High-Resolution Mapping of Biomass-Related Traits in Shrub Willow (Salix purpurea L.)

Shrub willow (Salix spp.) is a vigorous woody perennial feedstock bred for dedicated biofuel production. Recent genomic advances have provided the biomass feedstock community with new tools to improve traits related to biomass yield and wood chemical composition. Large mapping populations have been generated in order to locate QTL associated with these traits. In 2014, 497 progeny from an F₂ S. purpurea family were planted in a randomized complete block design at a location of uniform grade and soil type at the New York Agricultural Experiment Station, Geneva, NY. A total of 40 phenotypes and over 100,000 data points were measured during the establishment and first year post-coppice seasons. Family parents, grandparents, and progeny were genotyped via genotyping-by-sequencing (GBS) using the restriction enzymes, ApeKI and EcoT22I. Variant discovery was performed in the Tassel v3 GBS pipeline using the S. purpurea v1.0 genome (F₂ grandparent) as a reference. All SNPs were quality filtered and duplicate sites collapsed. Any SNPs deviating from expected segregation were removed. Of the initial SNPs, approximately 5,000 were considered informative. Linkage groups were constructed and markers ordered in MSTMap then imported into R/qtl for downstream analyses. Significant QTL were identified for numerous growth traits as well as those for insect and disease resistance. For instance, a major QTL for stem height (LOD=19.3, pve=19.03%) resides within a QTL cluster (1-3 cM) for multiple biomass-related traits. Beyond proof-of-concept, this work aims to provide tools for early selection of traits important for biofuel production in shrub willow bioenergy crops.