title: Regulatory network of secondary metabolism in Brassica rapa: insight into the glucosinolate pathway.
abstract: Brassica rapa studies towards metabolic variation have largely been focused on the profiling of the diversity of metabolic compounds in specific crop types or regional varieties, but none aimed to identify genes with regulatory function in metabolite composition. Here we followed a genetical genomics approach to identify regulatory genes for six biosynthetic pathways of health-related phytochemicals, i.e carotenoids, tocopherols, folates, glucosinolates, flavonoids and phenylpropanoids. Leaves from six weeks-old plants of a Brassica rapa doubled haploid population, consisting of 92 genotypes, were profiled for their secondary metabolite composition, using both targeted and LC-MS-based untargeted metabolomics approaches. Furthermore, the same population was profiled for transcript variation using a microarray containing EST sequences mainly derived from three Brassica species: B. napus, B. rapa and B. oleracea. The biochemical pathway analysis was based on the network analyses of both metabolite QTLs (mQTLs) and transcript QTLs (eQTLs). Co-localization of mQTLs and eQTLs lead to the identification of candidate regulatory genes involved in the biosynthesis of carotenoids, tocopherols and glucosinolates. We subsequently focused on the well-characterized glucosinolate pathway and revealed two hotspots of co-localization of eQTLs with mQTLs in linkage groups A03 and A09. Our results indicate that such a large-scale genetical genomics approach combining transcriptomics and metabolomics data can provide new insights into the genetic regulation of metabolite composition of Brassica vegetables.
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University & Research Centre, Wageningen, The Netherlands.
authors.forename: Dunia
authors.initials: D
authors.lastname: Pino Del Carpio
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University & Research Centre, Wageningen, The Netherlands.
authors.forename: Ram Kumar
authors.initials: RK
authors.lastname: Basnet
authors.affiliation: Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.
authors.forename: Danny
authors.initials: D
authors.lastname: Arends
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University & Research Centre, Wageningen, The Netherlands.
authors.forename: Ke
authors.initials: K
authors.lastname: Lin
authors.affiliation: BU Bioscience, Plant Research International, Wageningen, The Netherlands; Centre for BioSystems Genomics, Wageningen, The Netherlands; Netherlands Metabolomics Centre, Leiden, The Netherlands.
authors.forename: Ric C H
authors.initials: RC
authors.lastname: De Vos
authors.affiliation: BU Bioscience, Plant Research International, Wageningen, The Netherlands; Centre for BioSystems Genomics, Wageningen, The Netherlands; Netherlands Metabolomics Centre, Leiden, The Netherlands.
authors.forename: Dorota
authors.initials: D
authors.lastname: Muth
authors.affiliation: BU Bioscience, Plant Research International, Wageningen, The Netherlands.
authors.forename: Jan
authors.initials: J
authors.lastname: Kodde
authors.affiliation: BU Bioscience, Plant Research International, Wageningen, The Netherlands.
authors.forename: Kim
authors.initials: K
authors.lastname: Boutilier
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University & Research Centre, Wageningen, The Netherlands.
authors.forename: Johan
authors.initials: J
authors.lastname: Bucher
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China.
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
authors.affiliation: Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.
authors.forename: Ritsert
authors.initials: R
authors.lastname: Jansen
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University & Research Centre, Wageningen, The Netherlands; Centre for BioSystems Genomics, Wageningen, The Netherlands; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China.
authors.forename: Guusje
authors.initials: G
authors.lastname: Bonnema
mesh_terms: D029741:Brassica rapa / Q000235:genetics / Q000378:metabolism*; D002853:Chromatography, Liquid; D005419:Flavonoids / Q000378:metabolism; D018745:Genome, Plant; D005961:Glucosinolates / Q000378:metabolism*; D013058:Mass Spectrometry; D053858:Metabolic Networks and Pathways; D040641:Quantitative Trait Loci; D012333:RNA, Messenger / Q000378:metabolism; D059467:Transcriptome
chemical_list: D005419:Flavonoids; D005961:Glucosinolates; D012333:RNA, Messenger