References
Arsova, B., Kierszniowska, S., & Schulze, W. X. (2012). The use of heavy nitrogen in quantitative proteomics experiments in plants.Trends in Plant Science, 17 (2), 102-112. doi:10.1016/j.tplants.2011.11.001
Berendzen, K., Searle, I., Ravenscroft, D., Koncz, C., Batschauer, A., Coupland, G., . . . Ulker, B. (2005). A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thalianaecotypes Col-0 and Landsberg erecta. Plant Methods, 1 . doi:Artn 410.1186/1746-4811-1-4
Brachi, B., Faure, N., Bergelson, J., Cuguen, J., & Roux, F. (2013). Genome-wide association mapping of flowering time in Arabidopsis thaliana in nature: genetics for underlying components and reaction norms across two successive years. Acta Bot Gall, 160 (3-4), 205-219. doi:10.1080/12538078.2013.807302
Christie, J. M., Arvai, A. S., Baxter, K. J., Heilmann, M., Pratt, A. J., O’Hara, A., . . . Getzoff, E. D. (2012). Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science, 335 (6075), 1492-1496. doi:10.1126/science.1218091
de Jong, M., Tavares, H., Pasam, R. K., Butler, R., Ward, S., George, G., . . . Leyser, O. (2019). Natural variation in Arabidopsis shoot branching plasticity in response to nitrate supply affects fitness.Plos Genetics, 15 (9). doi:ARTN e100836610.1371/journal.pgen.1008366
Eprintsev, A. T., Fedorin, D. N., Sazonova, O. V., & Igamberdiev, A. U. (2016). Light inhibition of fumarase in Arabidopsis leaves is phytochrome A-dependent and mediated by calcium. Plant Physiol Biochem, 102 , 161-166. doi:10.1016/j.plaphy.2016.02.028
Evans, J. R., & Clarke, V. C. (2018). The nitrogen cost of photosynthesis. Journal of Experimental Botany, 70 (1), 7-15. doi:10.1093/jxb/ery366
Fredes, I., Moreno, S., Diaz, F. P., & Gutierrez, R. A. (2019). Nitrate signaling and the control of Arabidopsis growth and development.Current Opinion in Plant Biology, 47 , 112-118. doi:10.1016/j.pbi.2018.10.004
Grimm, D. G., Roqueiro, D., Salome, P. A., Kleeberger, S., Greshake, B., Zhu, W. S., . . . Borgwardt, K. M. (2017). easyGWAS: A cloud-based platform for comparing the results of genome-wide association studies.Plant Cell, 29 (1), 5-19. doi:10.1105/tpc.16.00551
Gu, Z. G., Eils, R., & Schlesner, M. (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data.Bioinformatics, 32 (18), 2847-2849. doi:10.1093/bioinformatics/btw313
Guignard, M. S., Leitch, A. R., Acquisti, C., Eizaguirre, C., Elser, J. J., Hessen, D. O., . . . Leitch, I. J. (2017). Impacts of nitrogen and phosphorus: from genomes to natural ecosystems and agriculture.Frontiers in Ecology and Evolution, 5 (70). doi:10.3389/fevo.2017.00070
Gutierrez, R. (2012). Nitrogen regulatory networks controlling plant root growth. Febs Journal, 279 , 35-35.
Hadjebi, O., Casas-Terradellas, E., Garcia-Gonzalo, F. R., & Rosa, J. L. (2008). The RCC1 superfamily: from genes, to function, to disease.Biochim Biophys Acta, 1783 (8), 1467-1479. doi:10.1016/j.bbamcr.2008.03.015
Horton, M. W., Hancock, A. M., Huang, Y. S., Toomajian, C., Atwell, S., Auton, A., . . . Bergelson, J. (2012). Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics, 44 (2), 212-216. doi:10.1038/ng.1042
Ikram, S., Bedu, M., Daniel-Vedele, F., Chaillou, S., & Chardon, F. (2012). Natural variation of Arabidopsis response to nitrogen availability. Journal of Experimental Botany, 63 (1), 91-105. doi:10.1093/jxb/err244
Ji, H., Wang, S., Cheng, C., Li, R., Wang, Z., Jenkins, G. I., . . . Li, X. (2019). The RCC1 family protein SAB1 negatively regulates ABI5 through multidimensional mechanisms during postgermination in Arabidopsis. New Phytologist, 222 (2), 907-922. doi:10.1111/nph.15653
Ji, H., Wang, Y., Cloix, C., Li, K., Jenkins, G. I., Wang, S., . . . Li, X. (2015). The Arabidopsis RCC1 family protein TCF1 regulates freezing tolerance and cold acclimation through modulating lignin biosynthesis.Plos Genetics, 11 (9), e1005471. doi:10.1371/journal.pgen.1005471
Kassambara, A. a. M., F. . (2020). factoextra: extract and visualize the results of multivariate data analyses. R package version 1.0.7. , https://CRAN.R-project.org/package=factoextra .
Kramer, U. (2015). Planting molecular functions in an ecological context with Arabidopsis thaliana . Elife, 4 . doi:ARTN e0610010.7554/eLife.06100
Krapp, A., Berthomé, R., Orsel, M., Mercey-Boutet, S., Yu, A., Castaings, L., . . . Daniel-Vedele, F. (2011). Arabidopsis roots and shoots show distinct temporal adaptation patterns toward nitrogen starvation. Plant Physiology, 157 (3), 1255-1282. doi:10.1104/pp.111.179838
Kuhlmann, M., Meyer, R. C., Jia, Z. T., Klose, D., Krieg, L. M., von Wiren, N., & Altmann, T. (2020). Epigenetic variation at a genomic locus affecting biomass accumulation under low nitrogen inArabidopsis thaliana . Agronomy-Basel, 10 (5). doi:ARTN 63610.3390/agronomy10050636
Kuhn, K., Carrie, C., Giraud, E., Wang, Y., Meyer, E. H., Narsai, R., . . . Whelan, J. (2011). The RCC1 family protein RUG3 is required for splicing of nad2 and complex I biogenesis in mitochondria ofArabidopsis thaliana . Plant Journal, 67 (6), 1067-1080. doi:10.1111/j.1365-313X.2011.04658.x
Laitinen, R. A. E., & Nikoloski, Z. (2019). Genetic basis of plasticity in plants. Journal of Experimental Botany, 70 (3), 739-745. doi:10.1093/jxb/ery404
Lark, R. M., Milne, A. E., Addiscott, T. M., Goulding, K. W. T., Webster, C. P., & O’Flaherty, S. (2004). Scale- and location-dependent correlation of nitrous oxide emissions with soil properties: an analysis using wavelets. European Journal of Soil Science, 55 (3), 611-627. doi:10.1111/j.1365-2389.2004.00620.x
Li, H., Hu, B., & Chu, C. C. (2017). Nitrogen use efficiency in crops: lessons from Arabidopsis and rice. Journal of Experimental Botany, 68 (10), 2477-2488. doi:10.1093/jxb/erx101
Lisec, J., Schauer, N., Kopka, J., Willmitzer, L., & Fernie, A. R. (2006). Gas chromatography mass spectrometry-based metabolite profiling in plants. Nature Protocols, 1 (1), 387-396. doi:10.1038/nprot.2006.59
Masclaux-Daubresse, C., & Chardon, F. (2011). Exploring nitrogen remobilization for seed filling using natural variation inArabidopsis thaliana . Journal of Experimental Botany, 62 (6), 2131-2142. doi:10.1093/jxb/erq405
McAllister, C. H., Beatty, P. H., & Good, A. G. (2012). Engineering nitrogen use efficient crop plants: the current status. Plant Biotechnology Journal, 10 (9), 1011-1025. doi:https://doi.org/10.1111/j.1467-7652.2012.00700.x
Meyer, R. C., Gryczka, C., Neitsch, C., Muller, M., Brautigam, A., Schlereth, A., . . . Altmann, T. (2019). Genetic diversity for nitrogen use efficiency in Arabidopsis thaliana . Planta, 250 (1), 41-57. doi:10.1007/s00425-019-03140-3
North, K. A., Ehlting, B., Koprivova, A., Rennenberg, H., & Kopriva, S. (2009). Natural variation in Arabidopsis adaptation to growth at low nitrogen conditions. Plant Physiology and Biochemistry, 47 (10), 912-918. doi:10.1016/j.plaphy.2009.06.009
Oldroyd, G. E. D., & Leyser, O. (2020). A plant’s diet, surviving in a variable nutrient environment. Science, 368 (6486), 45-+. doi:ARTN eaba019610.1126/science.aba0196
Pandey, P. K., Yu, J., Omranian, N., Alseekh, S., Vaid, N., Fernie, A. R., . . . Laitinen, R. A. E. (2019). Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations.Plant Direct, 3 (11). doi:ARTN e0018610.1002/pld3.186
Pennacchi, J. P., de Sousa Lira, J. M., Rodrigues, M., Garcia, F. H., Mendonca, A., & Delfino Barbosa, J. (2020). A systemic approach to the quantification of the phenotypic plasticity of plant physiological traits: the MVPi. J Exp Bot . doi:10.1093/jxb/eraa545
Perchlik, M., & Tegeder, M. (2017). Improving plant nitrogen use efficiency through alteration of amino acid transport processes.Plant Physiology, 175 (1), 235-247. doi:10.1104/pp.17.00608
Queitsch, C., Sangster, T. A., & Lindquist, S. (2002). Hsp90 as a capacitor of phenotypic variation. Nature, 417 (6889), 618-624. doi:DOI 10.1038/nature749
Revelle, W. (2020). psych: Procedures for psychological, psychometric, and personality research. In R package version 2.0.9 . Northwestern University, Evanston, Illinois.
Salathia, N., & Queitsch, C. (2007). Molecular mechanisms of canalization: Hsp90 and beyond. Journal of Biosciences, 32 (3), 457-463. doi:DOI 10.1007/s12038-007-0045-9
Sangster, T. A., & Queitsch, C. (2005). The HSP90 chaperone complex, an emerging force in plant development and phenotypic plasticity.Current Opinion in Plant Biology, 8 (1), 86-92. doi:10.1016/j.pbi.2004.11.012
Sangster, T. A., Salathia, N., Lee, H. N., Watanabe, E., Schellenberg, K., Morneau, K., . . . Lindquist, S. (2008). HSP90-buffered genetic variation is common in Arabidopsis thaliana . Proceedings of the National Academy of Sciences of the United States of America, 105 (8), 2969-2974. doi:10.1073/pnas.0712210105
Sasaki, E., Zhang, P., Atwell, S., Meng, D., & Nordborg, M. (2015). ”Missing” G x E variation controls flowering time in Arabidopsis thaliana . Plos Genetics, 11 (10), e1005597. doi:10.1371/journal.pgen.1005597
Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9 (7), 671-675. doi:10.1038/nmeth.2089
Stankovic, N., Schloesser, M., Joris, M., Sauvage, E., Hanikenne, M., & Motte, P. (2016). Dynamic distribution and interaction of the Arabidopsis SRSF1 subfamily splicing factors. Plant Physiology, 170 (2), 1000-1013. doi:10.1104/pp.15.01338
Sulpice, R., Nikoloski, Z., Tschoep, H., Antonio, C., Kleessen, S., Larhlimi, A., . . . Stitt, M. (2013). Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions. Plant Physiol, 162 (1), 347-363. doi:10.1104/pp.112.210104
Tam, V., Patel, N., Turcotte, M., Bosse, Y., Pare, G., & Meyre, D. (2019). Benefits and limitations of genome-wide association studies.Nature Reviews Genetics, 20 (8), 467-484. doi:10.1038/s41576-019-0127-1
Team, R. C. (2020). A language and environment for statistical computing. Vienna, Austria.
Vidal, E. A., & Gutierrez, R. A. (2008). A systems view of nitrogen nutrient and metabolite responses in Arabidopsis. Current Opinion in Plant Biology, 11 (5), 521-529. doi:10.1016/j.pbi.2008.07.003
Wei, T. a. S., W. . (2017). R package ”corrplot”: Visualization of a Correlation Matrix (Version 0.84).https://github.com/taiyun/corrplot .
Weigel, D. (2012). Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiology, 158 (1), 2-22. doi:10.1104/pp.111.189845
Wickham, H. (2009). ggplot2: elegant graphics for gata analysis.Ggplot2: Elegant Graphics for Data Analysis , 1-212. doi:10.1007/978-0-387-98141-3
Wickham, H. (2011). The split-apply-combine strategy for data analysis.Journal of Statistical Software, 40 (1), 1-29. doi:DOI 10.18637/jss.v040.i01
Wickham, H. (2020). tidyr: Tidy Messy Data. R package version 1.1.2. .https://CRAN.R-project.org/package=tidyr .
Wu, D., Hu, Q., Yan, Z., Chen, W., Yan, C., Huang, X., . . . Shi, Y. (2012). Structural basis of ultraviolet-B perception by UVR8.Nature, 484 (7393), 214-219. doi:10.1038/nature10931
Zabinsky, R. A., Mason, G. A., Queitsch, C., & Jarosz, D. F. (2019). It’s not magic-Hsp90 and its effects on genetic and epigenetic variation. Seminars in Cell & Developmental Biology, 88 , 21-35. doi:10.1016/j.semcdb.2018.05.015