title: Genetic mapping of semi-polar metabolites in pepper fruits (Capsicumsp.): towards unravelling the molecular regulation of flavonoid quantitative trait loci.
abstract: Untargeted LCMS profiling of semi-polar metabolites followed by metabolite quantitative trait locus (mQTL) analysis was performed in ripe pepper fruits of 113 F2 plants derived from a cross betweenCapsicum annuumAC1979 (no. 19) andCapsicum chinenseNo. 4661 Selection (no. 18). The parental accessions were selected based on their variation in fruit morphological characteristics and fruit content of some target phytonutrients. Clear segregation of fruit colour and fruit metabolite profiles was observed in the F2 population. The F2 plants formed three clusters based on their metabolite profiles. Of the total of 542 metabolites, 52 could be annotated, including a range of flavonoids, such as flavoneC-glycosides, flavonolO-glycosides and naringenin chalcone, as well as several phenylpropanoids, a capsaicin analogue, fatty acid derivatives and amino acid derivatives. Interval mapping revealed 279 mQTLs in total. Two mQTL hotspots were found on chromosome 9. These two chromosomal regions regulated the relative levels of 35 and 103 metabolites, respectively. Analysis also revealed an mQTL for a capsaicin analogue, located on chromosome 7. Confirmation of flavonoid mQTLs using a set of six flavonoid candidate gene markers and their corresponding expression data (expression QTLs) indicated theCa-MYB12transcription factor gene on chromosome 1 and the gene encoding flavone synthase (FS-2) on chromosome 6 as likely causative genes determining the variation in naringenin chalcone and flavoneC-glycosides, respectively, in this population. The combination of large-scale metabolite profiling and QTL analysis provided valuable insight into the genomic regions and genes important for the production of (secondary) metabolites in pepper fruit. This will impact breeding strategies aimed at optimising the content of specific metabolites in pepper fruit.
authors.affiliation: Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands ; Research Centre for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor KM. 46, Cibinong, Bogor, 16910 Indonesia.
authors.forename: Yuni
authors.initials: Y
authors.lastname: Wahyuni
authors.affiliation: Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands ; Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346, Florianópolis, SC 88034-001 Brazil.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Stahl-Hermes
authors.affiliation: Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands ; Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (IATA-CSIC), Avenida Agustín Escardino 7, 46980 Paterna, Valencia Spain.
authors.forename: Ana-Rosa
authors.initials: AR
authors.lastname: Ballester
authors.affiliation: Plant Research International, 6700 AA Wageningen, The Netherlands ; Netherlands Metabolomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
authors.forename: Ric C H
authors.initials: RC
authors.lastname: de Vos
authors.affiliation: Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands.
authors.forename: Roeland E
authors.initials: RE
authors.lastname: Voorrips
authors.affiliation: Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands ; Bogor Agricultural University, Jl. Raya Darmaga, 16680 Bogor, Indonesia.
authors.forename: Awang
authors.initials: A
authors.lastname: Maharijaya
authors.affiliation: Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands.
authors.forename: Jos
authors.initials: J
authors.lastname: Molthoff
authors.affiliation: Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands.
authors.forename: Marcela Viquez
authors.initials: MV
authors.lastname: Zamora
authors.affiliation: Research Centre for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor KM. 46, Cibinong, Bogor, 16910 Indonesia.
authors.forename: Enny
authors.initials: E
authors.lastname: Sudarmonowati
authors.affiliation: Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346, Florianópolis, SC 88034-001 Brazil.
authors.forename: Ana Carolina Maisonnave
authors.initials: AC
authors.lastname: Arisi
authors.affiliation: Laboratory of Plant Physiology, Wageningen University, 6700 AR Wageningen, The Netherlands.
authors.forename: Raoul J
authors.initials: RJ
authors.lastname: Bino
authors.affiliation: Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands ; Plant Research International, 6700 AA Wageningen, The Netherlands.
authors.forename: Arnaud G
authors.initials: AG
authors.lastname: Bovy
keywords: Capsicum; F2 population; Flavonoids; MYB12; Semi-polar metabolites; mQTL