Publications of A. R. Fernie

Fernie, A. R. & Bulut, M. SPOTLIGHT: Design of future climate smart crops by engineering heat stress-responsive gene expression. Molecular Plant (2025). doi:10.1016/j.molp.2025.03.012

Zhang, W. Y., Tariq, A., Jia, X. X., Yan, J. B., Fernie, A. R., Usadel, B. & Wen, W. W. Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points. Nature Protocols 20, 690–708 (2025).

Urrea-Castellanos, R., Calderan-Rodrigues, M. J., Artins, A., Musialak-Lange, M., Macharanda-Ganesh, A., Fernie, A. R., Wahl, V. & Caldana, C. The Regulatory-associated protein of target of rapamycin 1B (RAPTOR 1B) interconnects with the photoperiod pathway to promote flowering in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 122, (2025).

López, C. M., Alseekh, S., Rivas, F. J. M., Fernie, A. R., Prieto, P. & Alamillo, J. M. CRISPR/Cas9 editing of two adenine phosphoribosyl transferase coding genes reveals the functional specialization of adenine salvage proteins in common bean. Journal of Experimental Botany 76, 346–362 (2025).

D'Auria, J. C. & Fernie, A. R. The BAHD and the bold: the mitochondria's role in alkaloid artistry. Trends in Plant Science 29, 1290–1291 (2024).

Tiozon, R. J. N., Alseekh, S., Fernie, A. R., Bonto, A. P., Yu, J., Buenafe, R. J. Q. & Sreenivasulu, N. Comprehensive lipidomic insights of differentially accumulating lipids in large pigmented rice sprout collection and the changes in the starch composition upon germination. Food Chemistry 460, (2024).

Liu, F., Fernie, A. R. & Zhang, Y. Can a nitrogen-fixing organelle be engineered within plants? Trends in Plant Science 29, 1168–1171 (2024).

von Steimker, J., Tripodi, P., Wendenburg, R., Tringovska, I., Nankar, A. N., Stoeva, V., Pasev, G., Klemmer, A., Todorova, V., Bulut, M., Tikunov, Y., Bovy, A., Gechev, T., Kostova, D., Fernie, A. R. & Alseekh, S. The genetic architecture of the pepper metabolome and the biosynthesis of its signature capsianoside metabolites. Current Biology 34, 4209–4223 (2024).

Badoni, S., Pasion-Uy, E. A., Kor, S., Kim, S.-R., Tiozon, R. J. N., Misra, G., Buenafe, R. J. Q., Labarga, L. M., Ramos-Castrosanto, A. R., Pratap, V., Slamet-Loedin, I., von Steimker, J., Alseekh, S., Fernie, A. R., Kohli, A., Khush, G. S. & Sreenivasulu, N. Multiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein content. Proceedings of the National Academy of Sciences of the United States of America 121, (2024).

Hayashi, K. & Fernie, A. R. A neat wheat trick to hide genes from selection. Trends in Plant Science 29, 837–838 (2024).

Yin, Z., Huang, W., Li, K., Fernie, A. R. & Yan, S. Advances in mass spectrometry imaging for plant metabolomics—Expanding the analytical toolbox. The Plant Journal 119, 2168–2180 (2024).

Fernie, A. R. & Bulut, M. How cauliflower got its curd. Nature Genetics 56, 1042–1044 (2024).

Qiu, H., Zhang, X., Zhang, Y. J., Jiang, X., Ren, Y., Gao, D., Zhu, X., Usadel, B., Fernie, A. R. & Wen, W. Depicting the genetic and metabolic panorama of chemical diversity in the tea plant. Plant Biotechnology Journal 22, 1001–1016 (2024).

Liu, F., Fernie, A. R. & Zhang, Y. J. Plant gene co-expression defines the biosynthetic pathway of neuroactive alkaloids. Molecular Plant 17, 372–374 (2024).

Fernie, A. R. & Bulut, M. A delicate balance: transcriptional control of awn development and yield in barley. Trends in Plant Science 29, 946–947 (2024).

Gupta, S., Petrov, V., Garg, V., Mueller-Roeber, B., Fernie, A. R., Nikoloski, Z. & Gechev, T. The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments. Cellular and Molecular Life Sciences 81, (2024).

Rosa-Téllez, S., Alcántara-Enguídanos, A., Martinez-Seidel, F., Casatejada-Anchel, R., Saeheng, S., Bailes, C. L., Erban, A., Medeiros, D. B., Alepúz, P., Matus, J. T., Kopka, J., Muñoz-Bertomeu, J., Krueger, S., Roje, S., Fernie, A. R. & Ros, R. The serine-glycine-one carbon metabolic network orchestrates changes in nitrogen and sulfur metabolism and shapes plant development. The Plant Cell 36, 404–426 (2024).

Hayashi, K. & Fernie, A. R. Genomic evidence of a transposon-conferred adaptive response. Cell Reports 43, (2024).

Li, J., Martin, C. & Fernie, A. R. Biofortification’s contribution to mitigating micronutrient deficiencies. Nature Food 5, 19–27 (2024).

Zhang, Y. J., Wiese, L., Fang, H., Alseekh, S., de Souza, L. P., Scossa, F., Molloy, J., Christmann, M. & Fernie, A. R. Synthetic biology identifies the minimal gene set required for Paclitaxel biosynthesis in a plant chassis. Molecular Plant 16, 1951–1961 (2023).