@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{RodriguezCubillosTongAlseekhetal.2018,
  author    = {Rodriguez Cubillos, Andres Eduardo and Tong, Hao and Alseekh, Saleh and de Abreu e Lima, Francisco Anastacio and Yu, Jing and Fernie, Alisdair R. and Nikoloski, Zoran and Laitinen, Roosa A. E.},
  title     = {Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat},
  series = {Heredity},
  volume    = {120},
  journal   = {Heredity},
  number    = {5},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {0018-067X},
  doi       = {10.1038/s41437-017-0030-5},
  pages     = {463 -- 473},
  year      = {2018},
  abstract  = {Metabolism is a key determinant of plant growth and modulates plant adaptive responses. Increased metabolic variation due to heterozygosity may be beneficial for highly homozygous plants if their progeny is to respond to sudden changes in the habitat. Here, we investigate the extent to which heterozygosity contributes to the variation in metabolism and size of hybrids of Arabidopsis thaliana whose parents are from a single growth habitat. We created full diallel crosses among seven parents, originating from Southern Germany, and analysed the inheritance patterns in primary and secondary metabolism as well as in rosette size in situ. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed more pronounced non-additive inheritance patterns which could be attributed to epistasis. In addition, we showed that glucosinolates, among other secondary metabolites, were positively correlated with a proxy for plant size. Therefore, our study demonstrates that heterozygosity in local A. thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism.},
  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{TabatabaeiAlseekhShahidetal.2022,
  author    = {Tabatabaei, Iman and Alseekh, Saleh and Shahid, Mohammad and Leniak, Ewa and Wagner, Mateusz and Mahmoudi, Henda and Thushar, Sumitha and Fernie, Alisdair R. and Murphy, Kevin M. and Schm{\"o}ckel, Sandra M. and Tester, Mark and M{\"u}ller-R{\"o}ber, Bernd and Skirycz, Aleksandra and Balazadeh, Salma},
  title     = {The diversity of quinoa morphological traits and seed metabolic composition},
  series = {Scientific data},
  volume    = {9},
  journal   = {Scientific data},
  number    = {1},
  publisher = {Nature Research},
  address   = {Berlin},
  issn      = {2052-4463},
  doi       = {10.1038/s41597-022-01399-y},
  pages     = {7},
  year      = {2022},
  abstract  = {Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.},
  language  = {en}
}