Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies
Abstract
Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used a pre-filtered data set of 1,014 pure Populus trichocarpa entire genomes to identify rare and common small genetic variants across individual genomes. We compared variant calls between Platypus and HaplotypeCaller pipelines, and we further applied strict quality filters for improved genetic variant identification. Finally, we only retained genetic variants that were identified by both variantmore »
- Authors:
-
- Université Laval, Quebec (Canada). Department of Wood and Forest Sciences; Université Laval, Quebec (Canada).Institute for System and Integrated Biology (IBIS); Université Laval, Quebec (Canada). Centre for Forest Research
- Laurentian Forestry Centre, Quebec (Canada). Natural Resources Canada, Canadian Forest Service
- Scion, Rotorua (New Zealand)
- University of British Columbia, Vancouver (Canada). Department of Forest and Conservation Sciences, Faculty of Forestry
- Université Laval, Quebec (Canada). Centre for Forest Research; Université Laval, Quebec (Canada). Department of Biology
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1628043
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Genetics
- Additional Journal Information:
- Journal Volume: 10; Journal ID: ISSN 1664-8021
- Publisher:
- Frontiers
- Country of Publication:
- United States
- Language:
- English
- Subject:
- Genetics & Heredity
Citation Formats
Piot, Anthony, Prunier, Julien, Isabel, Nathalie, Klápště, Jaroslav, El-Kassaby, Yousry A., Villarreal Aguilar, Juan Carlos, and Porth, Ilga. Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies. United States: N. p., 2020.
Web. doi:10.3389/fgene.2019.01384.
Piot, Anthony, Prunier, Julien, Isabel, Nathalie, Klápště, Jaroslav, El-Kassaby, Yousry A., Villarreal Aguilar, Juan Carlos, & Porth, Ilga. Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies. United States. https://doi.org/10.3389/fgene.2019.01384
Piot, Anthony, Prunier, Julien, Isabel, Nathalie, Klápště, Jaroslav, El-Kassaby, Yousry A., Villarreal Aguilar, Juan Carlos, and Porth, Ilga. Tue .
"Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies". United States. https://doi.org/10.3389/fgene.2019.01384. https://www.osti.gov/servlets/purl/1628043.
@article{osti_1628043,
title = {Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies},
author = {Piot, Anthony and Prunier, Julien and Isabel, Nathalie and Klápště, Jaroslav and El-Kassaby, Yousry A. and Villarreal Aguilar, Juan Carlos and Porth, Ilga},
abstractNote = {Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used a pre-filtered data set of 1,014 pure Populus trichocarpa entire genomes to identify rare and common small genetic variants across individual genomes. We compared variant calls between Platypus and HaplotypeCaller pipelines, and we further applied strict quality filters for improved genetic variant identification. Finally, we only retained genetic variants that were identified by both variant callers increasing calling confidence. Based on these shared variants and after stringent quality filtering, we found high genomic diversity in P. trichocarpa germplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance of genomic diversity and the potential of rare defective genetic variants in explaining a significant portion of P. trichocarpa's phenotypic variability in association genetics. The ultimate goal is to associate both rare and common alleles with poplar's wood quality traits to support selective breeding for an improved bioenergy feedstock.},
doi = {10.3389/fgene.2019.01384},
journal = {Frontiers in Genetics},
number = ,
volume = 10,
place = {United States},
year = {Tue Jan 28 00:00:00 EST 2020},
month = {Tue Jan 28 00:00:00 EST 2020}
}
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FIGURE 1: The 1,038 P. trichocarpa individuals retrieved from the JGI Genome Portal are represented by red dots across northwestern America. P. trichocarpa natural range is defined in dark grey. P. trichocarpa natural range was drawn from Little (1971).
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