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Finding genetic variants in plants without complete genomes

View ORCID ProfileYoav Voichek, View ORCID ProfileDetlef Weigel
doi: https://doi.org/10.1101/818096
Yoav Voichek
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Detlef Weigel
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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  • For correspondence: weigel@weigelworld.org
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Abstract

Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the genetic variants detected in GWAS to include major deletions, insertions, and rearrangements. We first use raw sequencing data directly to derive short sequences, k-mers, that mark a broad range of polymorphisms independently of a reference genome. We then link k-mers associated with phenotypes to specific genomic regions. Using this approach, we re-analyzed 2,000 traits measured in Arabidopsis thaliana, tomato, and maize populations. Associations identified with k-mers recapitulate those found with single-nucleotide polymorphisms (SNPs), however, with stronger statistical support. Moreover, we identified new associations with structural variants and with regions missing from reference genomes. Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allow detection of a wider range of genetic variants responsible for phenotypic variation.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 25, 2019.
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Finding genetic variants in plants without complete genomes
Yoav Voichek, Detlef Weigel
bioRxiv 818096; doi: https://doi.org/10.1101/818096
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Finding genetic variants in plants without complete genomes
Yoav Voichek, Detlef Weigel
bioRxiv 818096; doi: https://doi.org/10.1101/818096

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