AUTHOR=Piot Anthony , Prunier Julien , Isabel Nathalie , Klápště Jaroslav , El-Kassaby Yousry A. , Villarreal Aguilar Juan Carlos , Porth Ilga TITLE=Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies JOURNAL=Frontiers in Genetics VOLUME=10 YEAR=2020 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.01384 DOI=10.3389/fgene.2019.01384 ISSN=1664-8021 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