Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
Abstract 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 e...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Springer Nature
2024-02-01
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| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s44320-024-00021-0 |
| _version_ | 1797219470391902208 |
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| author | Andreas Tsouris Gauthier Brach Anne Friedrich Jing Hou Joseph Schacherer |
| author_facet | Andreas Tsouris Gauthier Brach Anne Friedrich Jing Hou Joseph Schacherer |
| author_sort | Andreas Tsouris |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-24T12:34:09Z |
| format | Article |
| id | doaj.art-8a111588ffe7413683c2d11289da40b8 |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2024-04-24T12:34:09Z |
| publishDate | 2024-02-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-8a111588ffe7413683c2d11289da40b82024-04-07T11:35:05ZengSpringer NatureMolecular Systems Biology1744-42922024-02-0120436237310.1038/s44320-024-00021-0Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeastAndreas Tsouris0Gauthier Brach1Anne Friedrich2Jing Hou3Joseph Schacherer4Université de Strasbourg, CNRSUniversité de Strasbourg, CNRSUniversité de Strasbourg, CNRSUniversité de Strasbourg, CNRSUniversité de Strasbourg, CNRSAbstract 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.https://doi.org/10.1038/s44320-024-00021-0eQTLDiallelLow-frequency VariantsStructural VariantsYeast |
| spellingShingle | Andreas Tsouris Gauthier Brach Anne Friedrich Jing Hou Joseph Schacherer Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast Molecular Systems Biology eQTL Diallel Low-frequency Variants Structural Variants 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 | eQTL Diallel Low-frequency Variants Structural Variants Yeast |
| url | https://doi.org/10.1038/s44320-024-00021-0 |
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