Genomics approach to understanding silicon in ash trees (Fraxinus excelsior)

Silicon is a non-essential plant nutrient thought to be beneficial for improving resistance against a wide range of herbivores and pathogens. However, the genetics underlying silicon uptake, deposition and disease resistance are not fully understood, especially in tree species such as Common ash (Fraxinus excelsior), which is severely affected by the ash dieback epidemic.
Therefore, the project aims to improve our knowledge of silicon in ash trees using measurements of silicon in branch and leaf tissue. It also aims to identify gene markers for silicon content and understand the genetics associated with silicon. Finally, it aims to improve the genetic resources available for ash through genome assembly with long-read data.
Whole-genome sequencing and assembly resulted in a highly contiguous genome, using fewer contigs than the previous 2017 assembly. Realignment of cDNA sequences was used to update gene order, which was implemented into the associative transcriptomic (AT) analysis to visualise the results.
AT analysis of branch silicon data and differential gene expression analysis of leaf silicon revealed 9 genes significantly associated with branch silicon content and 22 genes with differential expression between trees with high or low leaf silicon levels. A diverse range of functions are predicted for these genes, with several functioning in the growth and development of leaf and root tissue. The differential gene expression analysis also identified three defence-associated genes and two secondary metabolite biosynthesis genes with possible pest repellent and antifungal activity, based on the functions of these metabolites in other species.
The results from the genome-wide silicon analyses provide a framework for additional studies investigating the genetics of silicon in ash and its association with disease resistance. Additionally, the production of an improved F. excelsior genome will assist future genetic studies of ash trees.