Special Issue: Root Architecture   

March 2016, Volume 58 Issue 3, Pages 189每279.

Cover Caption: Root Architecture
Water and mineral acquisitions from the soil under limiting conditions are strongly influenced by the architecture of the root system. Comparison of reconstructed 3D root architecture models for lowland IR64 and upland rice genotypes illustrates contrasting root traits adapted to different soil environments (see Piñeros et al. pp 230-241 for details). This special issue is dedicated to most recent advances in plant root architectural studies.


Root architecture  
Author: Leon V. Kochian
Journal of Integrative Plant Biology 2016 58(3): 190每192
Published Online: February 24, 2016
DOI: 10.1111/jipb.12471

Numerous research publications over the past 20 years have made it quite clear that a better understanding of the molecular and genetic basis for variation in root system architecture (RSA) will greatly aid the development of crop varieties with improved and more efficient nutrient and water acquisition under limiting conditions. In many parts of the world - especially in developing countries, food security is threatened by drought stress and poor soil fertility, which are major limitations to crop yields. These stresses are increasing in severity as climate change is resulting in more variable and extreme weather events (IPCC 4th Assessment Report 2007). Furthermore, due to the rising costs for fertilizer production and distribution and increasing water scarcity, as well as the negative environmental impacts associated with overuse of fertilizers, further increases in crop yields via increased agricultural inputs are not sustainable nor are they economically viable in many developing countries (Lynch 2007). Thus, identifying how plants control the development of root system architecture canl have a real impact on improving agricultural food production and world food security in the 21st century.

Abstract (Browse 573)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Invited Expert Reviews
Improving crop nutrient efficiency through root architecture modifications  
Author: Xinxin Li, Rensen Zeng and Hong Liao
Journal of Integrative Plant Biology 2016 58(3): 193每202
Published Online: October 12, 2015
DOI: 10.1111/jipb.12434

Improving crop nutrient efficiency becomes an essential consideration for environmentally friendly and sustainable agriculture. Plant growth and development is dependent on 17 essential nutrient elements, among them, nitrogen (N) and phosphorus (P) are the two most important mineral nutrients. Hence it is not surprising that low N and/or low P availability in soils severely constrains crop growth and productivity, and thereby have become high priority targets for improving nutrient efficiency in crops. Root exploration largely determines the ability of plants to acquire mineral nutrients from soils. Therefore, root architecture, the 3-dimensional configuration of the plant's root system in the soil, is of great importance for improving crop nutrient efficiency. Furthermore, the symbiotic associations between host plants and arbuscular mycorrhiza fungi/rhizobial bacteria, are additional important strategies to enhance nutrient acquisition. In this review, we summarize the recent advances in the current understanding of crop species control of root architecture alterations in response to nutrient availability and root/microbe symbioses, through gene or QTL regulation, which results in enhanced nutrient acquisition.


Li X, Zeng R, Liao H (2016) Improving crop nutrient efficiency through root architecture modifications. J Integr Plant Biol 58: 193– 202 doi: 10.1111/jipb.12434

Abstract (Browse 1176)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Root is essential for plant growth, nutrient and water acquisition and symbiosis with microflora in soils. Here, we summarized the recent advances in crop species' control of root architecture alterations in response to nutrient availability and root/microbe symbioses, through gene or QTL regulation, which results in enhanced nutrient efficiency.
Fine-tuning by strigolactones of root response to low phosphate  
Author: Yoram Kapulnik and Hinanit Koltai
Journal of Integrative Plant Biology 2016 58(3): 203每212
Published Online: December 15, 2015
DOI: 10.1111/jipb.12454

Strigolactones are plant hormones that regulate the development of different plant parts. In the shoot, they regulate axillary bud outgrowth and in the root, root architecture and root-hair length and density. Strigolactones are also involved with communication in the rhizosphere, including enhancement of hyphal branching of arbuscular mycorrhizal fungi. Here we present the role and activity of strigolactones under conditions of phosphate deprivation. Under these conditions, their levels of biosynthesis and exudation increase, leading to changes in shoot and root development. At least for the latter, these changes are likely to be associated with alterations in auxin transport and sensitivity. On the other hand, strigolactones may positively affect plant–mycorrhiza interactions and thereby promote phosphate acquisition by the plant. Strigolactones may be a way for plants to fine-tune their growth pattern under phosphate deprivation.

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Strigolactones and auxin are plant hormones that act in the plant to manipulate its response to phosphate conditions. Dependent on phosphate conditions, strigolactones manipulate auxin transport and perception whereas auxin positively regulates strigolactones biosynthesis. This crosstalk may affect lateral root formation, root hair density and elongation and activity of phosphate transporters.
How can we harness quantitative genetic variation in crop root systems for agricultural improvement?  
Author: Christopher N. Topp, Adam L. Bray, Nathanael A. Ellis and Zhengbin Liu
Journal of Integrative Plant Biology 2016 58(3): 213每225
Published Online: February 23, 2016
DOI: 10.1111/jipb.12470
Root systems are a black box obscuring a comprehensive understanding of plant function, from the ecosystem scale down to the individual. In particular, a lack of knowledge about the genetic mechanisms and environmental effects that condition root system growth hinders our ability to develop the next generation of crop plants for improved agricultural productivity and sustainability. We discuss how the methods and metrics we use to quantify root systems can affect our ability to understand them, how we can bridge knowledge gaps and accelerate the derivation of structure-function relationships for roots, and why a detailed mechanistic understanding of root growth and function will be important for future agricultural gains.
Abstract (Browse 602)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
This review article focuses on technologies and methodologies that allow us to measure root systems, the ※hidden-half§ of plants, and how we can utilize them to develop more stress resistant crop plants with fewer resources.
          Letter to the Editor
Long-distance nitrate signaling displays cytokinin dependent and independent branches  
Author: Sandrine Ruffel, Arthur Poitout, Gabriel Krouk, Gloria M. Coruzzi and Benoit Lacombe
Journal of Integrative Plant Biology 2016 58(3): 226每229
Published Online: December 1, 2015
DOI: 10.1111/jipb.12453

The long-distance signaling network allowing a plant to properly develop its root system is crucial to optimize root foraging in areas where nutrients are available. Cytokinin is an essential element of the systemic signaling network leading to the enhancement of lateral root proliferation in areas where nitrate is available. Here, we explore more precisely: (i) which particular traits of lateral root growth (density and length of emerged lateral roots) are the targets of systemic signaling in a context of heterogeneous nitrate supply; and (ii) if the systemic signaling depends only on cytokinin or on a combination of several signalings.

Abstract (Browse 846)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Heterogeneous nutrient availability is frequent during plant life cycle. Therefore, long-distance communication is crucial to properly tune root development according to local nutrient availability and whole-plant needs. Here, we show that multiple traits of root development are the targets of nitrate long-distance signaling, dependently or independently of cytokinin biosynthesis.
          Research Articles
Evolving technologies for growing, imaging and analyzing 3D root system architecture of crop plants  
Author: Miguel A. Piñeros, Brandon G. Larson, Jon E. Shaff, David J. Schneider, Alexandre Xavier Falcão, Lixing Yuan, Randy T. Clark, Eric J. Craft, Tyler W. Davis, Pierre-Luc Pradier, Nathanael M. Shaw, Ithipong Assaranurak, Susan R. McCouch, Craig Sturrock, Malcolm Bennett and Leon V. Kochian
Journal of Integrative Plant Biology 2016 58(3): 230每241
Published Online: December 18, 2015
DOI: 10.1111/jipb.12456
A plant's ability to maintain or improve its yield under limiting conditions, such as nutrient deficiency or drought, can be strongly influenced by root system architecture (RSA), the three-dimensional distribution of the different root types in the soil. The ability to image, track and quantify these root system attributes in a dynamic fashion is a useful tool in assessing desirable genetic and physiological root traits. Recent advances in imaging technology and phenotyping software have resulted in substantive progress in describing and quantifying RSA. We have designed a hydroponic growth system which retains the three-dimensional RSA of the plant root system, while allowing for aeration, solution replenishment and the imposition of nutrient treatments, as well as high-quality imaging of the root system. The simplicity and flexibility of the system allows for modifications tailored to the RSA of different crop species and improved throughput. This paper details the recent improvements and innovations in our root growth and imaging system which allows for greater image sensitivity (detection of fine roots and other root details), higher efficiency, and a broad array of growing conditions for plants that more closely mimic those found under field conditions.
Abstract (Browse 720)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Variation in root system architecture (RSA) plays a major role in efficient nutrient acquisition under limiting conditions. Here we describe improvements in the growth and digital imaging of root systems that allow for imaging and analysis of RSA traits for a wide range of crop species under diverse treatment conditions.
Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency  
Author: Pengcheng Li, Zhongjuan Zhuang, Hongguang Cai, Shuai Cheng, Ayaz Ali Soomro, Zhigang Liu, Riliang Gu, Guohua Mi, Lixing Yuan and Fanjun Chen
Journal of Integrative Plant Biology 2016 58(3): 242每253
Published Online: August 13, 2015
DOI: 10.1111/jipb.12384

Maize (Zea mays L.) root morphology exhibits a high degree of phenotypic plasticity to nitrogen (N) deficiency, but the underlying genetic architecture remains to be investigated. Using an advanced BC4F3 population, we investigated the root growth plasticity under two contrasted N levels and identified the quantitative trait loci (QTLs) with QTL-environment (Q × E) interaction effects. Principal components analysis (PCA) on changes of root traits to N deficiency (ΔLN-HN) showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC, while root traits scattered highly on PC2 and PC3. Hierarchical cluster analysis on traits for ΔLN-HN further assigned the BC4F3 lines into six groups, in which the special phenotypic responses to N deficiency was presented. These results revealed the complicated root plasticity of maize in response to N deficiency that can be caused by genotype-environment (G × E) interactions. Furthermore, QTL mapping using a multi-environment analysis identified 35 QTLs for root traits. Nine of these QTLs exhibited significant Q × E interaction effects. Taken together, our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N deficiency, which will be useful for developing maize tolerance cultivars to N deficiency.

Abstract (Browse 1092)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
This study reveals the complicated root plasticity of maize in response to nitrogen deficiency that can be caused by genotype-environment (G ℅ E) interactions. QTL mapping identified nine root QTLs exhibited significant Q ℅ E interaction effects that will be useful for developing maize cultivars to N deficiency.
Statistical modeling of nitrogen-dependent modulation of root system architecture in Arabidopsis thaliana  
Author: Takao Araya, Takuya Kubo, Nicolaus von Wirén and Hideki Takahashi
Journal of Integrative Plant Biology 2016 58(3): 254每265
Published Online: October 1, 2015
DOI: 10.1111/jipb.12433
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 as 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.
Abstract (Browse 887)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Nutrient and water supplies affect plant root architecture in the soil environment. Statistical modeling of root architectural traits provides evidence for root elongation and branching patterns being modulated in response to different forms and availabilities of nitrogen source in the environment.
Genetic dissection of maize seedling root system architecture traits using an ultra-high density bin-map and a recombinant inbred line population  
Author: Weibin Song, Baobao Wang, Andrew L Hauck, Xiaomei Dong, Jieping Li and Jinsheng Lai
Journal of Integrative Plant Biology 2016 58(3): 266每279
Published Online: November 23, 2015
DOI: 10.1111/jipb.12452

Maize (Zea mays) root system architecture (RSA) mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study, a set of 204 recombinant inbred lines (RILs) was derived from the widely adapted Chinese hybrid ZD958(Zheng58 × Chang7-2), genotyped by sequencing (GBS) and evaluated as seedlings for 24 RSA related traits divided into primary, seminal and total root classes. Significant differences between the means of the parental phenotypes were detected for 18 traits, and extensive transgressive segregation in the RIL population was observed for all traits. Moderate to strong relationships among the traits were discovered. A total of 62 quantitative trait loci (QTL) were identified that individually explained from 1.6% to 11.6% (total root dry weight/total seedling shoot dry weight) of the phenotypic variation. Eighteen, 24 and 20 QTL were identified for primary, seminal and total root classes of traits, respectively. We found hotspots of 5, 3, 4 and 12 QTL in maize chromosome bins 2.06, 3.02-03, 9.02-04, and 9.05-06, respectively, implicating the presence of root gene clusters or pleiotropic effects. These results characterized the phenotypic variation and genetic architecture of seedling RSA in a population derived from a successful maize hybrid.

Abstract (Browse 919)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Maize root system architecture (RSA) mediates key functions of plant anchorage and acquisition of nutrients and water. Our study suggested that many of the 24 characterized RSA related traits were highly correlated. We also identified 62 QTLs, including four gene clusters, for these root traits.
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