intervals. We note ten candidate genes of interest, including a BAHD-type acyltransferase that has been potentially linked to SPGs. Our results complement other recent studies in with implications for gene discovery and the evolution of defensive chemistry in a model genus. To our knowledge, this is the first study to use a full-sib mapping population to identify QTL intervals and gene lists associated with SPGs.