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PLoS Genet. 2019 Nov 6;15(11):e1008392. doi: 10.1371/journal.pgen.1008392. eCollection 2019 Nov.

Systems genomics approaches provide new insights into Arabidopsis thaliana root growth regulation under combinatorial mineral nutrient limitation.

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BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France.
Evolutionary Genomics, Center for Computational and Theoretical Biology (CCTB), University Würzburg, Würzburg, Germany.
Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
Plant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America.
Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America.


The molecular mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using Arabidopsis thaliana accessions, we analyzed RGR variation under combinatorial mineral nutrient deficiencies involving phosphorus (P), iron (Fe), and zinc (Zn). While -P stimulated early RGR of most accessions, -Fe or -Zn reduced it. The combination of either -P-Fe or -P-Zn led to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, root growth responses of the reference accession Columbia (Col-0) were not representative of the species under -P nor -Zn. Using a systems approach that combines GWAS, network-based candidate identification, and reverse genetic screen, we identified new genes that regulate root growth in -P-Fe: VIM1, FH6, and VDAC3. Our findings provide a framework to systematically identifying favorable allelic variations to improve root growth, and to better understand how plants sense and respond to multiple environmental cues.

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