@article{PandeyYuOmranianetal.2019,
  author    = {Pandey, Prashant K. and Yu, Jing and Omranian, Nooshin and Alseekh, Saleh and Vaid, Neha and Fernie, Alisdair R. and Nikoloski, Zoran and Laitinen, Roosa A. E.},
  title     = {Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations},
  series = {Plant Direct},
  volume    = {3},
  journal   = {Plant Direct},
  number    = {11},
  publisher = {John Wiley \& sonst LTD},
  address   = {Chichester},
  issn      = {2475-4455},
  doi       = {10.1002/pld3.186},
  pages     = {6},
  year      = {2019},
  abstract  = {Nitrogen (N) is central for plant growth, and metabolic plasticity can provide a strategy to respond to changing N availability. We showed that two local A. thaliana populations exhibited differential plasticity in the compounds of photorespiratory and starch degradation pathways in response to three N conditions. Association of metabolite levels with growth-related and fitness traits indicated that controlled plasticity in these pathways could contribute to local adaptation and play a role in plant evolution.},
  language  = {en}
}
@article{NunesNesiAlseekhdeOliveiraSilvaetal.2019,
  author    = {Nunes-Nesi, Adriano and Alseekh, Saleh and de Oliveira Silva, Franklin Magnum and Omranian, Nooshin and Lichtenstein, Gabriel and Mirnezhad, Mohammad and Romero Gonzalez, Roman R. and Sabio y Garcia, Julia and Conte, Mariana and Leiss, Kirsten A. and Klinkhamer, Peter Gerardus Leonardus and Nikoloski, Zoran and Carrari, Fernando and Fernie, Alisdair R.},
  title     = {Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds},
  series = {Metabolomics},
  volume    = {15},
  journal   = {Metabolomics},
  number    = {46},
  publisher = {Springer},
  address   = {New York},
  issn      = {1573-3882},
  doi       = {10.1007/s11306-019-1503-8},
  pages     = {13},
  year      = {2019},
  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.},
  language  = {en}
}
@article{AlseekhTohgeWendenbergetal.2015,
  author    = {Alseekh, Saleh and Tohge, Takayuki and Wendenberg, Regina and Scossa, Federico and Omranian, Nooshin and Li, Jie and Kleessen, Sabrina and Giavalisco, Patrick and Pleban, Tzili and M{\"u}ller-R{\"o}ber, Bernd and Zamir, Dani and Nikoloski, Zoran and Fernie, Alisdair R.},
  title     = {Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato},
  series = {The plant cell},
  volume    = {27},
  journal   = {The plant cell},
  number    = {3},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {1040-4651},
  doi       = {10.1105/tpc.114.132266},
  pages     = {485 -- 512},
  year      = {2015},
  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.},
  language  = {en}
}