Genomic diversity evaluation of Populus trichocarpa germplasm by screening 1,014 full genomes

Forest trees may harbor naturally occurring exon disruptive variants (DVs)
in their gene sequences, which potentially impact important ecological and
economic phenotypic traits. However, the abundance and molecular
regulation of these variants remain largely unexplored. Here, 24,420 DVs
were identified by screening 1014 Populus trichocarpa full genomes. The
identified DVs were predominantly heterozygous with allelic frequencies
below 5% (only 26% of DVs had frequencies greater than 5%). Using common
garden-grown trees, DVs were assessed for gene expression variation in the
developing xylem, revealing that their gene expression can be
significantly altered, particularly for homozygous DVs (in the range of
27%-38% of cases depending on the studied common garden). DVs were further
investigated for their correlations with 13 wood quality traits, revealing
that, among the 148 discovered DV associations, 15 correlated with more
than one wood property and six genes had more than one DV in their coding
sequences associated with wood traits. Approximately one-third of DVs
correlated with wood property variation also showed significant gene
expression variation, confirming their non-spurious impact. These findings
offer potential avenues for targeted introduction of homozygous mutations
using tree biotechnology, and while the exact mechanisms by which DVs may
directly influence wood formation remain to be unraveled, this study lays
the groundwork for further investigation.