Recent advances in -omics technologies such as transcriptomics, metabolomics, and proteomics along with genotypic profiling have permitted dissection of the genetics of complex traits represented by molecular phenotypes in nonmodel species. To identify the genetic factors underlying variation in primary metabolism in potato (Solanum tuberosum), we have profiled primary metabolite content in a diploid potato mapping population, derived from crosses between S. tuberosum and wild relatives, using gas chromatography-time of flight-mass spectrometry. In total, 139 polar metabolites were detected, of which we identified metabolite quantitative trait loci for approximately 72% of the detected compounds. In order to obtain an insight into the relationships between metabolic traits and classical phenotypic traits, we also analyzed statistical associations between them. The combined analysis of genetic information through quantitative trait locus coincidence and the application of statistical learning methods provide information on putative indicators associated with the alterations in metabolic networks that affect complex phenotypic traits.The variation observed in phenotypic trait values in plants is often of quantitative nature, and it remains challenging to unravel the genetic basis of these traits. Quantitative trait locus (QTL) mapping is currently the most commonly used approach to dissect the genetic factors underlying complex traits. The goal of QTL mapping is to identify genomic regions associated with a specific complex phenotype by statistical analysis of the associations between genetic markers and phenotypic variation (Doerge, 2002). Recently, advances in highthroughput analysis and analytical detection methods have facilitated more integrated approaches to measure global phenotypic variation at the molecular level. Metabolite profiling is a rapidly evolving technology that has significantly increased the possibilities of performing high-throughput analysis of hundreds to thousands of compounds in a range of plants, including complex crop species. Metabolite composition is of great importance in crop plants, as a number of important traits such as biotic and abiotic stress resistance, postharvest processing, and nutritional value are largely dependent on the metabolic content (Fernie and Schauer, 2009).In potato (Solanum tuberosum) breeding, metabolomic studies have progressively increased in importance, as many potato tuber traits such as content and quality of starch, chipping quality, flesh color, taste, and glycoalkaloid content have been shown to be linked to a wide range of metabolites (Coffin et al., 1987;Dobson et al., 2008). As a result, tuber quality can be assessed by assaying a range of metabolites. Gas chromatography-time of flight-mass spectrometry (GC-TOF-MS) has been shown to be useful for the rapid and highly sensitive detection of a large fraction of plant metabolites covering the central pathways of primary metabolism (Roessner et al., 2000;Lisec et al., 2006). In potato, untargeted metab...

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Several root-colonizing bacterial species can simultaneously promote plant growth and induce systemic resistance. How these rhizobacteria modulate plant metabolism to accommodate the carbon and energy demand from these two competing processes is largely unknown. Here, we show that strains of three Paraburkholderia species, P. graminis PHS1 (Pbg), P. hospita mHSR1 (Pbh), and P. terricola mHS1 (Pbt), upon colonization of the roots of two Broccoli cultivars led to cultivar-dependent increases in biomass, changes in primary and secondary metabolism and induced resistance against the bacterial leaf pathogen Xanthomonas campestris. Strains that promoted growth led to greater accumulation of soluble sugars in the shoot and particularly fructose levels showed an increase of up to 280-fold relative to the non-treated control plants. Similarly, a number of secondary metabolites constituting chemical and structural defense, including flavonoids, hydroxycinnamates, stilbenoids, coumarins and lignins, showed greater accumulation while other resource-competing metabolite pathways were depleted. High soluble sugar generation, efficient sugar utilization, and suppression or remobilization of resource-competing metabolites potentially contributed to curb the tradeoff between the carbon and energy demanding processes induced by Paraburkholderia-Broccoli interaction. Collectively, our results provide a comprehensive and integrated view of the temporal changes in plant metabolome associated with rhizobacteria-mediated plant growth promotion and induced resistance.