Genome-Wide Association of Essential Oil Traits in Eucalyptus polybractea using a Low-Depth WGS Pipeline

Blue mallee (Eucalyptus polybractea) is one of a handful of dedicated tree species grown for the commercial production of Eucalyptus oil, but is mostly un-domesticated. Essential oil yield is a complex quantitative trait made up of several component traits including foliar oil concentration, foliar biomass, oil profile, regrowth after coppicing, survival in adverse environmental conditions and resistance to pests and pathogens.

We sampled 480 individual mallees from 40 open-pollinated half-sib families in a commercial progeny trial. Phenotypes included quantitative and qualitative variation of foliar essential oils and biomass over two years. Oil concentration varied widely (12 fold) within and between families and between individuals. Family ranking of commercially harvested oil yield was well predicted (r = 0.74) from phenotypic mixed models.

We re-sequenced all 480 whole genomes (ca. 650 Mb) to an average of 4x (1.3 Tb total) and aligned them to the E. grandis genome. Sites in E. grandis that were fixed in E. polybractea were then replaced with the E. polybractea alleles to generate a pseudo E. polybractea reference genome. All data was then mapped to the pseudo reference. Variants were called with an LD-aware pipeline to minimise genotyping errors due to low depth. The final SNP dataset was used to associate SNPs to essential oil yield related traits, and to perform genomic prediction. This is the first assessment of the genetic architecture of oil traits on a genome-wide scale in Eucalyptus, enabling detection of genetic variation in regulatory elements as well as structural genes of oil biosynthesis.