JXB Advance Access originally published online on September 24, 2004
Journal of Experimental Botany 2004 55(407):2343-2351; doi:10.1093/jxb/erh276
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RESEARCH PAPER |
Root growth maintenance during water deficits: physiology to functional genomics*

1Department of Agronomy, Plant Sciences Unit, 1-87 Agriculture Building, University of Missouri, Columbia, MO 65211, USA
2Department of Plant Biology and Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
3Department of Computer Science, University of Missouri, Columbia, MO 65211, USA
To whom correspondence should be addressed. Fax: +1 573 882 1469. E-mail: SharpR{at}missouri.edu
Received 16 July 2004; Accepted 23 August 2004
| Abstract |
|---|
Progress in understanding the network of mechanisms involved in maize primary root growth maintenance under water deficits is reviewed. These include the adjustment of growth zone dimensions, turgor maintenance by osmotic adjustment, and enhanced cell wall loosening. The role of the hormone abscisic acid (ABA) in maintaining root growth under water deficits is also addressed. The research has taken advantage of kinematic analysis, i.e. characterization of spatial and temporal patterns of cell expansion within the root growth zone. This approach revealed different growth responses to water deficits and ABA deficiency in distinct regions of the root tip. In the apical 3 mm region, elongation is maintained at well-watered rates under severe water deficit, although only in ABA-sufficient roots, whereas the region from 37 mm from the apex exhibits maximum elongation in well-watered roots, but progressive inhibition of elongation in roots under water deficit. This knowledge has greatly facilitated discovery of the mechanisms involved in regulating the responses. The spatial resolution with which this system has been characterized and the physiological knowledge gained to date provide a unique and powerful underpinning for functional genomics studies. Characterization of water deficit-induced changes in transcript populations and cell wall protein profiles within the growth zone of the maize primary root is in progress. Initial results from EST and unigene analyses in the tips of well-watered and water-stressed roots highlight the strength of the kinematic approach to transcript profiling.
Key words: Abscisic acid, cell wall extensibility, ESTs, expansins, kinematics, osmotic adjustment
| Introduction |
|---|
Drought is the major abiotic stress factor limiting crop productivity worldwide, and understanding the genetic and biochemical mechanisms which control drought tolerance is a central question in plant biology. As water resources for agricultural uses become more limiting, the development of drought-tolerant lines will become increasingly important. One aspect of principal importance in this arena is the response of root growth and development to water-deficit conditions.
The physiology of maize primary root elongation at low water potentials has been studied extensively by Sharp and co-workers, and the findings are summarized in this report. This work has provided the foundation for an understanding of the complex network of responses involved. The research has taken advantage of a kinematic approach, i.e. the study of spatial and temporal patterns of cell expansion within the growth zone (Erickson and Silk, 1980
; Silk, 1984
), which has greatly facilitated discovery of the mechanisms involved in the growth responses. The spatial resolution with which this system has been characterized and the physiological knowledge gained to date provide a unique and powerful underpinning for functional genomics studies which are underway and will be introduced here. This combined approach can be expected to yield much novel and valuable information towards the goal of a comprehensive understanding of the regulation of root growth during water deficits.
| Root growth maintenance during water deficits |
|---|
In plants growing in drying soil, the development of the root system is usually less inhibited than shoot growth, and may even be promoted (Sharp and Davies, 1989
An important feature of the root system response to soil drying is the ability of some roots to continue elongation at water potentials that are low enough to inhibit shoot growth completely. For example, this occurs in nodal (adventitious) roots of maize, which must penetrate through dry surface soil (Sharp and Davies, 1979
; Westgate and Boyer, 1985
), and in primary roots of a range of species, which helps seedling establishment under dry conditions by ensuring a supply of water before shoot emergence (Sharp et al., 1988
; Spollen et al., 1993
; van der Weele et al., 2000
). Figure 1 shows for several agronomic species that the primary root maintains substantial elongation rates at water potentials lower than 1.5 MPa, whereas shoot growth is completely inhibited at much higher water potentials.
|
| Taking advantage of a kinematic approach |
|---|
As emphasized by Erickson and Silk (1980)
|
In addition, roots growing at low water potential become thinner (Sharp et al., 1988
| Osmotic adjustment |
|---|
Early work showed that there is substantial osmotic adjustment in the tips of both maize nodal roots (Sharp and Davies, 1979
| Enhanced cell wall loosening |
|---|
The extent of osmotic adjustment in the maize primary root tip, although substantial, is insufficient to maintain turgor at well-watered levels in roots growing under severe water deficits. At a water potential of 1.6 MPa, turgor is reduced by over 50% throughout the growth zone (Spollen and Sharp, 1991
Cell wall-loosening proteins are believed to play key roles in controlling cell wall extension. Therefore, the activities of expansins and xyloglucan endotransglycosylase (XET) were examined to see if they correlated with the increase in wall extensibility in the apical region of the water-stressed roots. Expansin activity and extractable expansin protein increased substantially in the apical 5 mm of water-stressed compared with well-watered roots (Wu et al., 1996
). The susceptibility to expansin action also increased, indicating changes in wall structure or chemistry that facilitated expansin accessibility or action. A subsequent study (Wu et al., 2001
) showed that four expansin genes are expressed specifically in the growth zone in well-watered roots, and that three of these are rapidly up-regulated in the apical 5 mm and down-regulated in the 510 mm region after transplanting to low water potential (Fig. 3), correlating with the maintenance of elongation and the increase in cell wall extensibility in the apical region. These results illustrate the advantage of using a kinematic approach, because the up- and down-regulation of expression of the same genes in adjacent regions would have precluded observation of these changes if the whole tip had been studied. XET activity was also enhanced specifically in the apical 5 mm of the water-stressed roots, and this response was shown to be dependent on ABA accumulation (Wu et al., 1994
). By contrast, the evidence suggested that the changes in expansin gene expression are not mediated by ABA. Proteomic analyses are in progress to gain a comprehensive understanding of how cell wall protein composition changes in association with the differential growth responses to water deficits in the different regions of the root tip.
|
| Growth-maintaining role of ABA accumulation in water-stressed roots |
|---|
Hormones are likely to play important regulatory roles in the adaptation of root growth to water deficits, but the involvement of most of these compounds has not been elucidated. The exception is the accumulation of ABA, which has been shown to be required for the maintenance of maize primary root elongation at low water potentials (reviewed in Sharp, 2002
|
It is important to note that the conclusion that the accumulation of ABA in water-stressed roots helps to maintain elongation cannot be inferred by applying ABA to well-watered seedlings in order to simulate the increase in content under water stress (Sharp et al., 1994
The role of ABA in determining plant growth responses to water deficits is a long-standing question, and the finding that the accumulation of ABA is necessary for root growth maintenance at low water potentials contrasts with the commonly proposed growth-inhibitory function of increased ABA concentrations in water-stressed plants (Trewavas and Jones, 1991
). Recent studies have also shown that the normal ABA levels in well-watered plants are required to maintain shoot growth in tomato (Sharp et al., 2000
) and Arabidopsis (LeNoble et al., 2004
). In all cases, the action of ABA has been shown to involve the suppression of ethylene production (Sharp et al., 2000
; Spollen et al., 2000
, LeNoble et al., 2004
), but taken together, the studies indicate that water-deficient compared with well-watered plants require increased levels of ABA to prevent excess ethylene production (Sharp, 2002
). This difference may be related to a role of ABA accumulation in promoting the antioxidant system to maintain reactive oxygen species (ROS) at non-damaging levels during water deficits (Fig. 5). This hypothesis is based on evidence that ROS are produced in greater amounts in stressed tissues, that ABA treatments have been shown to increase expression of genes for antioxidant enzymes, for example, catalase in maize leaves (Guan et al., 2000
), and that excess ROS levels can cause increased ethylene synthesis (Overmyer et al., 2000
).
|
In recent studies, the effect of ABA deficiency on levels of ROS in the maize primary root growth zone was studied using the vp14 mutant, in which ABA levels are deficient in water-stressed but not well-watered roots (I-J Cho, M Sivaguru, RE Sharp, unpublished data). Under well-watered conditions, ROS levels were low in roots of both wild-type and vp14 seedlings. Under water deficits, ROS levels were slightly greater in the growth zone of wild-type roots and increased dramatically in vp14. The increased ROS levels in vp14 were prevented when ABA was restored to the wild-type level by exogenous application. The effect of ABA deficiency on ROS levels occurred specifically in the region 13 mm from the root apex where cell elongation is normally maintained under water deficits but is inhibited by ABA deficiency (Saab et al., 1992
| From physiology to functional genomics |
|---|
As detailed above, the maize primary root system is ideally suited for the application of genomic analyses to gain a comprehensive understanding of the mechanisms that control the responses of root growth to water stress. Characterization of water deficit-induced changes in transcript populations within the growth zone of the maize primary root is in progress. Initial results from expressed sequence tag (EST) and unigene analyses in the tips of well-watered and water-stressed roots highlight the strength of the kinematic approach to transcript profiling.
At 5 h and 48 h after transplanting to well-watered or water deficit (water potential of 1.6 MPa) conditions, primary roots were harvested and cut into four regions from the apex (Fig. 6): region 1 (03 mm), in which elongation rates are completely maintained under water deficit; region 2 (37 mm), in which elongation rates are maximal in well-watered roots but progressively inhibited under water deficit; region 3 (712 mm), in which elongation decelerates in well-watered roots and is completely inhibited under water deficit; and region 4 (1220 mm), which is non-elongating in well-watered and water-stressed roots.
|
By comparison with regions 13, region 4 helps to identify stress-induced changes that are specifically associated with growth, and its maintenance or inhibition (as in the similar studies of expansin expression shown in Fig. 3). The 48 h time point was chosen to characterize changes that are associated with the steady-state patterns of relative elongation rate in acclimated seedlings (Figs 2, 6). The 5 h time point was chosen to facilitate identification of regulatory/primary changes in gene expression (as opposed to secondary effects) after the initiation of the water-stress treatment. The well-watered samples from 5 h and 48 h were combined, and 12 primary cDNA libraries (well-watered; water-stressed 5 h; water-stressed 48 h; four regions each) were generated such that each library carried a region-identifying sequence tag. After combining the libraries for each condition, three normalized libraries were generated and
6000 ESTs from each were sequenced. The whole 3'-EST collection was then grouped into clusters of sequences with high similarity. The relative size of each cluster in a library-region combination was calculated and the distribution of cluster sizes for each of the 12 combinations then compared to produce similarity scores. These scores are represented in the hierarchical tree shown in Fig. 6. The results illustrate that EST populations were distinctly different both in adjacent regions within a treatment and in particular regions between treatments. The most distinct profile was found in region 2 of the well-watered roots, corresponding to the uniqueness of this region in exhibiting maximal elongation rates under well-watered conditions. Under water-deficit conditions, region 2 acquired a transcript profile which was more similar to that of the decelerating region (region 3) of well-watered roots. By contrast, the overall sequence collections from region 1 clustered together for the well-watered and water-stressed treatments (both 5 h and 48 h), which underscores that the transcriptional programme in this region was less disturbed by water stress than in other regions. This finding corresponds to the maintenance of relative elongation rate in region 1 of the water-stressed roots, although it is important to note that the overall similarity in EST populations does not entail that gene expression in this region was identical between the treatments. Indeed, it is anticipated that in region 1 microarray profiling and quantitative PCR studies will reveal significant changes in expression which are associated with mechanisms of root growth maintenance under water deficits.
Functional annotations of the EST populations indicate that processes which reflect the active root apical meristem, including translation, post-translational modification, RNA processing and modification, chromatin structure and dynamics, and cell cycle control were not greatly affected by the water-deficit treatment. However, water deprivation for 48 h led to the repression of transcripts in categories of intracellular trafficking and carbohydrate metabolism and to significant up-regulation of transcripts related to lipid metabolism. Transcripts associated with the cytoskeleton and cell wall formation declined during water stress in regions 24, although region 2 exhibited recovery in the expression of these transcripts at 48 h, indicating acclimation. Similarly, transcripts involved in ethylene response were more abundant after 5 h of water stress, but at 48 h the abundance was the same as that found in the well-watered roots. A number of ABA-responsive transcripts were found at a somewhat higher frequency in both 5 h and 48 h-stressed roots. It should be noted that these statements must be viewed with caution, because the nature of efficiently normalized cDNA libraries distorts transcript abundance.
To date, a total of 7688 unigenes have been identified in the root tips from the well-watered and water-stressed roots, including 992 from a subtracted cDNA library in which transcripts present under well-watered conditions were removed. Of the total of 6696 unigenes identified in the three tagged libraries, a surprisingly high number, 4517, were specific to individual libraries, and moreover, the majority of those were also specific to individual regions within the individual libraries (Table 1). These results again illustrate the advantage of the kinematic approach to this study. While experiments in the 1980s estimated the number of genes expressed in roots to be fewer than 10 000 (Kamalay and Goldberg, 1980
, 1984
), recent analyses have altered these estimates. The analysis of SAGE tags and an analysis of microarray data in Arabidopsis indicated a much higher number of genes expressed in (total) root tissues; at least 15 000 expressed sequence tags or transcripts have been identified (Birnbaum et al., 2003
; Ekman et al., 2003
). Accordingly, results of the present study suggest that from the sampling of
21 000 sequenced ESTs from which the root tip unigene set was derived, approximately half of the maize root transcriptome has been obtained.
|
Probing the maize root transcriptome by SAGE
An additional dimension has been introduced by the generation of a SAGE library from well-watered roots (regions 14). SAGE (Serial Analysis of Gene Expression) technology results in concatenated clones that may contain 3'-end located portions of up to 70 genes per clone (Velculescu et al., 1995
To identify genes corresponding with the different SAGE tags, the maize root EST database was queried to obtain a virtual maize root transcript population. In total, >18 000 maize cDNA sequences that had been determined in the EST sequencing project were analysed, resulting in the identification of 5630 cDNAs that could be assigned to SAGE tags. Correlating SAGE tag and EST number in each library provided an interesting aspect (Fig. 7). Although the SAGE tags were derived from well-watered root RNA, they were almost evenly distributed between the libraries, indicating that transcript complexity is largely unchanged by water stress and that most genes are expressed irrespective of the physiological state of the root. What is different, however, is transcript abundance. This observation suggests that gene expression, affected by water stress, primarily alters abundance levels (reported as the number of a SAGE tag) and does not completely alter the structure of the expressed part of the genome. Closer inspection (Fig. 7) indicates that complexity changes after longer-term water stress (48 h), with extrapolation indicating that approximately 20% of the transcriptome could be specific for the water-stressed state.
|
| Conclusion |
|---|
The studies reviewed here illustrate the complexity of mechanisms involved in root growth maintenance during water deficits. Understanding is being enhanced by an integrated approach, working across disciplines from physiology to functional genomics to gain a comprehensive knowledge of the gene networks, proteins, and metabolites involved. This knowledge will lead to novel approaches for improving drought tolerance through genetic and metabolic engineering of root function.
| Acknowledgements |
|---|
This work was supported by National Science Foundation Plant Genome Program grant no. DBI-0211842, by the University of Missouri Food for the 21st Century Program, and by University of Illinois at Urbana-Champaign institutional grants. We thank In-Jeong Cho for supplying Fig. 5, and Dr Mary LeNoble for useful discussions and helpful comments on the manuscript.
| Footnotes |
|---|
* This paper was also presented at the 4th International Crop Science Congress, Brisbane, Australia, September 2004.
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J. Zhu, S. Chen, S. Alvarez, V. S. Asirvatham, D. P. Schachtman, Y. Wu, and R. E. Sharp Cell Wall Proteome in the Maize Primary Root Elongation Zone. I. Extraction and Identification of Water-Soluble and Lightly Ionically Bound Proteins Plant Physiology, January 1, 2006; 140(1): 311 - 325. [Abstract] [Full Text] [PDF] |
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S. Park, J. Li, J. K. Pittman, G. A. Berkowitz, H. Yang, S. Undurraga, J. Morris, K. D. Hirschi, and R. A. Gaxiola Up-regulation of a H+-pyrophosphatase (H+-PPase) as a strategy to engineer drought-resistant crop plants PNAS, December 27, 2005; 102(52): 18830 - 18835. [Abstract] [Full Text] [PDF] |
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S. Giuliani, M. C. Sanguineti, R. Tuberosa, M. Bellotti, S. Salvi, and P. Landi Root-ABA1, a major constitutive QTL, affects maize root architecture and leaf ABA concentration at different water regimes J. Exp. Bot., December 1, 2005; 56(422): 3061 - 3070. [Abstract] [Full Text] [PDF] |
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C. Zhu, D. Schraut, W. Hartung, and A. R. Schaffner Differential responses of maize MIP genes to salt stress and ABA J. Exp. Bot., November 1, 2005; 56(421): 2971 - 2981. [Abstract] [Full Text] [PDF] |
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V. Poroyko, L.G. Hejlek, W.G. Spollen, G.K. Springer, H.T. Nguyen, R.E. Sharp, and H.J. Bohnert The Maize Root Transcriptome by Serial Analysis of Gene Expression Plant Physiology, July 1, 2005; 138(3): 1700 - 1710. [Abstract] [Full Text] [PDF] |
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