Editable Plant Root Modeling and Growth Simulation

We have identified new potential regulators of xylem cell-type determination and cellular proliferation in cassava and studied their expression in roots. Results are highly relevant for cassava biotechnology. Cassava's root system is composed of two types of root that coexist in every individual: the fibrous and the storage roots. Whether a root becomes fibrous or storage depends on the xylem cell types that it develops: fibrous roots develop xylem fibres and vessels while storage roots develop parenchyma xylem, the starch-storing tissue. A crucial question in cassava root development is how the specific xylem cell types differentiate and proliferate in the fibrous and storage roots. Using phylogenetic, protein sequence and synteny analyses we identified (1) MeVND6, MeVND7.1, MeVND7.2, MeNST3.1 and MeNST3.2 as the potential cassava orthologues of the Arabidopsis regulators of xylem cell type determination AtVND6, AtVND7 and AtNST3; and (2) MeWOX4.1 and MeWOX4.2 as the potential cassava orthologues of the Arabidopsis cambium regulator AtWOX4. Fibrous and storage roots were anatomically characterised and tested for the expression of the identified genes. Results revealed that (1) MeVND7.1 and MeVND7.2 are expressed in the fibrous but not in the storage roots; (2) MeVND6 shows low expression in both root types; (3) MeNST3.1 is not expressed in the fibrous or storage roots, while MeNST3.2 is highly expressed in both root-types and (4) MeWOX4.1 and, to a higher level, MeWOX4.2 are expressed in both the fibrous and storage roots. Results open new avenues for research in cassava root development and for food security-oriented biotechnology programmes.

1. Length of day determines the type of root system formed by cuttings for 6 varieties of dahlia, heavy root storage being correlated with a short day, and a fibrous root system being correlated with a long day. 2. Flowering was found to be independent of storage root formation, although certain varieties, such as Jersey's Beauty and Mrs. I. de ver Warner, flowered and formed storage roots concurrently on a short day. 3. Certain varieties, such as Arthur and Summer Red, flowered independently of day length; while others, such as Jersey's Beauty and Warner, flowered only on a short day. 4. Cuttings taken during late September and October developed various types of storage organs along the stem without forming either typical storage roots or fibrous roots. 5. Nitrates accumulated in the leaves and stems of short day plants, but were absent or present in only small amounts in long day plants. 6. The hydrogen-ion concentration of stems or leaves of long and short day plants varied only slightly from pH 5.4.

SUMMARYDevelopment of the fibrous root system of sugar beet was studied by washing soil samples taken from field experiments through the growing season. At the beginning of June the root system was still poorly developed but during June there was rapid proliferation. In the top 70 cm there was only little further increase in root density after the end of June. Below 70 cm root density increased up to the end of August. Throughout the season fibrous root density decreased with depth. Despite the origin of the lateral roots from two grooves on the storage root, fibrous root distributions at each depth around individual plants were essentially uniform from mid-June onwards. In the absence of nitrogen fertilizer, fibrous root development exceeded that of a crop given fertilizer, particularly at depths greater than 50 cm early in the season. The maximum value of root density was 2·8 cm/cm3 soil recorded in the top 10 cm in mid-September. Compared with published data for other crops, the sugar-beet root system was sparser than that of winter wheat or maize but denser than that of a soya bean or cassava.Soil water content was measured with a neutron probe. Inflows to roots were calculated from soil water content changes in different soil layers. In the top 30 cm, inflows ranged up to 10·8 μl water/cm root.day and were up to five times higher than published inflows for winter wheat. At 30–100 cm sugar beet and winter wheat inflows were generally similar. The 0–30 and 30–120 cm layers contributed about 80 and 20% respectively of the total water use by sugar beet while no uptake was recorded below 110 cm. Previous studies have shown that sugar beet often takes up water from soil deeper than 110 cm, although it is not unknown for the depth of water removal to be restricted.

ABSTRACTThe rice root system consists of three types of roots; main root, L-type and S-type lateral root (LR). These component roots are morphologically and histologically different, which is termed as heterorhizy. Root system hydraulic architecture is related to the unique features of component roots. We hypothesized that each component root contributes in different degrees to water uptake of the whole root system. Rice varieties IRAT 109 and Taichung 65 were grown in pots filled with soil under continuous waterlogged (CWL) and drought (CD) conditions until two weeks after heading. Morphology and histological structures of roots, which may regulate radial water movement, were compared among the three component roots. Moreover, hydraulic conductivity (Lpr) of the root system, which represents the water uptake ability, were measured with a pressure chamber. Based on a model that Lpr of the whole root system is a product of Lpr of each of the component roots and their surface areas, we found that the differences in Lpr between the two varieties and the plants grown under different soil water conditions for any of the component roots did not support the corresponding differences in the measured Lpr of the whole root system. In contrast, a significant and positive correlation was found between Lpr of the whole root system and the percentage of surface area of S-type LR but not for the other component roots. These results indicate S-type LR might have a higher contribution to Lpr of the whole root system than the other component roots.

BackgroundSweet potato (Ipomoea batatas L.) is the sixth most important food crop in the world. The formation and development of storage roots in sweet potato is a highly complicated and genetically programmed process. However, the underlying mechanisms of storage root development have not yet been elucidated.ResultsTo better understand the molecular mechanisms involved in storage root development, a combined analysis of the transcriptome and proteome of sweet potato fibrous roots (F) and storage roots at four different stages (D1, D3, D5 and D10) was performed in the present study. A total of 26,273 differentially expressed genes were identified in a comparison between the fibrous root library and four storage root libraries, while 2558 proteins showed a 1.0-fold or greater expression difference as indicated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis. The combination of the transcriptome and proteome analyses and morphological and physiological data revealed several critical pathways involved in storage root formation and development. First, genes/proteins involved in the development of meristems/cambia and starch biosynthesis were all significantly upregulated in storage roots compared with fibrous roots. Second, multiple phytohormones and the genes related to their biosynthesis showed differential expression between fibrous roots and storage roots. Third, a large number of transcription factors were differentially expressed during storage root initiation and development, which suggests the importance of transcription factor regulation in the development of storage roots. Fourth, inconsistent gene expression was found between the transcriptome and proteome data, which indicated posttranscriptional regulatory activity during the development of storage roots.ConclusionOverall, these results reveal multiple events associated with storage root development and provide new insights into the molecular mechanisms underlying the regulatory networks involved in storage root development.

Two-dimensional gel electrophoresis analysis was performed on adventitious and storage root in cassava (Manihot esculenta Crantz). Adventitious root lacking swelling formation and swelled storage root were obtained from the accession WU104 grown in the green house of the Department of Biology in Washington University in St. Louis (MO-USA). Saline buffer-soluble proteins were extracted, separated in a high-resolution 2-D electrophoresis system, visualized with silver staining gel procedure, and digital image generate for further analysis. Quantitative and qualitative protein spots analysis was performed with a computer assisted image software system. Results revealed large variation in the complexity of the gel protein profile between the two root systems. About 90% of the protein spots appeared in the pI range value of 4.0 to 6.5 and between 14 to 80 Kda of molecular mass. Detailed computer assisted analysis of this gel allowed us to establish 5 distinct classes of protein based on spot quantification that could be associated with swelling and non-swelling roots. Variation in the complexity of protein pattern was related with different type of root. Whereas the adventitious root showed a more simple profile related to primary growth, the storage root showed to be a more complex profile related to secondary growth and starch accumulation.

Effects of woody plant roots on migration of ciprofloxacin and tylosin in soil.

Well‐adapted root systems allow plants to grow under resource‐limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below‐ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts‐list of elements that function together in an integrated root system to promote survival and crop productivity.

Root systems of woody plants generally display a strong relationship between the cross-sectional area or cross-sectional diameter (CSD) of a root and the dry weight of biomass (DWd) or root volume (Vd) that has grown (i.e., is descendent) from a point. Specification of this relationship allows one to quantify root architectural patterns and estimate the amount of material lost when root systems are extracted from the soil. However, specifications of this relationship generally do not account for the fact that root systems are comprised of multiple types of roots. We assessed whether the relationship between CSD and Vd varies as a function of root type. Additionally, we sought to identify a more accurate and time-efficient method for estimating missing root volume than is currently available. We used a database that described the 3D root architecture of Pinus pinaster root systems (5, 12, or 19 years) from a stand in southwest France. We determined the relationship between CSD and Vd for 10,000 root segments from intact root branches. Models were specified that did and did not account for root type. The relationships were then applied to the diameters of 11,000 broken root ends to estimate the volume of missing roots. CSD was nearly linearly related to the square root of Vd, but the slope of the curve varied greatly as a function of root type. Sinkers and deep roots tapered rapidly, as they were limited by available soil depth. Distal shallow roots tapered gradually, as they were less limited spatially. We estimated that younger trees lost an average of 17% of root volume when excavated, while older trees lost 4%. Missing volumes were smallest in the central parts of root systems and largest in distal shallow roots. The slopes of the curves for each root type are synthetic parameters that account for differentiation due to genetics, soil properties, or mechanical stimuli. Accounting for this differentiation is critical to estimating root loss accurately.

Quantifying root water uptake is essential to understanding plant water use and responses to different environmental conditions. However, non-destructive measurement of water transport and related hydraulics in the soil-root system remains a challenge. Neutron imaging, with its high sensitivity to hydrogen, has become an unparalleled tool to visualize and quantify root water uptake in vivo. In combination with isotopes (e.g., deuterated water) and a diffusion-convection model, root water uptake and hydraulic redistribution in root and soil can be quantified. Here, we review recent advances in utilizing neutron imaging to visualize and quantify root water uptake, hydraulic redistribution in roots and soil, and root hydraulic properties of different plant species. Under uniform soil moisture distributions, neutron radiographic studies have shown that water uptake was not uniform along the root and depended on both root type and age. For both tap (e.g., lupine [Lupinus albus L.]) and fibrous (e.g., maize [Zea mays L.]) root systems, water was mainly taken up through lateral roots. In mature maize, the location of water uptake shifted from seminal roots and their laterals to crown/nodal roots and their laterals. Under non-uniform soil moisture distributions, part of the water taken up during the daytime maintained the growth of crown/nodal roots in the upper, drier soil layers. Ultra-fast neutron tomography provides new insights into 3D water movement in soil and roots. We discuss the limitations of using neutron imaging and propose future directions to utilize neutron imaging to advance our understanding of root water uptake and soil-root interactions.

The effect of inoculation with Azospirillum brasilense strain Cd on mineral concentration in sweetpotato, [Ipomeo batatas (L) Lam cv. TI-155] tissue and ionic composition of plant nutrient solution was investigated in a greenhouse study. In the field, inoculation of sweetpotato with Azospirillum spp. has been reported to enhance. sweetpotato yield. In this study, 48-h old broth cultures were used as inoculum at a population density of approx. 1 × 108 cfu/ml. The inoculum (0.20 L) was added to the reservoirs containing 30.4 L of a modified half Hoagland's plant nutrient solution at 28 days after the start of the experiment Results indicate that percent total nitrogen in sweetpotato foliage tended to be higher for the inoculated fibrous mat than in the fibrous mat for non-inoculated plants. The percent total nitrogen in storage roots for the non-inoculated treatment tended to be higher than in storage roots for inoculated plants. Inoculation resulted in a slight increase in foliar phosphorus concentration but had no effect on phosphorus concentration in sweetpotato storage and fibrous root samples. Inoculation tended to reduce foliar calcium concentration. Magnesium concentration in leaf tissue was not influenced by inoculation. Foliar potassium concentration tended to increase slightly. The effect of inoculation on potassium concentration in sweetpotato root tissue was not well-defined; potassium concentration tended to be higher in fibrous root tissue for the inoculated treatment. But in storage root tissue, potassium concentration was higher for the non-inoculated treatment than for the inoculated treatment. Inoculation did not affect foliar concentrations of any of the micronutrients measured. This study indicates no effect of inoculation on ionic strength of nutrients in solution reservoirs.

Aggregate stability is considered an essential indicator of changes in the physical properties of soils, and vegetation roots play a crucial role in the stability of shallow soil aggregates in ionic rare earth tailings piles during ecological remediation. In this paper, the influence of the law of ecologically restored vegetation roots on the stability of shallow aggregates of ionic rare earth tailing piles was investigated by means of field investigation tests, indoor experiments and mathematical statistics. The influence of different types of root systems on the stability of the shallow depth range aggregates of tailings piles was investigated; the correlation between vegetation root systems and the main physical parameters of rare earth tailings was clarified; and a mathematical correlation model characterizing the characteristic parameters of vegetation root systems was constructed. The evaluation index of the stability of rare earth tailings piles was constructed, and the influence of the law of the ecological restoration of vegetation root systems on the strength of shallow aggregates of ionic rare earth tailings piles was revealed. The results of the study showed that compared with the RD (root density), the root characteristic parameter with the largest response weight to the rare earth tailings pile is the RL (root length density), and the root characteristic parameter with the largest response weight to the water content is the RV (root volume). Suitable vegetation roots can effectively enhance the content of shallow large aggregates of rare ionic earth tailing piles. With the increase of the depth of a tailing pile, the content of large aggregates continues to decrease, and the content of micro aggregates continues increasing. This indicates that the vegetation root system changed the shallow soil of the rare earth tailing pile from disorderly to orderly through its own growth pattern, which effectively improved the stability of the shallow aggregates of the tailing pile and improved the physical properties of the tailing.

Root morphological and proteomic responses to growth restriction in maize plants supplied with sufficient N

ABSTRACTVegetal species are potentially effective at stabilising soil against water erosion due to the beneficial effects of their root system. In this regard, fibrous roots increase soil aggregation and improve its physical properties. However, the literature about the variability in particle detachment capacity in rills (the prevalent erosion form on steep and long hillslopes) with species with fibrous roots is not abundant. To fill this gap, this study has analysed the effects of fibrous roots of four herbaceous species (Hypericum androsaemum, Urtica dioica L., Epipactis latifolia All. and Danae racemosa (L.) Moench.) that are typical of Northern Iran on water flow velocity (V) and rill detachment capacity (Dc) by flume experiments. The results showed that plants with fibrous roots significantly reduced the mean V, but not Dc (except for Danae racemosa (L.) Moench.) between two positions located upstream and downstream of a rill. Only Dc of Epipactis latifolia All. was significantly different (−30% to −40%) compared with the other species. High correlations were found among the plant root characteristics. The associations between those vegetal parameters and Dc were significant but weaker. Linear regressions between Dc and shear stress allowed the estimation of rill erodibility and the critical value of the shear stress for all species, while equations set up to predict Dc from the stream power of the water flow showed a very high accuracy in all cases. Despite some limitations (linked to the small scale of the experiments), the study has demonstrated that the root system of herbaceous species may play an important role in rill erosion, but this erosion form may be driven by factors other than root system morphology.

A Comparison of Two Approaches for Modelling Cassava (Manihot esculenta Crantz.) Crop Growth