Conservation of single nucleotide polymorphisms in 44 wood quality candidate genes of Eucalyptus globulus, Eucalyptus pyrocarpa and Eucalyptus pilularis
Sexton, TR, Henry, RJ, McManus, LJ, Thomas, D & Shepherd, M 2010, 'Conservation of single nucleotide polymorphisms in 44 wood quality candidate genes of Eucalyptus globulus, Eucalyptus pyrocarpa and Eucalyptus pilularis', paper presented to the Plant and Animal Genomes XVIII Conference, San Diego, California, USA, 9-13 January.
Single Nucleotide Polymorphisms (SNPs) code for much of the morphological variation observed between individuals. The aim of this experiment was to identify SNPs conserved among three species of interest Eucalyptus globulus, Eucalyptus pyrocarpa and Eucalyptus pilularis. Encompassing the Eucalyptus and Symphyomyrtus subgenera, conserved SNPs are of particular interest as they will transfer between many of the ~700 Eucalyptus species and are valuable candidates for genotyping in association studies. They also provide a valuable insight into the evolution and divergence of the species examined. Genomic DNA from 30 diverse individuals from each species was pooled. A total of 44 candidate genes for wood quality were amplified by PCR, with amplicons ranging in size from 400bp to 9kb. At equimolar concentrations amplicons were then pooled back into their respective species groups. The pooled PCR products were sheared, before preparation of paired-end libraries. Deep sequencing of each gene was achieved up to a level of 10,000X coverage using both 75bp paired end reads and 36bp single reads from the Illumina Genome Analyser IIx. Using this approach several thousand SNPs were identified. Relationships of conserved SNPs will be reported along with findings from association studies.