Higher Non-Synonymous Substitution Rates in Disease Resistance, Wood Synthesis and Stress-Responsive Genes in Clonal Varieties of Woody Biomass Species

Several woody species are promising candidates for field trials for the production of biomass in short-rotation coppice plantations. In an attempt to relate the general level of sequence polymorphisms in selected genes to performance, sequence polymorphisms in a set of 15 genes involved in wood synthesis, disease resistance, and suggested to be useful for species discrimination were analysed by a hybrid PCR/next generation sequencing approach in a small series of clonal trials of Populus (poplar/cottonwood species and hybrids) and willows (Salix sp. and hybrids), established in 2010. PCR fragments longer than 500 bp were enzymatically fragmentised, then mixed with the shorter ones and processed with separate DNA barcodes for identification of the sequences of the individual clones. Next generation sequencing was done on an Illumina MySeq (250 bp reads per direction). Sequences were quality trimmed and mapped to the P. trichocarpa and Salix purpurea genome. SNPs and other polymorphisms were called in CLC Bio’s Genome Workbench. A total of 1188 sequence variants (relative to P. trichocarpa) were found in fragments of 32 genes for poplar, and similar results were obtained in Salix. A higher number of non-synonymous substitutions were identified in ASSYMETRIC LEAVES, GLUTAMATE DECARBOXYLASE, MELAMPSORA-INFECTION RELATED, PHENYL ALANINE LYASE, and in a group of anionic peroxidases. We will discuss opportunities and challenges of this approach.