A REFERENCE GENOME SEQUENCE FOR WILLOW
Decoding the genome sequence of Salix viminalis – a willow species of importance as a renewable bioenergy source.
Wednesday, January 1, 2003 - 16:00
In this project we are generating a high quality reference genome sequence for Salix viminalis, an important willow species that is used as a dedicated bioenergy crop.
This species grows extremely rapidly and accumulates biomass with minimal inputs; attributes that make it ideal for this use. It has been a key species in European willow breeding efforts and has also been the focus of a significant amount of research in recent years.
Willow is recognised as one of the most advanced dedicated bioenergy crops in temperate regions and as such, is the focus of an increasing amount of research in the UK and worldwide. Considerable genetic and molecular resources are already available for this crop and research is well poised to take full advantage of a reference genome sequence once available. Molecular markers and detailed linkage maps are available, as are permanent, well-characterised germplasm collections. In addition, several large mapping populations for use in both quantitative trait locus (QTL) and linkage disequilibrium (LD) mapping are established and under study with genome targets identified for a number of key bioenergy traits.
Willows and poplars comprise the Salicaceae family, with poplar (Populus trichocarpa) being the first tree genome sequenced. Synteny and collinearity between willow and poplar genomes is largely maintained. Although nucleotide sequence is highly conserved within coding regions, sequence is not always conserved at useful levels elsewhere in the genome. Thus, while the poplar genome is clearly of value as a reference in willow studies that focus on genes, it is not as useful for comparative analysis across the entire genome.
To address this, we are sequencing a female, diploid individual (NWC663) from the UK National Willow Collection. With our collaborators at the Earlham Institute, we aim to generate a high quality assembly and annotation for this genotype. This genome would serve as a scaffold for assembly of re-sequenced willow lines of particular interest in research and breeding and would greatly improve the efficiency with which polymorphisms can be identified for subsequent screening in biparental QTL and association mapping populations - the currently employed route to associating genotype to phenotype in willow and the first stage in the development of molecular tools for selection of improved crop varieties
The reference genome assembly, annotation and variant databases will be made available to the research community once completed.