Root Growth Angle Research Articles

Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging.

Precise measurements of root system architecture traits are an important requirement for plant phenotyping. Most of the current methods for analyzing root growth require either artificial growing conditions (e.g. hydroponics), are severely restricted in the fraction of roots detectable (e.g. rhizotrons), or are destructive (e.g. soil coring). On the other hand, modalities such as magnetic resonance imaging (MRI) are noninvasive and allow high-quality three-dimensional imaging of roots in soil. Here, we present a plant root imaging and analysis pipeline using MRI together with an advanced image visualization and analysis software toolbox named NMRooting. Pots up to 117 mm in diameter and 800 mm in height can be measured with the 4.7 T MRI instrument used here. For 1.5 l pots (81 mm diameter, 300 mm high), a fully automated system was developed enabling measurement of up to 18 pots per day. The most important root traits that can be nondestructively monitored over time are root mass, length, diameter, tip number, and growth angles (in two-dimensional polar coordinates) and spatial distribution. Various validation measurements for these traits were performed, showing that roots down to a diameter range between 200 μm and 300 μm can be quantitatively measured. Root fresh weight correlates linearly with root mass determined by MRI. We demonstrate the capabilities of MRI and the dedicated imaging pipeline in experimental series performed on soil-grown maize (Zea mays) and barley (Hordeum vulgare) plants.

Comparison of root growth angles of wheat cultivars grown in a hydrogel polymer medium

Comparison of root growth angles of wheat cultivars grown in a hydrogel polymer medium

Genetic variation in seminal and nodal root angle and their association with grain yield of maize under water-stressed field conditions

Root angles are widely recognized to play an important role in determining rooting depth and drought tolerance in crop plants. But there has been no report revealing any association between root angle and yield performance under drought conditions in maize. There is also no simple method available to screen root angles. The objectives of this study were to evaluate genetic variation in seminal and nodal root angles in maize in greenhouse condition and their association with drought tolerance in field condition. Eighteen hybrids, of which nine were higher-yielding and nine were lower-yielding under water-stressed condition in field, were evaluated for root angle variation. Root angle was estimated as the distance between the horizontal soil surface line and slope of the root at 2 cm position from root base using a protractor. Significant phenotypic variation was observed among hybrids for seminal and nodal root angles and primary root diameter. These root traits showed strong positive correlations with grain yield under drought condition. All the higher-yielding hybrids had steeper root growth angle than the lower-yielding hybrids. A strong correlation between seminal and nodal root angles was observed. A strong correlation was also observed between 5th and 4th node nodal root angles. Either seminal or nodal root angle could be used for selection for the improvement drought tolerance. The current screening system for root angle is simple and inexpensive, and could be used for screening a large number of genotypes.

QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1.

BackgroundThe functional allele of the rice gene DEEPER ROOTING 1 (DRO1) increases the root growth angle (RGA). However, wide natural variation in RGA is observed among rice cultivars with the functional DRO1 allele. To elucidate genetic factors related to such variation, we quantitatively measured RGA using the basket method and analyzed quantitative trait loci (QTLs) for RGA in three F2 mapping populations derived from crosses between the large RGA–type cultivar Kinandang Patong and each of three accessions with varying RGA: Momiroman has small RGA and was used to produce the MoK-F2 population; Yumeaoba has intermediate RGA (YuK-F2 population); Tachisugata has large RGA (TaK-F2 population). All four accessions belong to the same haplotype group of functional DRO1 allele.ResultsWe detected the following statistically significant QTLs: one QTL on chromosome 4 in MoK-F2, three QTLs on chromosomes 2, 4, and 6 in YuK-F2, and one QTL on chromosome 2 in TaK-F2. Among them, the two QTLs on chromosome 4 were located near DRO2, which has been previously reported as a major QTL for RGA, whereas the two major QTLs for RGA on chromosomes 2 (DRO4) and 6 (DRO5) were novel. With the LOD threshold reduced to 3.0, several minor QTLs for RGA were also detected in each population.ConclusionNatural variation in RGA in rice cultivars carrying functional DRO1 alleles may be controlled by a few major QTLs and by several additional minor QTLs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0049-2) contains supplementary material, which is available to authorized users.

Phene synergism between root hair length and basal root growth angle for phosphorus acquisition.

Shallow basal root growth angle (BRGA) increases phosphorus acquisition efficiency by enhancing topsoil foraging because in most soils, phosphorus is concentrated in the topsoil. Root hair length and density (RHL/D) increase phosphorus acquisition by expanding the soil volume subject to phosphorus depletion through diffusion. We hypothesized that shallow BRGA and large RHL/D are synergetic for phosphorus acquisition, meaning that their combined effect is greater than the sum of their individual effects. To evaluate this hypothesis, phosphorus acquisition in the field in Mozambique was compared among recombinant inbred lines of common bean (Phaseolus vulgaris) having four distinct root phenotypes: long root hairs and shallow basal roots, long root hairs and deep basal roots, short root hairs and shallow basal roots, and short root hairs and deep basal roots. The results revealed substantial synergism between BRGA and RHL/D. Compared with short-haired, deep-rooted phenotypes, long root hairs increased shoot biomass under phosphorus stress by 89%, while shallow roots increased shoot biomass by 58%. Genotypes with both long root hairs and shallow roots had 298% greater biomass accumulation than short-haired, deep-rooted phenotypes. Therefore, the utility of shallow basal roots and long root hairs for phosphorus acquisition in combination is twice as large as their additive effects. We conclude that the anatomical phene of long, dense root hairs and the architectural phene of shallower basal root growth are synergetic for phosphorus acquisition. Phene synergism may be common in plant biology and can have substantial importance for plant fitness, as shown here.

A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1.

BackgroundRoot growth angle (RGA) is an important trait that influences the ability of rice to avoid drought stress. DEEPER ROOTING 1 (DRO1), which is a major quantitative trait locus (QTL) for RGA, is responsible for the difference in RGA between the shallow-rooting cultivar IR64 and the deep-rooting cultivar Kinandang Patong. However, the RGA differences between these cultivars cannot be fully explained by DRO1. The objective of this study was to identify new QTLs for RGA explaining the difference in RGA between these cultivars.ResultsBy crossing IR64 (which has a non-functional allele of DRO1) with Kinandang Patong (which has a functional allele of DRO1), we developed 26 chromosome segment substitution lines (CSSLs) that carried a particular chromosome segment from Kinandang Patong in the IR64 genetic background. Using these CSSLs, we found only one chromosomal region that was related to RGA: on chromosome 9, which includes DRO1. Using an F2 population derived from a cross between Kinandang Patong and the Dro1-NIL (near isogenic line), which had a functional DRO1 allele in the IR64 genetic background, we identified a new QTL for RGA (DRO3) on the long arm of chromosome 7.ConclusionsDRO3 may only affect RGA in plants with a functional DRO1 allele, suggesting that DRO3 is involved in the DRO1 genetic pathway.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0044-7) contains supplementary material, which is available to authorized users.

Genetic improvement for root growth angle to enhance crop production.

The root system is an essential organ for taking up water and nutrients and anchoring shoots to the ground. On the other hand, the root system has rarely been regarded as breeding target, possibly because it is more laborious and time-consuming to evaluate roots (which require excavation) in a large number of plants than aboveground tissues. The root growth angle (RGA), which determines the direction of root elongation in the soil, affects the area in which roots capture water and nutrients. In this review, we describe the significance of RGA as a potential trait to improve crop production, and the physiological and molecular mechanisms that regulate RGA. We discuss the prospects for breeding to improve RGA based on current knowledge of quantitative trait loci for RGA in rice.

A major QTL controlling deep rooting on rice chromosome 4

Drought is the most serious abiotic stress that hinders rice production under rainfed conditions. Breeding for deep rooting is a promising strategy to improve the root system architecture in shallow-rooting rice cultivars to avoid drought stress. We analysed the quantitative trait loci (QTLs) for the ratio of deep rooting (RDR) in three F2 mapping populations derived from crosses between each of three shallow-rooting varieties (‘ARC5955', ‘Pinulupot1', and ‘Tupa729') and a deep-rooting variety, ‘Kinandang Patong'. In total, we detected five RDR QTLs on chromosomes 2, 4, and 6. In all three populations, QTLs on chromosome 4 were found to be located at similar positions; they explained from 32.0% to 56.6% of the total RDR phenotypic variance. This suggests that one or more key genetic factors controlling the root growth angle in rice is located in this region of chromosome 4.

Basal root whorl number: a modulator of phosphorus acquisition in common bean (Phaseolus vulgaris).

Root architectural phenes enhancing topsoil foraging are important for phosphorus acquisition. In this study, the utility of a novel phene is described, basal root whorl number (BRWN), that has significant effects on topsoil foraging in common bean (Phaseolus vulgaris). Whorls are defined as distinct tiers of basal roots that emerge in a tetrarch fashion along the base of the hypocotyl. Wild and domesticated bean taxa as well as two recombinant inbred line (RIL) populations were screened for BRWN and basal root number (BRN). A set of six RILs contrasting for BRWN was evaluated for performance under low phosphorus availability in the greenhouse and in the field. In the greenhouse, plants were grown in a sand-soil media with low or high phosphorus availability. In the field, plants were grown in an Oxisol in Mozambique under low and moderate phosphorus availability. Wild bean accessions tended to have a BRWN of one or two, whereas cultivated accessions had BRWN reaching four and sometimes five. BRWN and BRN did not vary with phosphorus availability, i.e. BRWN was not a plastic trait in these genotypes. Greater BRWN was beneficial for phosphorus acquisition in low phosphorus soil. Genotypes with three whorls had almost twice the shoot biomass, greater root length and greater leaf area than related genotypes with two whorls. In low phosphorus soil, shoot phosphorus content was strongly correlated with BRWN (R(2) = 0.64 in the greenhouse and R(2) = 0.88 in the field). Genotypes with three whorls had shallower root systems with a greater range of basal root growth angles (from 10 to 45 ° from horizontal) than genotypes with two whorls (angles ranged from 60 to 85 ° from horizontal). The results indicate that BRWN is associated with increased phosphorus acquisition and that this trait may have value for selection of genotypes with better performance in low phosphorus soils.

Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions

The genetic improvement of drought resistance is essential for stable and adequate crop production in drought-prone areas. Here we demonstrate that alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 (DRO1), a rice quantitative trait locus controlling root growth angle. DRO1 is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar. Our experiments suggest that control of root system architecture will contribute to drought avoidance in crops.

Integration of root phenes for soil resource acquisition

Suboptimal availability of water and nutrients is a primary limitation to plant growth in terrestrial ecosystems. The acquisition of soil resources by plant roots is therefore an important component of plant fitness and agricultural productivity. Plant root systems comprise a set of phenes, or traits, that interact. Phenes are the units of the plant phenotype, and phene states represent the variation in form and function a particular phene may take. Root phenes can be classified as affecting resource acquisition or utilization, influencing acquisition through exploration or exploitation, and in being metabolically influential or neutral. These classifications determine how one phene will interact with another phene, whether through foraging mechanisms or metabolic economics. Phenes that influence one another through foraging mechanisms are likely to operate within a phene module, a group of interacting phenes, that may be co-selected. Examples of root phene interactions discussed are: (1) root hair length × root hair density, (2) lateral branching × root cortical aerenchyma (RCA), (3) adventitious root number × adventitious root respiration and basal root growth angle (BRGA), (4) nodal root number × RCA, and (5) BRGA × root hair length and density. Progress in the study of phenes and phene interactions will be facilitated by employing simulation modeling and near-isophenic lines that allow the study of specific phenes and phene combinations within a common phenotypic background. Developing a robust understanding of the phenome at the organismal level will require new lines of inquiry into how phenotypic integration influences plant function in diverse environments. A better understanding of how root phenes interact to affect soil resource acquisition will be an important tool in the breeding of crops with superior stress tolerance and reduced dependence on intensive use of inputs.

Maize root growth angles become steeper under low N conditions

Root traits that increase the speed and effectiveness of subsoil foraging may enhance nitrogen acquisition in leaching environments. We investigated root depth distribution of maize genotypes across the cropping cycle, effects of root angles on plant performance and potential plastic responses of root growth angles to nitrogen fertilization. We focus on genetic variation for growth angles of crown and brace roots among 108 inbred lines of maize in high and low nitrogen field environments in the USA and South Africa. Root angles of crown roots were significantly associated with rooting depth calculated as the depth containing 95% of the root mass (D95). The number of brace roots as well as rooting depth (D95) increased between 43 days after planting (DAP) and flowering, but did not show any major changes between flowering and physiological maturity. Brace root branching increased between 43 DAP and flowering and showed reductions between flowering and physiological maturity. Under well-fertilized conditions genotypes initially selected as ‘steep’ and ‘shallow’ did not alter their root angles. Brace and crown root angles became up to 18° steeper under nitrogen deficient conditions. Increases in root angles under nitrogen deficient conditions were more accentuated for shallow genotypes, resulting in root angles and rooting depths similar to the ones measured for steep genotypes. Steeper root angles enabled plastic genotypes to potentially explore similar soil volumes under nitrogen deficient conditions as steep genotypes, thereby not incurring any reductions in grain yield compared to genotypes constitutively forming steep root angles. Additive main and multiplicative interaction effects (AMMI) analysis revealed that out of 29 genotypes best adapted to 4 different nitrogen fertilizer treatment-by-location combinations, 11 were steep, 11 were plastic and 7 were shallow genotypes. The number of plastic genotypes among the adapted entries was disproportionately high compared to 6 that could be anticipated based on the distribution in the entire genotypic set. We postulate that modulation of rooting depth by root growth angles is important for nitrogen acquisition by positioning roots in soil domains with the greatest nitrogen availability. Genotypic variation in root growth angles and the plasticity of root growth angles in response to nitrogen may be useful in breeding crops with improved nitrogen acquisition.

Novel QTLs for growth angle of seminal roots in wheat (Triticum aestivum L.)

Because plants cannot change their environmental circumstances by changing their location, they must instead adapt to a wide variety of environmental conditions, especially soil conditions. One of the most effective ways for a plant to adapt to a given soil condition is by modifying its root system architecture. We aim to identify the genetic factors controlling root growth angle, a trait that affects root system architecture. The present study consisted of a genetic analysis of the seminal root growth angle in wheat; the parental varieties of the doubled haploid lines (DHLs) used in this study exhibited significantly different root growth directions. Using the ‘basket’ method, the ratio of deep roots (DRR; the proportion of total roots with GA > 45 degrees) was observed for evaluating deep rooting. We were able to identify novel quantitative trait loci (QTLs) controlling the gravitropic and hydrotropic responses of wheat roots. Moreover, we detected one QTL for seminal root number per seedling (RN) on chromosome 5A and two QTLs for seminal root elongation rate (ER) on chromosomes 5D and 7D. Gravitropic and hydrotropic responses of wheat roots, which play a significant role in establishing root system architecture, are controlled by independent genetic factors.

Identification of qSOR1, a major rice QTL involved in soil-surface rooting in paddy fields

Specific Indonesian lowland rice (Oryza sativa L.) cultivars elongate thick primary roots on the soil surface of paddy fields. To clarify the genetic factors controlling soil-surface rooting, we performed quantitative trait locus (QTL) analyses using 124 recombinant inbred lines (RILs) derived from a cross between Gemdjah Beton, an Indonesian lowland rice cultivar with soil-surface roots, and Sasanishiki, a Japanese lowland rice cultivar without soil-surface roots. These cultivars and the RILs were tested for soil-surface rooting in a paddy field. We identified four regions of chromosomes 3, 4, 6, and 7 that were associated with soil-surface rooting in the field. Among them, one major QTL was located on the long arm of chromosome 7. This QTL explained 32.5-53.6% of the total phenotypic variance across three field evaluations. To perform fine mapping of this QTL, we measured the basal root growth angle of crown roots at the seedling stage in seven BC(2)F(3) recombinant lines grown in small cups in a greenhouse. The QTL was mapped between markers RM21941 and RM21976, which delimit an 812-kb interval in the reference cultivar Nipponbare. We have designated this QTL qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1).

Spatio-temporal analysis of development of basal roots of common bean (Phaseolus vulgaris L.)

Temporal development of roots is key to the understanding of root system architecture of plants which influences nutrient uptake, anchorage and plant competition. Using time lapse imaging we analyzed developmental patterns of length, growth angle, depth and curvature of Phaseolus basal roots from emergence till 48 h in two genotypes, B98311 and TLP19 with contrasting growth angles. In both genotypes all basal roots appeared almost simultaneously, but their growth rates varied which accounted for differences in root length. The growth angles of the basal roots fluctuated rapidly during initial development due to oscillatory root growth causing local bends. Beyond 24 h, as the root curvature stabilized, so did the growth angle. Therefore growth angle of basal roots is not a very reliable quantity for characterizing root architecture, especially during early seedling development. Comparatively, tip depth is a more robust measure of vertical distribution of the basal roots even during early seedling development.

Detailed quantitative analysis of architectural traits of basal roots of young seedlings of bean in response to auxin and ethylene.

Vertical placement of roots within the soil determines their efficiency of acquisition of heterogeneous belowground resources. This study quantifies the architectural traits of seedling basal roots of bean (Phaseolus vulgaris), and shows that the distribution of root tips at different depths results from a combined effect of both basal root growth angle (BRGA) and root length. Based on emergence locations, the basal roots are classified in three zones, upper, middle, and lower, with each zone having distinct architectural traits. The genotypes characterized as shallow on BRGA alone produced basal roots with higher BRGA, greater length, and more vertically distributed roots than deep genotypes, thereby establishing root depth as a robust measure of root architecture. Although endogenous indole-3-acetic acid (IAA) levels were similar in all genotypes, IAA and 1-N-naphthylphthalamic acid treatments showed different root growth responses to auxin because shallow and deep genotypes tended to have optimal and supraoptimal auxin levels, respectively, for root growth in controls. While IAA increased ethylene production, ethylene also increased IAA content. Although differences in acropetal IAA transport to roots of different zones can account for some of the differences in auxin responsiveness among roots of different emergence positions, this study shows that mutually dependent ethylene-auxin interplay regulates BRGA and root growth differently in different genotypes. Root length inhibition by auxin was reversed by an ethylene synthesis inhibitor. However, IAA caused smaller BRGA in deep genotypes, but not in shallow genotypes, which only responded to IAA in the presence of an ethylene inhibitor.

Effect of arbuscular mycorrhizal fungal inoculation on root system architecture of trifoliate orange ( Poncirus trifoliata L. Raf.) seedlings

Plant root system architecture is essential characteristics in relation to nutrient acquisition by root system from soil volume. Many environmental factors can affect the establishment of root system architecture, e.g. arbuscular mycorrhizal (AM) fungi. We inoculated the trifoliate orange ( Poncirus trifoliata L. Raf.) seedlings with four AM fungal species in rhizoboxes, with non-inoculated seedlings as control. Using the WinRHIZO ® image analysis system, the root system architecture of seedlings was characterized. Results indicated that AM colonization did not affect the tap root length, the average root diameter, the basal root growth angle in spite that four AM fungal species exerted differential influence on the plant growth. Contrastingly, AM colonization significantly reduced the total root length, the root volume, the root surface area, but promoted the formation of lateral roots of high order. In addition, AM colonization induced more fine roots and less coarse roots. To our knowledge, it is the first report on the influence of AM fungi on the distribution of root diameter size classes. The mechanisms and implication of AM fungi on root system architecture is discussed.

Ethylene modulates genetic, positional, and nutritional regulation of root plagiogravitropism.

Plagiogravitropic growth of roots strongly affects root architecture and topsoil exploration, which are important for the acquisition of water and nutrients. Here we show that basal roots of Phaseolus vulgaris L. develop from 2-3 definable whorls at the root-shoot interface and exhibit position-dependent plagiogravitropic growth. The whorl closest to the shoot produces the shallowest roots, and lower whorls produce deeper roots. Genotypes vary in both the average growth angles of roots within whorls and the range of growth angles, i.e. the difference between the shallowest and deepest basal roots within a root system. Since ethylene has been implicated in both gravitropic and edaphic stress responses, we studied the role of ethylene and its interaction with phosphorus availability in regulating growth angles of genotypes with shallow or deep basal roots. There was a weak correlation between growth angle and ethylene production in the basal rooting zone, but ethylene sensitivity was strongly correlated with growth angle. Basal roots emerging from the uppermost whorl were more responsive to ethylene treatment than the lower-most whorl, displaying shallower angles and inhibition of growth. Ethylene sensitivity is greater for shallow than for deep genotypes and for plants grown with low phosphorus compared with those supplied with high phosphorus. Ethylene exposure increased the range of angles, although deep genotypes grown in low phosphorus were less affected. Our results identify basal root whorl number as a novel architectural trait, and show that ethylene mediates regulation of growth angle by position of origin, genotype and phosphorus availability.

根の伸長角度が異なるコムギ実験系統群の不耕起圃場における収量性

根の伸長角度が異なるコムギ実験系統群の不耕起圃場における収量性

Genotypic Variation in Root Growth Angle in Rice (Oryza sativa L.) and its Association with Deep Root Development in Upland Fields with Different Water Regimes

Deep root development, which is important for the drought resistance in rice (Oryza sativa L.), is a complex trait combining various root morphologies. The objective of this study was to elucidate genotypic variation in deep root development in relation to morphological indicators such as vertical root distribution and root growth angle. Two experiments were conducted: one on upland fields, and one in pots and fields. In experiment 1, the root systems of six rice cultivars on upland fields were physio-morphologically analyzed under different water regimes (irrigated and intermittent drought conditions during panicle development). In experiment 2, cultivar differences in root growth angles were evaluated with 12 cultivars using the basket method under irrigated conditions. No cultivar × environment interactions were found for total root length or deep root length between irrigated and drought conditions in experiment 1. This suggests that constitutive root growth, which is genetically determined, is important for deep root development under intermittent drought conditions during reproductive stage. Among root traits, the deep root ratio (i.e., deep root weight divided by total root weight) was most closely related to deep root length under both water regimes. This suggested that vertical root distribution constitutively affects deep root length. Significant genotypic variation existed in the nodal root diameter and root growth angle of upland rice in experiment 2. It was considered that genotypes with thick roots allocated more assimilates to deep roots through root growth angles higher to the horizontal plane on upland fields. This is the first report on genotypic variation in the root growth angle of rice on upland fields. It should prove useful for rough estimations of genotypic variation in the vertical root distribution of upland rice because root growth angle is rapidly and easily measured.