Systems Biology for Enhanced Plant Nitrogen Nutrition

FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago, Chile.
Science (Impact Factor: 33.61). 06/2012; 336(6089):1673-5. DOI: 10.1126/science.1217620
Source: PubMed


Nitrogen (N)-based fertilizers increase agricultural productivity but have detrimental effects on the environment and human health. Research is generating improved understanding of the signaling components plants use to sense N and regulate metabolism, physiology, and growth and development. However, we still need to integrate these regulatory factors into signal transduction pathways and connect them to downstream response pathways. Systems biology approaches facilitate identification of new components and N-regulatory networks linked to other plant processes. A holistic view of plant N nutrition should open avenues to translate this knowledge into effective strategies to improve N-use efficiency and enhance crop production systems for more sustainable agricultural practices.

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Available from: Rodrigo A Gutierrez, Jan 21, 2014
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    • "In contrast, lateral roots elongate for N foraging when they locally receive an adequate amount of NO 3 (Zhang and Forde 1998; Remans et al. 2006a). The function of the NPF6.3 nitrate/auxin transporter and the action of its downstream networks further corroborate the roles of NO 3 -dependent signals associated with the development of lateral roots following transfer of plants from N-deprived to N-replete conditions (Vidal et al. 2010; Gutiérrez 2012; Vidal et al. 2013; Bouguyon et al. 2015; Giehl and von Wirén 2015). Besides these morphological responses to NO 3 supply , plant roots display different architectures in the presence of alternative N sources. "
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    ABSTRACT: Plant root development is strongly affected by nutrient availability. Despite the importance of structure and function of roots in nutrient acquisition, statistical modeling approaches to evaluate dynamic and temporal modulations of root system architecture in response to nutrient availability have remained widely open and exploratory areas in root biology. In this study, we developed a statistical modeling approach to investigate modulations of root system architecture in response to nitrogen availability. Mathematical models were designed for quantitative assessment of root growth and root branching phenotypes and their dynamic relationships based on hierarchical configuration of primary and lateral roots formulating the fishbone-shaped root system architecture in Arabidopsis thaliana. Time-series datasets reporting dynamic changes in root developmental traits on different nitrate or ammonium concentrations were generated for statistical analyses. Regression analyses unraveled key parameters associated with (i) inhibition of primary root growth under nitrogen limitation or on ammonium, (ii) rapid progression of lateral root emergence in response to ammonium, and (iii) inhibition of lateral root elongation in the presence of excess nitrate or ammonium. This study provides a statistical framework for interpreting dynamic modulation of root system architecture, supported by meta-analysis of datasets displaying morphological responses of roots to diverse nitrogen supplies.
    Journal of Integrative Plant Biology 09/2015; DOI:10.1111/jipb.12433 · 3.34 Impact Factor
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    • "These contradictory results may be attributed to differences in soil sampling points, number of samples, time of sampling, and analytical methods. Up to now, effects of K fertilizer use have not attracted concerns like N and P (Guttierrez, 2012; MacDonald et al., 2011; Pinder et al., 2012; Liu et al., 2010; Zhang et al., 2013). The national soil survey conducted in the early 1980s in China could not reflect soil K status in reality. "
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    ABSTRACT: Potassium (K) fertilizers are non-renewable resources and cannot be synthesized from other chemicals. Understanding soil K status in China is crucial for the efficient use of K resources, and the resulting food security and resource sustainability. We analyzed temporal and spatial changes in soil K from 58,559 soil samples, and yield responses from 2055 field experiments compiled from the International Plant Nutrition Institute (IPNI) China Program database from 1990 to 2012. The results indicated that on average soil available K increased from 79.8 mg L−1 in the 1990s, to 93.4 mg L−1 in the 2000s, with the increase for cash crops faster than that for grain crops. In fact the average increase in soil available K over time was attributed to increases in soil K for cash crop fields with high K fertilizer application (1.4 to 2.6 times more than for grain crops). The study found great variation in soil available K across different regions and over time in China. Soil available K varied over space with values of 76.8, 99.8, 118.0, 83.9 and 81.3 mg L−1 for northeast (NE), north central (NC), northwest (NW), southeast (SE) and southwest (SW), respectively. While no difference in soil available K over the time period of the study was observed in NE China, the values increased by 34.8%, 17.9% and 30.2% for NC, SE and SW, respectively, and decreased by 75.9% for NW China between the 1990s and 2000s. Great temporal and spatial variation existed for relative yield as well, which followed similar trends to soil available K. Potassium fertilizer application continued to be recommended for grain crops due to the low soil available K falling short of critical values, and cash crops where a larger yield response to K fertilizer has been recorded. This great variation observed in soil available K across the different regions in China demonstrated the urgent need for site-specific K nutrient management.
    Field Crops Research 03/2015; 173. DOI:10.1016/j.fcr.2015.01.003 · 2.98 Impact Factor
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    • "Although much more informative than conventional transcriptome studies, such whole-genome expression approaches have remained confined to deciphering regulatory circuits at the transcriptional level, since only the steady state of transcripts has been considered. Such an approach, originally developed for Arabidopsis by virtue of the wealth of information available, when transferred to crops may help in identifying key master genes involved in the control of NUE (Gutiérrez, 2012). Nevertheless, transcriptome, metabolome, and even fluxome co-expression network analyses will certainly be necessary in order to enhance our knowledge of the genes and metabolic pathways linked to NUE in crops such as maize (Saito and Matsuda, 2010). "

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