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Journal Article

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

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Naake,  T.
Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Zhu,  F.
Central Metabolism, Department Gutjahr, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Alseekh,  S.       
The Genetics of Crop Metabolism, Department Gutjahr, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Scossa,  F.
Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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de Souza,  L. P.       
Central Metabolism, Department Gutjahr, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Borghi,  M.
Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Fernie,  A. R.       
Central Metabolism, Department Gutjahr, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Citation

Naake, T., Zhu, F., Alseekh, S., Scossa, F., de Souza, L. P., Borghi, M., et al. (2024). Genome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis. Plant Physiology, 194(3), 1705-1721. doi:10.1093/plphys/kiad511.


Cite as: https://hdl.handle.net/21.11116/0000-000D-EACF-3
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 (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 ALKENYL HYDROXYALKYL PRODUCING loci (GS-ALK and GS-OHP) on chromosome 4 containing alkenyl hydroxyalkyl producing 2 (AOP2) and 3 (AOP3) 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 dataset generated here is a high-quality resource that can be investigated in further studies.