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

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