Publications of the Group

1.

Journal Article

Zhang, F.; Wu, J.; Sade, N.; Wu, S.; Egbaria, A.; Fernie, A. R.; Yan, J.; Qin, F.; Chen, W.; Brotman, Y. et al.; Dai, M.: Genomic basis underlying the metabolome-mediated drought adaptation of maize. Genome Biology 22 (1), 260 (2021)

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2.

Journal Article

Aarabi, F.; Rakpenthai, A.; Barahimipour, R.; Gorka, M.; Alseekh, S.; Zhang, Y.; Salem, M.A.; Brückner, F.; Omranian, N.; Watanabe, M. et al.; Nikoloski, Z.; Giavalisco, P.; Tohge, T.; Graf, A.; Fernie, A. R.; Hoefgen, R.: Sulfur Deficiency Induced genes affect seed protein accumulation and composition under sulfate deprivation. Plant Physiology (2021)

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3.

Journal Article

Zhang, Y.; Scossa, Federico, F.; Fernie, A. R.: The genomes of Taxus species unveil novel candidates in the biosynthesis of taxoids. Molecular Plant (2021)

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4.

Journal Article

Bellucci, E.; Aguilar, O. M.; Alseekh, S.; Bett, K.; Brezeanu, C.; Cook, D.; De la Rosa, L.; Delledonne, M.; Dostatny, D. F.; Ferreira, J. J. et al.; Geffroy, V.; Ghitarrini, S.; Kroc, M.; Kumar Agrawal, S.; Logozzo, G.; Marino, M.; Mary-Huard, T.; McClean, P.; Meglič, V.; Messer, T.; Muel, F.; Nanni, L.; Neumann, K.; Servalli, F.; Străjeru, S.; Varshney, R. K.; Vasconcelos, M. W.; Zaccardelli, M.; Zavarzin, A.; Bitocchi, E.; Frontoni, E.; Fernie, A. R.; Gioia, T.; Graner, A.; Guasch, L.; Prochnow, L.; Opperman, M.; Susek, K.; Tenaillon, M.; Papa, R.: The INCREASE project: Intelligent Collections of Food-Legume Genetic Resources for European Agrofood Systems. The Plant Journal (2021)

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5.

Journal Article

Zhu, F.; Fernie, A. R.: Plants upcycle gene functions to suit their roots. Trends in Plant Science (2021)

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6.

Journal Article

Alseekh, S.; Aharoni, A.; Brotman, Y.; Contrepois, K.; D’Auria, J.; Ewald, J.; C. Ewald, J.; Fraser, P. D.; Giavalisco, P.; Hall, R. D. et al.; Heinemann, M.; Link, H.; Luo, J.; Neumann, S.; Nielsen, J.; de Souza, L. P.; Saito, K.; Sauer, U.; Schroeder, F. C.; Schuster, S.; Siuzdak, G.; Skirycz, A.; Sumner, L. W.; Snyder, M. P.; Tang, H.; Tohge, T.; Wang, Y.; Wen, W.; Wu, S.; Xu, G.; Zamboni, N.; Fernie, A. R.: Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. Nature Methods 18 (7), pp. 747 - 756 (2021)

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7.

Journal Article

Guadalupe Dominguez, P.; Conti, G.; Duffy, T.; Insani, M.; Alseekh, S.; Asurmendi, S.; Fernie, A. R.; Carrari, F.: Multi-omics analyses reveal the roles of the ASR1 transcription factor in tomato fruits. Journal of Experimental Botany (2021)

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8.

Journal Article

Moreno, J.C.; Rojas, B.E.; Vicente, R.; Gorka, M.; Matz, T.; Kosmacz, M.; Peralta-Ariza, J.S.; Zhang, Y.; Alseekh, S.; Childs, D. et al.; Luzarowski, M.; Nikoloski, Z.; Zarivach, R.; Walther, D.; Hartman, M.D.; Figueroa, C.M.; Iglesias, A.A.; Fernie, A. R.; Skirycz, A.: Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism. EMBO Journal, e106800 (2021)

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9.

Journal Article

Altman, A.; Fan, L.; Foyer, C.; Cowling, W.; Mittler, R.; Qaim, M.; Weber, A.; Reynolds, M.; Varshney, R.; Fernie, A. R.: Past and Future Milestones of Plant Breeding. Trends in Plant Science 26 (6), pp. 530 - 538 (2021)

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10.

Journal Article

Ancín, M.; Larraya, L.; Florez-Sarasa, I. D.; Bénard, C.; Fernández-San Millán, A.; Veramendi, J.; Gibon, Y.; Fernie, A. R.; Aranjuelo, I.; Farran, I.: Thioredoxin m overexpression in chloroplasts alters carbon and nitrogen partitioning in tobacco plants. Journal of Experimental Botany (2021)

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11.

Journal Article

Ashraf, M.; Mao, Q.; Hong, J.; Shi, L.; Ran, X.; Liaquat, F.; Uzair, M.; Liang, W.; Fernie, A. R.; Shi, J.: HSP70-16 and VDAC3 jointly inhibit seed germination under cold stress in Arabidopsis. Plant, Cell and Environment (2021)

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12.

Journal Article

Zimmermann, S. E.; Benstein, R. M.; Flores-Tornero, M.; Blau, S.; Anoman, A. D.; Rosa-Téllez, S.; Gerlich, S. C.; Salem, M.A.; Alseekh, S.; Kopriva, S. et al.; Wewer, V.; Flügge, U.-I.; Jacoby, R. P.; Fernie, A. R.; Giavalisco, P.; Ros, R.; Krueger, S.: The phosphorylated pathway of serine biosynthesis links plant growth with nitrogen metabolism. Plant Physiology 186 (3), pp. 1487 - 1506 (2021)

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13.

Journal Article

de Souza, L. P.; Alseekh, S.; Scossa, F.; Fernie, A. R.: Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research. Nature Methods 18, pp. 733 - 746 (2021)

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14.

Journal Article

Borghi, M.; Fernie, A. R.: From flowers to seeds: how the metabolism of flowers frames plant reproduction. The biochemist: the bulletin of the Biochemical Society 43 (3), pp. 14 - 18 (2021)

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15.

Journal Article

Cortinovis, G.; Oppermann, M.; Neumann, K.; Graner, A.; Gioia, T.; Marsella, M.; Alseekh, S.; Fernie, A. R.; Papa, R.; Bellucci, E. et al.; Bitocchi, E.: Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Common Bean. Current Protocols in Plant Biology 1 (5), e133 (2021)

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16.

Journal Article

Fernie, A. R.: Associating primary and specialized metabolism with salt induced osmotic stress tolerance in maize. New Phytologist 230 (6), pp. 2991 - 2093 (2021)

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17.

Journal Article

Zhang, Y.; Giese, J.; Kerbler, S.M.-L.; Siemiatkowska, B.; de Souza, L. P.; Alpers, J.; Medeiros, D.B.; Hincha, D. K.; Daloso, D. M.; Stitt, M. et al.; Finkemeier, I.; Fernie, A. R.: Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis. Molecular Plant 14 (7), pp. 1104 - 1118 (2021)

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18.

Journal Article

Baptistella, J. L. C.; Llerena, J. P. P.; Domingues-Júnior, A. P.; Fernie, A. R.; Favarin, J. L.; Mazzafera, P.: Differential responses of three Urochloa species to low phosphorus availability. Annals of Applied Biology 179 (2), pp. 216 - 230 (2021)

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19.

Journal Article

Scossa, F.; Fernie, A. R.: When a Crop Goes Back to the Wild: Feralization. Trends in Plant Science 26 (6), pp. 543 - 545 (2021)

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20.

Journal Article

Alseekh, S.; Kostova, D.; Bulut, M.; Fernie, A. R.: Genome-wide association studies: assessing trait characteristics in model and crop plants. Cellular and Molecular Life Sciences 78 (15), pp. 5743 - 5754 (2021)

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21.

Journal Article

Ancín, M.; Larraya, L.; Florez-Sarasa, I. D.; Bénard, C.; Fernández-San Millán, A.; Veramendi, J.; Gibon, Y.; Fernie, A. R.; Aranjuelo, I.; Farran, I.: Overexpression of thioredoxin m in chloroplasts alters carbon and nitrogen partitioning in tobacco. Journal of Experimental Botany 72 (13), pp. 4949 - 4964 (2021)

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22.

Journal Article

Aneklaphakij, C.; Saigo, T.; Watanabe, M.; Naake, T.; Fernie, A. R.; Bunsupa, S.; Satitpatipan, V.; Tohge, T.: Diversity of Chemical Structures and Biosynthesis of Polyphenols in Nut-Bearing Species. Frontiers in Plant Science 12, 642581 (2021)

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23.

Journal Article

Barja, M.V.; Ezquerro, M.; Beretta, S.; Diretto, G.; Florez-Sarasa, I.; Feixes, E.; Fiore, A.; Karlova, R.; Fernie, A. R.; Beekwilder, J. et al.; Rodríguez-Concepción, M.: Several geranylgeranyl diphosphate synthase isoforms supply metabolic substrates for carotenoid biosynthesis in tomato. New Phytologist 231 (1), pp. 255 - 272 (2021)

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24.

Journal Article

Bottcher, A.; Domingues Júnior, A.P.; de Souza, L. P.; Tohge, T.; Araujo, W. L.; Fernie, A. R.; Mazzafera, P.: Sugarcane cell suspension reveals major metabolic changes under different nitrogen starvation regimes. BRAGANTIA 80, e2921 (2021)

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25.

Journal Article

Breitel, D.; Brett, P.; Alseekh, S.; Fernie, A. R.; Butelli, E.; Martin, C.: Diverting tyrosine: Data from untargeted metabolic analysis of tomato fruit accumulating L-DOPA. Data in Brief 34, 106678 (2021)

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26.

Journal Article

Brotman, Y.; Llorente-Wiegand, C.; Oyong, G.; Badoni, S.; Misra, G.; Anacleto, R.; Parween, S.; Pasion, E.; Tiozon Jr., R. N.; Anonuevo, J. J. et al.; Krishna deGuzman, M.; Alseekh, S.; Mbanjo, E. G.N.; Boyd, L. A.; Fernie, A. R.; Sreenivasulu, N.: The genetics underlying metabolic signatures in a brown rice diversity panel and their vital role in human nutrition. The Plant Journal 106 (2), pp. 507 - 527 (2021)

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27.

Journal Article

Bulut, M.; Fernie, A. R.; Alseekh, S.: Large-scale Multi-omics Genome-wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization. Journal of Visualized Experiments 173, e62732 (2021)

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28.

Journal Article

Cárcamo-Fincheira, P.; Reyes-Díaz, M.; Omena-García, R.P.; Vargas, J.R.; Alvear, M.; Florez-Sarasa, I.; Rosado-Souza, L.; Rengel, Z.; Fernie, A. R.; Nunes-Nesi, A. et al.; Inostroza-Blancheteau, C.: Metabolomic analyses of highbush blueberry (Vaccinium corymbosum L.) cultivars revealed mechanisms of resistance to aluminum toxicity. Environmental and Experimental Botany 183, 104338 (2021)

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29.

Journal Article

Casatejada-Anchel, R.; Munoz-Bertomeu, J.; Rosa-Tellez, S.; Anoman, A. D.; Nebauer, S. G.; Torres-Moncho, A.; Fernie, A. R.; Ros, R.: Phosphoglycerate dehydrogenase genes differentially affect Arabidopsis metabolism and development. Plant Science 306, 110863 (2021)

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30.

Journal Article

Cervela-Cardona, L.; Yoshida, T.; Zhang, Y.; Okada, M.; Fernie, A. R.; Mas, P.: Circadian Control of Metabolism by the Clock Component TOC1. Frontiers in Plant Science 12, 683516 (2021)

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31.

Journal Article

Chen, J.; Xue, M.; Liu, H.; Fernie, A. R.; Chen, W.: Exploring the genic resources underlying metabolites through mGWAS and mQTL in wheat: From large-scale gene identification and pathway elucidation to crop improvement. Plant Communications 2 (4), 100216 (2021)

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32.

Journal Article

da Fonseca-Pereira, P.; Souza, P. V. L.; Fernie, A. R.; Timm, S.; Daloso, D. M.; Araújo, W. L.: Thioredoxin-mediated regulation of (photo)respiration and central metabolism. Journal of Experimental Botany (2021)

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33.

Journal Article

Duarte, G. T.; Pandey, P. K.; Vaid, N.; Alseekh, S.; Fernie, A. R.; Nikoloski, Z.; Laitinen, R.: Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein. Plant, Cell and Environment (2021)

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34.

Journal Article

Fernie, A. R.: Using landrace transcription factor alleles to increase yield in modern rice under low input agriculture. Journal of Plant Physiology 258-259, 153362 (2021)

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35.

Journal Article

Fernie, A. R.; Alseekh, S.; Liu, J.; Yan, J.: Using Precision Phenotyping to Inform de novo Domestication. Plant Physiology 186 (3), pp. 1397 - 1411 (2021)

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36.

Journal Article

Fernie, A. R.; Sonnewald, U.: Plant biotechnology for sustainable agriculture and food safety. Journal of Plant Physiology 261, 153416 (2021)

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37.

Journal Article

Filippou, P.; Zarza, X.; Antoniou, C.; Obata, T.; Villarroel, C.A.; Ganopoulos, I.; Harokopos, V.; Gohari, G.; Aidinis, V.; Madesis, P. et al.; Christou, A.; Fernie, A. R.; Tiburcio, A.F.; Fotopoulos, V.: Systems biology reveals key tissue-specific metabolic and transcriptional signatures involved in the response of Medicago truncatula plant genotypes to salt stress. Computational and Structural Biotechnology Journal 19, pp. 2133 - 2147 (2021)

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38.

Journal Article

Florez-Sarasa, I.; Welchen, E.; Racca, S.; Gonzalez, D.H.; Vallarino, J. G.; Fernie, A. R.; Ribas-Carbo, M.; Del-Saz, N.F.: Cytochrome c deficiency differentially affects the in vivo mitochondrial electron partitioning and primary metabolism depending on the photoperiod. Plants 10 (3), 444 (2021)

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39.

Journal Article

Freire, F.B.S.; Bastos, R.L.G.; Bret, R.S.C.; Cândido-Sobrinho, S.A.; Medeiros, D.B.; Antunes, W.C.; Fernie, A. R.; Daloso, D.M.: Mild reductions in guard cell sucrose synthase 2 expression leads to slower stomatal opening and decreased whole plant transpiration in Nicotiana tabacum L. Environmental and Experimental Botany 184, 104370 (2021)

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40.

Journal Article

Gill, R. A.; Scossa, F.; King, G. J.; Golicz, A.; Tong, C.; Snowdon, R. J.; Fernie, A. R.; Liu, S.: On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes. Critical Reviews in Plant Sciences 40 (2), pp. 157 - 189 (2021)

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41.

Journal Article

Heyneke, E.; Hoefgen, R.: Meeting the complexity of plant nutrient metabolism with multi-omics approaches. Journal of Experimental Botany 72 (7), pp. 2261 - 2265 (2021)

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42.

Journal Article

Israeli, A.; Burko, Y.; Shleizer-Burko, S.; Zelnik, I. D.; Sela, N.; Hajirezaei, M. R.; Fernie, A. R.; Tohge, T.; Ori, N.; Bar, M.: Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium. PLoS Genetics 17 (4), e1009537 (2021)

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43.

Journal Article

Jiang, L.; Yoshida, T.; Stiegert, S.; Yu, J.; Alseekh, S.; Lenhard, M.; Pérez-Alfocea, F.; Fernie, A. R.: Multi-omics approach reveals the contribution of KLU to leaf longevity and drought tolerance. Plant Physiology 185 (2), pp. 352 - 368 (2021)

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44.

Journal Article

Jorge, T. F.; Ramalho, J. C.; Alseekh, S.; Pais, I. P.; Leitão, A. E.; Rodrigues, A. P.; Scotti-Campos, P.; Ribeiro-Barros, A. I.; Fernie, A. R.; António, C.: Will Casuarina glauca Stress Resilience Be Maintained in the Face of Climate Change? Metabolites 11 (9), 593 (2021)

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45.

Journal Article

Kerbler, S.M.-L.; Natale, R.; Fernie, A. R.; Zhang, Y.: From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants. International Journal of Molecular Sciences 22 (13), 7101 (2021)

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46.

Journal Article

Koessler, S.; Armarego-Marriott, T.; Tarkowska, D.; Tureckova, V.; Agrawal, S.; Mi, J.; Perez da Sousa, L.; Schöttler, M. A.; Schadach, A.; Fröhlich, A. et al.; Bock, R.; Al-Babili, S.; Ruf, S.; Sampathkumar, A.; Moreno, J.C.: Lycopene β-cyclase expression influences plant physiology, development and metabolism in tobacco plants. Journal of Experimental Botany 72 (7), pp. 2544 - 2569 (2021)

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47.

Journal Article

Krahmer, J.; Abbas, A.; Mengin, V.; Ishihara, H.; Romanowski, A.; Furniss, J. J.; Moraes, T. A.; Krohn, N.; Annunziata, M. G.; Feil, R. et al.; Alseekh, S.; Obata, T.; Fernie, A. R.; Stitt, M.; Halliday, K. J.: Phytochromes control metabolic flux, and their action at the seedling stage determines adult plant biomass. Journal of Experimental Botany 72 (8), pp. 3263 - 3278 (2021)

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48.

Journal Article

Kroc, M.; Tomaszewska, M.; Czepiel, K.; Bitocchi, E.; Oppermann, M.; Neumann, K.; Guasch, L.; Bellucci, E.; Alseekh, S.; Graner, A. et al.; Fernie, A. R.; Papa, R.; Susek, K.: Towards Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Lupins. Current Protocols in Plant Biology 1 (7), e191 (2021)

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49.

Journal Article

Lazare, S.; Bechar, D.; Garbowicz, K.; Fernie, A. R.; Brotman, Y.; Zaccai, M.: When vegetation indicates reproduction: the affinity between leaf morphology and flowering commitment in the lily meristem. Physiologia Plantarum 172 (4), pp. 2022 - 2033 (2021)

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50.

Journal Article

Liu, J.; Fernie, A. R.; Yan, J.: Crop breeding – From experience-based selection to precision design. Journal of Plant Physiology 256, 153313 (2021)

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Publications of the Group

Journal Article (980)