Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16

• Published in: Journal of experimental botany Vol. 63; no. 8; pp. 2895 - 2908
• Main Authors: Khan, Sabaz Ali, Chibon, Pierre-Yves, de Vos, Ric C.H., Schipper, Bert A., Walraven, Evert, Beekwilder, Jules, van Dijk, Thijs, Finkers, Richard, Visser, Richard G.F., van de Weg, Eric W., Bovy, Arnaud, Cestaro, Alessandro, Velasco, Riccardo, Jacobsen, Evert, Schouten, Henk J.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01-05-2012
• Subjects: Alleles; anthocyanidin reductase; Arabidopsis - genetics; Biological and medical sciences; Chromosome Mapping; cisgenic plants; Crosses, Genetic; developing grape berries; flavonoid biosynthesis; Flavonoids; Fruit - genetics; Fruit - metabolism; Fruits; Fundamental and applied biological sciences. Psychology; Genes; Genes, Plant - genetics; Genetic Linkage; Genetic loci; Genotype; Glycosides; Humans; Hydrogen-Ion Concentration; Malus - genetics; Malus - metabolism; malus-pumila mill; mass-spectrometry; Metabolic Networks and Pathways - genetics; Metabolites; microsatellite markers; Peels; Phenols - metabolism; Plant physiology and development; proanthocyanidin biosynthesis; quantitative trait loci; Quantitative Trait Loci - genetics; RESEARCH PAPER; Research Papers; Segregation; Transcription factors; Transcription Factors - genetics; x-domestica borkh; Cartography; Metabolomics; Fruit; Metabolite; untargeted and targeted mQTL mapping; Rosaceae; Liquid chromatography; Malus domestica; Malus×domestica Borkh; Genetic determinism; Apple; LC-MS; Dicotyledones; Linkage group; Angiospermae; Botany; Phenols; MetaNetwork; Spermatophyta; Fruit tree; Mass spectrometry; MapQTL; genetical metabolomics
• ISSN: 0022-0957; 1460-2431
• DOI: 10.1093/jxb/err464

Apple (Malus×domesticaBorkh) is among the main sources of phenolic compounds in the human diet. The genetic basis of the quantitative variations of these potentially beneficial phenolic compounds was investigated. A segregating F₁ population was used to map metabolite quantitative trait loci (mQTLs). Untargeted metabolic profiling of peel and flesh tissues of ripe fruits was performed using liquid chromatography–mass spectrometry (LC-MS), resulting in the detection of 418 metabolites in peel and 254 in flesh. In mQTL mapping using MetaNetwork, 669 significant mQTLs were detected: 488 in the peel and 181 in the flesh. Four linkage groups (LGs), LG1, LG8, LG13, and LG16, were found to contain mQTL hotspots, mainly regulating metabolites that belong to the phenylpropanoid pathway. The genetics of annotated metabolites was studied in more detail using MapQTL®. A number of quercetin conjugates had mQTLs on LG1 or LG13. The most important mQTL hotspot with the largest number of metabolites was detected on LG16: mQTLs for 33 peel-related and 17 flesh-related phenolic compounds. Structural genes involved in the phenylpropanoid biosynthetic pathway were located, using the apple genome sequence. The structural geneleucoanthocyanidin reductase(LAR1) was in the mQTL hotspot on LG16, as were seven transcription factor genes. The authors believe that this is the first time that a QTL analysis was performed on such a high number of metabolites in an outbreeding plant species.