Abstract
A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.
Highlights
Over the last 20 or so years, the adoption of quantitative trait locus (QTL) analysis of natural variation in segregating populations has become an increasingly popular approach (Jansen, 1993; Frary et al, 2000; Koornneef et al, 2004; Ashikari et al, 2005; Xue et al, 2008; Bagheri et al, 2012)
This study identified numerous mQTLs for secondary metabolite accumulation in tomato fruit pericarp
While only a handful of studies have used broad genetic crosses to identify mQTLs for a broad range of secondary metabolites (Kliebenstein et al, 2001a, 2001b; Keurentjes et al, 2006; Morreel et al, 2006; Khan et al, 2012; Matsuda et al, 2012; Routaboul et al, 2012; Gong et al, 2013; Wahyuni et al, 2014) and previous studies have largely been focused on Arabidopsis, considerable research has been focused on defining QTLs for volatile organic compounds from tomato fruit (Tieman et al, 2006; Mathieu et al, 2009; Mageroy et al, 2012; Rambla et al, 2014) and acyl-sugars in tomato leaf trichomes (Schilmiller et al, 2012, 2010)
Summary
Over the last 20 or so years, the adoption of quantitative trait locus (QTL) analysis of natural variation in segregating populations has become an increasingly popular approach (Jansen, 1993; Frary et al, 2000; Koornneef et al, 2004; Ashikari et al, 2005; Xue et al, 2008; Bagheri et al, 2012). While the majority of these studies have been performed in segregating populations of Arabidopsis thaliana, In tomato, the majority of both natural variance and metabolite quantitative trait loci (mQTL) studies have focused on primary metabolism (Schauer et al, 2005, 2006, 2008; Stevens et al, 2007; Do et al, 2010; Maloney et al, 2010; Quadrana et al, 2013, 2014) They have revealed the critical importance of cell wall invertase and fruit yield (Fridman et al, 2004; Ruan et al, 2012) and have identified the genomic regions underlying vitamin content in fruit (Stevens et al, 2007; Fitzpatrick et al, 2013; Quadrana et al, 2013, 2014). Screens of natural variance have focused on a similar range of compounds
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