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 thei..., A total of 1,014 pure Populus trichocarpa entire genomes were used to identify rare and common small genetic variants across individual genomes. Variant calls were compared between Platypus and HaplotypeCaller 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 P. trichocarpa germplasm, with 7.4 million small genetic variants was found. Importantly, 377k non-synonymous variants (5% of the total) were uncovered., , # 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)).

林木的基因序列中可能天然存在外显子干扰变异（exon disruptive variants, DVs），此类变异或对重要的生态与经济表型性状产生影响。然而，此类变异的丰度与分子调控机制目前仍未得到充分探究。本研究通过对1014份毛果杨（*Populus trichocarpa*）全基因组进行筛选，共鉴定得到24420个外显子干扰变异（DVs）。所鉴定得到的DVs大多为杂合型，等位基因频率低于5%（仅26%的DVs频率高于5%）。本研究借助同质园种植的毛果杨，对发育中的木质部组织中的基因表达变异与DVs的关联进行了分析，结果表明DVs所在基因的表达水平可发生显著改变，纯合型DVs的这种效应尤为明显（根据所研究的同质园不同，该比例介于27%~38%之间）。研究还对DVs与13项木材品质性状的相关性进行了分析，结果显示，在已发现的148个DV关联中，有15个与不止一项木材性状相关，另有6个基因携带不止一个DV……

总计1014份纯种毛果杨全基因组被用于鉴定各基因组中的罕见与常见小型遗传变异。将变异检出结果在Platypus与HaplotypeCaller两种分析流程之间进行了比对，并进一步施加严格的质量过滤步骤以提升遗传变异鉴定的准确性。最终仅保留两种变异检出工具共同鉴定得到的遗传变异，以提高变异检出的置信度。基于这些共有的变异并经过严格的质量过滤后，本研究在毛果杨种质资源中发现了极高的基因组多样性，共鉴定出740万个小型遗传变异。值得注意的是，本次研究还发现了37.7万个非同义变异（占总变异数的5%）。

# 用于罕见变异遗传关联研究的毛果杨大规模种质资源基因型数据集
[https://doi.org/10.5061/dryad.g79cnp5wb](https://doi.org/10.5061/dryad.g79cnp5wb)

本基因型数据集包含了覆盖毛果杨（*Populus trichocarpa*）绝大多数分布范围的1014份个体的小型遗传变异（1~3bp），涵盖罕见变异与常见变异两类。原始基因组数据下载自JGI基因组门户（[https://genome.jgi.doe.gov/portal/](https://genome.jgi.doe.gov/portal/)）。

本次提供的文件（Variant_calling_P_trichocarpa_1014.vcf）采用VCF格式。遗传变异的鉴定使用了platypus与GATK的HaplotypeCaller两种变异检出工具。最终得到的VCF文件已通过SnpEff，基于毛果杨参考基因组v3.0完成了注释。

关于本数据集的完整获取流程，已在相关研究论文中进行了详细阐述（[https://doi.org/10.3389/fgene.2019.01384](https://doi.org/10.3389/fgene.2019.01384)）。