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Examining Shrub Willow Genomics and Genetics

Expanding the genetic and genomic resources available for shrub willow will not only facilitate improvements of the crop through breeding, but will also contribute to our understanding of woody plant biology.  At the forefront of this is the sequencing of the willow genome.  Larry Smart’s research group together with lead PI Dr. Gerald Tuskan and Dr. Chris Town is directing the sequencing of the genome of Salix purpurea L. clone 94006 at the US Department of Energy Joint Genome Institute using next-generation sequencing technology.  To complement the next-generation sequencing of the genome, we are developing BAC and fosmid libraries in collaboration with Dr. Chris Town and Dr. Haiying Liang.  Transcriptome analysis of different tissue types from S. purpurea is underway, which will allow for the identification and functional characterization of thousands of new genes in willow.  


The genetic basis for specific traits in shrub willow is being investigated to assist in the development of marker assisted selection for willow breeding.   Molecular markers such as SNPs and SSRs as well as candidate genes linked to traits combined with phenotypic analysis can be vital tools for future breeding efforts and help predict the performance of particular varieties in certain environments and allow for major improvements to the willow bioenergy crop.  Among some of the characteristics of willow being investigated at the molecular level are cell wall composition and biosynthesis, phosphorus and arsenic uptake and detoxification, and the unique “corkscrew” trait observed in S. matsudana (Lin et al 2007).




DNA from willow variety 94006

In order to make marker assisted selection successful in willow breeding, mapping populations are being produced through controlled breeding.  Future research goals include the development of a linkage map for S. purpurea using SSRs and SNPs, many of which have been used successfully for the mapping of S. viminalis and alignment with the P. trichocarpa linkage map by Hanley et al 2006 and by Berlin et al 2010.  Segregating populations for future QTL and eQTL mapping are also in development. 

The natural dioecious sexual reproductive habit of shrub willow within large populations of overlapping generations has allowed the species to maintain high levels of genetic diversity and heterozygosity within the population as well as between populations.  Thorough sampling of natural populations has provided a large gene pool of variation for potential genetic improvement.  Breeding strategies for willow benefit from maximizing the phenotypic variation in progeny families to increase the probability of identifying exceptional individuals.  Research on willow breeding populations has focused on genetic diversity studies as well as heritability studies (Lin et al 2009; Cameron et al 2008; Kopp et al 2005).  In addition, a complete phylogenetic analysis of important willow varieties used in our willow breeding program is now in progress using matK and ITS sequences.  This will provide us a better understanding of the taxonomic relationship between many of the different species and individuals currently used for breeding. 



For more information on willow genomics and genetics research, contact Michelle Serapiglia

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