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Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast

Unraveling the genetic sources of gene expression variation is essential to better understand the origins of phenotypic diversity in natural populations. Genome-wide association studies identified thousands of variants involved in gene expression variation, however, variants detected only explain pa...

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Autores principales: Tsouris, Andreas, Brach, Gauthier, Friedrich, Anne, Hou, Jing, Schacherer, Joseph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10370210/
https://www.ncbi.nlm.nih.gov/pubmed/37503053
http://dx.doi.org/10.1101/2023.07.21.550015
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author Tsouris, Andreas
Brach, Gauthier
Friedrich, Anne
Hou, Jing
Schacherer, Joseph
author_facet Tsouris, Andreas
Brach, Gauthier
Friedrich, Anne
Hou, Jing
Schacherer, Joseph
author_sort Tsouris, Andreas
collection PubMed
description Unraveling the genetic sources of gene expression variation is essential to better understand the origins of phenotypic diversity in natural populations. Genome-wide association studies identified thousands of variants involved in gene expression variation, however, variants detected only explain part of the heritability. In fact, variants such as low-frequency and structural variants (SVs) are poorly captured in association studies. To assess the impact of these variants on gene expression variation, we explored a half-diallel panel composed of 323 hybrids originated from pairwise crosses of 26 natural Saccharomyces cerevisiae isolates. Using short- and long-read sequencing strategies, we established an exhaustive catalog of single nucleotide polymorphisms (SNPs) and SVs for this panel. Combining this dataset with the transcriptomes of all hybrids, we comprehensively mapped SNPs and SVs associated with gene expression variation. While SVs impact gene expression variation, SNPs exhibit a higher effect size with an overrepresentation of low-frequency variants compared to common ones. These results reinforce the importance of dissecting the heritability of complex traits with a comprehensive catalog of genetic variants at the population level.
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spelling pubmed-103702102023-07-27 Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast Tsouris, Andreas Brach, Gauthier Friedrich, Anne Hou, Jing Schacherer, Joseph bioRxiv Article Unraveling the genetic sources of gene expression variation is essential to better understand the origins of phenotypic diversity in natural populations. Genome-wide association studies identified thousands of variants involved in gene expression variation, however, variants detected only explain part of the heritability. In fact, variants such as low-frequency and structural variants (SVs) are poorly captured in association studies. To assess the impact of these variants on gene expression variation, we explored a half-diallel panel composed of 323 hybrids originated from pairwise crosses of 26 natural Saccharomyces cerevisiae isolates. Using short- and long-read sequencing strategies, we established an exhaustive catalog of single nucleotide polymorphisms (SNPs) and SVs for this panel. Combining this dataset with the transcriptomes of all hybrids, we comprehensively mapped SNPs and SVs associated with gene expression variation. While SVs impact gene expression variation, SNPs exhibit a higher effect size with an overrepresentation of low-frequency variants compared to common ones. These results reinforce the importance of dissecting the heritability of complex traits with a comprehensive catalog of genetic variants at the population level. Cold Spring Harbor Laboratory 2023-07-25 /pmc/articles/PMC10370210/ /pubmed/37503053 http://dx.doi.org/10.1101/2023.07.21.550015 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Tsouris, Andreas
Brach, Gauthier
Friedrich, Anne
Hou, Jing
Schacherer, Joseph
Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
title Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
title_full Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
title_fullStr Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
title_full_unstemmed Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
title_short Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
title_sort diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10370210/
https://www.ncbi.nlm.nih.gov/pubmed/37503053
http://dx.doi.org/10.1101/2023.07.21.550015
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