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Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Siwen Deng, Daniel Caddell, Jinliang Yang, Lindsay Dahlen, Lorenzo Washington, Devin Coleman-Derr
doi: https://doi.org/10.1101/2020.02.21.960377
Siwen Deng
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
2Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
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Daniel Caddell
2Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
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Jinliang Yang
3Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
4Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
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Lindsay Dahlen
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
5Department of Plant Sciences, University of California, Davis, CA, USA
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Lorenzo Washington
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Devin Coleman-Derr
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
2Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
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  • For correspondence: colemanderr@berkeley.edu
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Abstract

Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome wide association studies (GWAS) represent a potentially powerful, unbiased method to identify microbes sensitive to host genotype, and to connect them with the genetic loci that influence their colonization. Here, we conducted a population-level microbiome analysis of the rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify significant overlap between these lineages and heritable taxa recently identified in maize. Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can be used to predict rhizosphere microbiome structure for an independent panel of sorghum genotypes based solely on knowledge of host genotypic information.

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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-ND 4.0 International license.
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Posted February 23, 2020.
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Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome
Siwen Deng, Daniel Caddell, Jinliang Yang, Lindsay Dahlen, Lorenzo Washington, Devin Coleman-Derr
bioRxiv 2020.02.21.960377; doi: https://doi.org/10.1101/2020.02.21.960377
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Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome
Siwen Deng, Daniel Caddell, Jinliang Yang, Lindsay Dahlen, Lorenzo Washington, Devin Coleman-Derr
bioRxiv 2020.02.21.960377; doi: https://doi.org/10.1101/2020.02.21.960377

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