DOI: 10.5061/dryad.g79cnp5wb
title: Genomic diversity evaluation of Populus trichocarpa germplasm by screening 1,014 full genomes

description: 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.
description: A total of 1,014 pure <em>Populus trichocarpa</em>
 entire genomes were used to identify rare and common small genetic
 variants across individual genomes. Variant calls were compared between
 <em>Platypus</em> and <em>HaplotypeCaller</em>
 pipelines, and strict quality filters were further applied for improved
 genetic variant identification. Finally, only genetic variants that were
 identified by both variant callers were retained for increasing calling
 confidence. Based on these shared variants and after stringent quality
 filtering, a high genomic diversity in <em>P. trichocarpa</em>
 germplasm, with 7.4 million small genetic variants was found. Importantly,
 377k non-synonymous variants (5% of the total) were uncovered.
description: # Genotypic Dataset of a Large Populus trichocarpa Germplasm for Rare
 Variant Genetic Association Studies
 [https://doi.org/10.5061/dryad.g79cnp5wb](https://doi.org/10.5061/dryad.g79cnp5wb) This genotypic dataset contains rare and common small genetic variations (1-3bp) from 1014 *Populus trichocarpa* individuals sampled across most of the species range. Original genomes have been download from the JGI Genome Portal ([https://genome.jgi.doe.gov/portal/](https://genome.jgi.doe.gov/portal/)). The file (Variant_calling_P_trichocarpa_1014.vcf) is in the *VCF* format. Genetic variants have been identified using the *platypus* and *GATK's Haplotype Caller* variant callers. The resulting VCF file has been annotated using *SnpEff* with *P. trichocarpa* reference genome v3.0. A complete description of how the dataset has been obtained is detailed in the associated publication ([https://doi.org/10.3389/fgene.2019.01384](https://doi.org/10.3389/fgene.2019.01384)).