Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds

Adriano Nunes-Nesi,Julia Sabio Y Garcia,Saleh Alseekh,Franklin Magnum De Oliveira Silva,Fernando Carrari,Zoran Nikoloski,Mohammad Mirnezhad,Mariana Conte,Kirsten A Leiss,Peter G L Klinkhamer,Nooshin Omranian,Roman R Romero González,Gabriel Lichtenstein,Alisdair R Fernie

doi:10.1007/s11306-019-1503-8

Abstract

IntroductionTo date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism.ObjectiveThis study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues.MethodsThe analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses.ResultsChanges in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism.ConclusionsOverall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.

Highlights

To date, most studies of natural variation and metabolite quantitative trait loci in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism
Several studies suggest that metabolite levels are heritable and might be controlled by multiple genes (Schauer et al 2008; Chan et al 2010; Alseekh et al 2015; Wen et al 2015) and can be considered as quantitative traits regulated by metabolite quantitative trait loci
By counting the number of the introgression lines (ILs) that exhibited the same alteration in both experiments, we verified that the highest percentage of ILs with stable changes in amino acids levels occurred for threonine, asparagine and glutamate (10.8, 9.8 and 8.6%, respectively)

Summary

Introduction

Most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Conclusions Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits. Some groups have reported genome wide association studies in tomato fruits (Sauvage et al 2014; Tieman et al 2017) or on leaf metabolism for a range of wild species Most mQTL research has been carried out by investigating introgression lines (ILs) or recombinant inbred lines (Schauer et al 2006, 2008; Zanor et al 2009; Do et al 2010)

Methods

Results

Conclusion