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Genome-wide association studies of seed metabolites identify loci controlling specialized metabolites in Arabidopsis thaliana

View ORCID ProfileThomas Naake, View ORCID ProfileFederico Scossa, View ORCID ProfileLeonardo Perez de Souza, View ORCID ProfileMonica Borghi, View ORCID ProfileYariv Brotman, View ORCID ProfileTetsuya Mori, View ORCID ProfileRyo Nakabayashi, View ORCID ProfileTakayuki Tohge, View ORCID ProfileAlisdair R. Fernie
doi: https://doi.org/10.1101/2022.09.23.509130
Thomas Naake
1Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
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Federico Scossa
1Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
2Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
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Leonardo Perez de Souza
1Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
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Monica Borghi
1Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
3Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84321-5305, USA
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Yariv Brotman
4Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
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Tetsuya Mori
5RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
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Ryo Nakabayashi
5RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
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Takayuki Tohge
6Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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Alisdair R. Fernie
1Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
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  • For correspondence: fernie@mpimp-golm.mpg.de
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Abstract

Plants synthesize specialized metabolites to facilitate environmental and ecological interactions. During evolution, plants diversified in their potential to synthesize these metabolites. Quantitative differences in metabolite levels of natural Arabidopsis thaliana accessions can be employed to unravel the genetic basis for metabolic traits using genome-wide association studies (GWAS). Here, we performed metabolic GWAS (mGWAS) on seeds of a panel of 315 A. thaliana natural accessions, including the reference genotypes C24 and Col-0, for polar and semi-polar seed metabolites using untargeted ultra-performance liquid chromatography-mass spectrometry. As a complementary approach, we performed quantitative trait locus (QTL) mapping of near-isogenic introgression lines between C24 and Col-0 for specific seed specialized metabolites. Besides common QTL between seeds and leaves, GWAS revealed seed-specific QTL for specialized metabolites indicating differences in the genetic architecture of seeds and leaves. In seeds, aliphatic methylsulfinylalkyl and methylthioalkyl glucosinolates associated with the GS-ALK and GS-OHP locus on chromosome 4 containing alkenyl hydroxyalkyl producing 2 (AOP2) and 3 (AOP3) and/or with the GS-ELONG locus on chromosome 5 containing methylthioalkyl malate synthase (MAM1) and MAM3. We detected two unknown sulfur-containing compounds that were also mapped to these loci. In GWAS, some of the annotated flavonoids (kaempferol 3-O-rhamnoside-7-O-rhamnoside, quercetin 3-O-rhamnoside-7-O-rhamnoside) were mapped to transparent testa 7 (AT5G07990), encoding a cytochrome P450 75B1 monooxygenase. Three additional mass signals corresponding to quercetin-containing flavonols were mapped to UGT78D2 (AT5G17050). The association of the loci and associating metabolic features were functionally verified in knockdown mutant lines. By performing GWAS and QTL mapping, we were able to leverage variation of natural populations and parental lines to study seed specialized metabolism. The GWAS data set generated here is a high-quality resource that can be interrogated in further studies.

Competing Interest Statement

The authors have declared no competing interest.

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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 4.0 International license.
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Posted September 26, 2022.
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Genome-wide association studies of seed metabolites identify loci controlling specialized metabolites in Arabidopsis thaliana
Thomas Naake, Federico Scossa, Leonardo Perez de Souza, Monica Borghi, Yariv Brotman, Tetsuya Mori, Ryo Nakabayashi, Takayuki Tohge, Alisdair R. Fernie
bioRxiv 2022.09.23.509130; doi: https://doi.org/10.1101/2022.09.23.509130
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Genome-wide association studies of seed metabolites identify loci controlling specialized metabolites in Arabidopsis thaliana
Thomas Naake, Federico Scossa, Leonardo Perez de Souza, Monica Borghi, Yariv Brotman, Tetsuya Mori, Ryo Nakabayashi, Takayuki Tohge, Alisdair R. Fernie
bioRxiv 2022.09.23.509130; doi: https://doi.org/10.1101/2022.09.23.509130

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