Ice-cap. A high-throughput method for capturing plant tissue samples for genotype analysis

High-throughput genotype screening is rapidly becoming a standard research tool in the post-genomic era. A major bottleneck currently exists, however, that limits the utility of this approach in the plant sciences. The rate-limiting step in current high-throughput pipelines is that tissue samples from living plants must be collected manually, one plant at a time. In this article I describe a novel method for harvesting tissue samples from living seedlings that eliminates this bottleneck. The method has been named Ice-Cap to reflect the fact that ice is used to capture the tissue samples. The planting of seeds, growth of seedlings, and harvesting of tissue are all performed in a 96-well format. I demonstrate the utility of this system by using tissue harvested by Ice-Cap to genotype a population of Arabidopsis seedlings that is segregating a previously characterized mutation. Because the harvesting of tissue is performed in a nondestructive manner, plants with the desired genotype can be transferred to soil and grown to maturity. I also show that Ice-Cap can be used to analyze genomic DNA from rice (Oryza sativa) seedlings. It is expected that this method will be applicable to high-throughput screening with many different plant species, making it a useful technology for performing marker assisted selection.     

In vitro freezing in microtitre plates applied to tobacco plants transformed with the inaZ gene of Pseudomonas syringae

High throughput assays have been developed to measure the ice nucleation activity of transgenic tobacco, Nicotiana tabacum L. cv. Petit Havana SR1 plants expressing the ice nucleation gene, inaZ, from Pseudomonas syringae at a young seedling stage, as well as in leaf tissue. Both assays are carried out in 96-well microtitre plates. The first assay involves direct seeding in vitro, one seed per microtitre plate well containing Murashige-Skoog agar. When seedlings reach the two-leaf stage, they are exposed to freezing temperatures by floating the plates on a circulating alcohol bath set at temperatures colder than -9 degrees C. The second assay involves placing small leaf discs individually in microtitre plate wells containing sterile distilled water. The assays complement each other, give highly reproducible results, are technically simple and enable the detection of freezing events in large numbers of plants. The utility and limitations of these assays are discussed.     

An In Vitro Test for Temperature Sensitivity and Resistance to Meloidogyne incognita in Tomato

An in vitro root explant tissue culture technique is described for determining susceptibility of tomato (Lycopersicon esculentum Mill.) breeding lines and cultivars to the root-knot nematode Meloidogyne incognita. Root explants were taken from 2-day-old seedlings cultured for 30 days at 28 C on Gamborg''s B-5 medium with or without nematode inoculum. The remaining portion of the root and stem from the excised root explants was transferred to soil in pots and grown to maturity in the greenhouse. In vitro root explants were evaluated for growth and occurrence of juveniles, adults, and egg masses. The regenerated plants were used to produce more seed, The proposed technique is simple, reliable, and adapted to routine screening of large numbers of F₁ and F₂ samples, and it utilizes less space than tests performed on intact plants in the greenhouse or growth chamber. Evidence is presented also on the breakdown of resistance to M. incognita under high temperature stress using this in vitro root explant technique.     

Rapid,noninvasive screening for perturbations of metabolism and plant growth using chlorophyll fluorescence imaging

A rapid, noninvasive technique involving imaging of chlorophyll fluorescence parameters for detecting perturbations of leaf metabolism and growth in seedlings is described. Arabidopsis seedlings were grown in 96-well microtitre plates for 4 d and then treated with eight herbicides with differing modes of action to induce perturbations in a range of different metabolic processes. Imaging of chlorophyll fluorescence emissions from 96 seedlings growing on a microtitre plate enabled images of a number of fluorescence parameters to be rapidly and simultaneously produced for the plants in each well. Herbicideinduced perturbations in metabolism, even in metabolic reactions not directly associated with photosynthetic metabolism, were detected from the changes in the images of fluorescence parameters considerably before any visual effects on seedling growth were observed. Evaluations of seedling growth were made from measurements of the area of chlorophyll fluorescence emission in images of plants growing in the 96-well plates. Decreased seedling growth related directly to herbicideinduced changes in the imaged chlorophyll fluorescence parameters. The applicability of this rapid-screening technique for metabolic perturbations in monocotyledonous species was demonstrated by treating Agrostis tenuis seedlings with Imazapyr, an inhibitor of branched-chain amino acid synthesis.     

A Bioassay to Estimate Root Penetration by Nematodes

An in vitro bioassay with a 96-well microtiter plate was used to study the effect of lectins on burrowing nematode penetration of citrus roots. In each well, one 4-mm root segment, excised from the zone of elongation of rough lemon roots, was buried in 0.88 g dry sand. Addition of a Radopholus citrophilus suspension containing ca. 300 nematodes in 50 μ1 test solution completely moistened the sand in each well. The technique assured uniform treatment concentration throughout the medium. Within 16-24 hours, burrowing nematodes penetrated citrus root pieces, primarily through the cut ends. The lectins (100 μg/ml) Concanavalin A (Con A), soybean agglutinin (SBA), wheat germ agglutinin (WGA), and Lotus tetragonolobus agglutinin (LOT) stimulated an increase in penetration of citrus root segments by Radopholus citrophilus. Concentrations as low as 12.5 μg/ml Con A, LOT, and WGA stimulated burrowing nematode penetration of citrus roots. Heat denaturation of the lectins reversed their effect on penetration; however, incubation of nematodes in lectin (25 μg/ml) with 25 mM competitive sugars did not. The reason for enhanced penetration associated with lectins is unclear.     

Growth,root colonization and nutrient status of Helianthemum sessiliflorum Desf. inoculated with a desert truffle Terfezia boudieri Chatin

This study aims to investigate the effects of inoculation using Terfezia boudieri Chatin ascospores (ectomycorrhizal fungus) on growth, root colonization and nutrient status of Helianthemum sessiliflorum Desf. seedlings grown in pots on two-soil types (gypseous and sandy loam). Mycorrhizal seedlings had significantly increased their height and leaf number compared to non-mycorrhizal ones. Regardless of mycorrhizal inoculation treatments, the plants growing on gypseous soil showed higher growth as compared to sandy loam one. It appears that inoculation with T. boudieri changed root morphology, increasing branching of first-order lateral roots of H. sessiliflorum seedlings. The highest root mycorrhizal colonization was recorded in inoculated seedlings on sandy loam soil (89%) when compared to gypseous one (52%). N, P and K concentrations in mycorrhizal seedlings were significantly improved by fungal inoculation. It can be concluded that inoculation of H. sessiliflorum with T. boudieri increased growth attributes and improved plant nutritional status.     

Carbon Partitioning in Soybean Infected with Meloidogyne incognita and M. javanica

Seven-day-old seedlings of two cultivars (Cristalina and UFV ITM1) of Glycine max were inoculated with 0, 3,000, 9,000, or 27,000 eggs of Meloidogyne incognita race 3 or M. javanica and maintained in a greenhouse. Thirty days later, plants were exposed to ¹⁴CO₂ for 4 hours. Twenty hours after ¹⁴CO₂ exposure, the root fresh weight, leaf dry weight, nematode eggs per gram of root, total and specific radioactivity of carbohydrates in roots, and root carbohydrate content were evaluated. Meloidogyne javanica produced more eggs than M. incognita on both varieties. A general increase in root weight and a decrease in leaf weight with increased inoculum levels were observed. Gall tissue appeared to account for most of the root mass increase in seedlings infected with M. javanica. For both nematodes there was an increase of total radioactivity in the root system with increased levels of nematodes, and this was positively related to the number of eggs per gram fresh weight and to the root fresh weight, but negatively related to leaf dry weight. In most cases, specific radioactivities of sucrose and reducing sugars were also increased with increased inoculum levels. Highest specific radioactivities were observed with reducing sugars. Although significant changes were not observed in endogenous levels of carbohydrates, sucrose content was higher than reducing sugars. The data show that nematodes are strong metabolic sinks and significantly change the carbon distribution pattern in infected soybean plants. Carbon partitioning in plants infected with nematodes may vary with the nematode genotype.     

Effects of Population Densities of Meloidogyne hapla on Growth and Yield of Tomato

Growth and yield of ''Veebrite'' tomato were studied in 20-cm (i.d.) clay-tile microplots containing initially 260, 1,840, 6,120, or 27,950 Meloidogyne hapla larvae/kg of soil. Low nematode numbers stimulated, and the highest nematode population suppressed, vegetative plant growth. More tomatoes, with a higher total weight, were harvested from plants infested with 260 and 1,840 nematode larvae at planting than from those with initial densities of 6,120 and 27,950 larvae. At the two highest densities, the cumulative fruit production (weight) was suppressed by 10% and 40%, respectively. The increase in growth and yield at the lower densities appeared to be due to an increase in the size of the root systent. However, at the higher densities, yield was no longer directly related to root weight. The reproduction factor of M. hapla was negatively correlated with initial density; for the lowest and highest initial densities, it was 96X and 7X at midseason, and 354X and 3X at harvest, respectively. The equilibrium density was 63,000 larvae/kg of soil; initial densities larger than 2,000 larvae/kg of soil may require control.     

Influence of Mycorrhizal Fungus, Phosphorus,and Burrowing Nematode Interactions on Growth of Rough Lemon Citrus Seedlings

Rough lemon seedlings were grown in mycorrhizal-infested or phosphorus-amended soil (25 and 300 mg P/kg) in greenhouse experiments. Plants Were inoculated with the citrus burrowing nematode, Radopholus citrophilus (0, 50, 100, or 200 nematodes per pot). Six months later, mycorrhizal plants and nonmycorrhizal, high-P plants had larger shoot and root weights than did non-mycorrhizal, low-P plants. Burrowing nematode population densities were lower in roots of mycorrhizal or nonmycorrhizal, high-P plants than in roots of nonmycorrhizal, low-P plants; however, differences in plant growth between mycorrhizal and nonmycorrhizal plants were not significant with respect to initial nematode inoculum densities. Phosphorus content in leaf tissue was significantly greater in mycorrhizal and nonmycorrhizal, high-P plants compared with nonmycorrhizal, low-P plants. Nutrient concentrations of K, Mg, and Zn were unaffected by nematode parasitism, whereas P, Ca, Fe, and Mn were less in nematode-infected plants. Enhanced growth associated with root colonization by the mycorrhizal fungus appeared to result from improved P nutrition and not antagonism between the fungus and the nematode.     

Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, phosphorus, sulfate and trace elements that plants acquire from the soil. If we want to develop sustainable approaches to producing high crop yield, we need to better understand how the root develops, takes up a wide spectrum of nutrients, and interacts with symbiotic and pathogenic organisms. To accomplish these goals, we need to be able to explore roots in microscopic detail over time periods ranging from minutes to days.We developed the RootChip, a polydimethylsiloxane (PDMS)- based microfluidic device, which allows us to grow and image roots from Arabidopsis seedlings while avoiding any physical stress to roots during preparation for imaging¹ (Figure 1). The device contains a bifurcated channel structure featuring micromechanical valves to guide the fluid flow from solution inlets to each of the eight observation chambers². This perfusion system allows the root microenvironment to be controlled and modified with precision and speed. The volume of the chambers is approximately 400 nl, thus requiring only minimal amounts of test solution.Here we provide a detailed protocol for studying root biology on the RootChip using imaging-based approaches with real time resolution. Roots can be analyzed over several days using time lapse microscopy. Roots can be perfused with nutrient solutions or inhibitors, and up to eight seedlings can be analyzed in parallel. This system has the potential for a wide range of applications, including analysis of root growth in the presence or absence of chemicals, fluorescence-based analysis of gene expression, and the analysis of biosensors, e.g. FRET nanosensors³.     

A simple physiologically relevant double-agar-layer method for post-germination treatment of seedlings

Arabidopsis thaliana is frequently grown on semisolid medium in Petri dishes, for various experiments that usually consist of two stages on two distinct growth media. Seedlings are germinated under favorable conditions followed by their transfer to another medium containing the given treatment(s). This often causes secondary effects on seedlings due to root shock, or direct and unavoidable contact of the shoot with the second medium. We have developed a simple and efficient method for the transfer of seedlings grown on semisolid medium with minimal damage. In this double-agar-layer method, seeds are germinated on a thin growth-medium-containing agar layer. Subsequently, medium blocks containing the embedded seedlings are excised and placed on the second semisolid medium supplemented with the treatment agent. Differential agar concentrations allow easy penetration of the roots into the second medium, but do not allow the shoots to come into contact with it. This unique method offers several advantages over others that are in common use, in which the seedlings are individually transferred to the second medium or alternatively grown on transfer-carrier matrices, such as filter paper, mesh and cellophane. In the presented method, the entire root system faces the growth medium, the shoots are surrounded by air at all growth stages and transfer of the seedlings is much easier. In addition, a large number of seedlings can be transferred in a single step, without stressing the plants or damaging the delicate root system. This method can also be applied to other plant species grown on semisolid media.     

Microplate screening assay for binding of ligands to bovine or reindeer beta-lactoglobulins

Several analytical methods have been used to determine whether ligands bind to bovine beta-lactoglobulin (betaLG). The most common methods are based on fluorescence quenching. We have miniaturised this method from a quartz cell to a 96-well plate. The miniaturisation was evaluated using retinol. The binding constants between the two methods demonstrated a good correlation. The 96-well plate method is much faster and allows many references to be used in the same analysis. The miniaturised method was used to study the binding of three different ligands (4-HPR, arotinoid, warfarinyl palmitate) modelled to bind to betaLG. The binding data showed that all of these ligands bound to betaLG. The method was further used to demonstrate that reindeer betaLG could also bind the four ligands in the same way as bovine betaLG. Because one aim is to use bovine and reindeer betaLG as a binder molecule for aliments in e.g. functional food or for drugs, the influence of pH was also studied and demonstrated that short-term acidic conditions had only a slight effect on the binding properties.     

Cloning grills: High throughput cloning for structural genomics

Cloning grills are aluminum grids designed to divide an agar plate into segments, thereby multiplying the number of E. coli cultures which can be streaked out on a single plate. The grills are autoclaved and placed in square petri dishes immediately after hot agar is poured. When the agar solidifies, the grill remains embedded in the media, and each of the 12 lanes accommodates the streaking out of a single culture. As the spacing of the grill lanes is the same as that of a 96-well plate, 12 cultures can be streaked at a time using a 12-channel pipette. This allows a plate of 96 cultures to be rapidly and accurately plated for colony isolation on only eight agar plates.     

Cereal DNA: A rapid high-throughput extraction method for marker assisted selection

A rapid, automated and novel method is presented to extract DNA suitable for polymerase chain reaction (PCR) from small amounts of cereal leaf tissue in a high-throughput cost-effective way. The method uses a 96-well plate in which leaf samples are frozen, mechanically crushed using a matrix mill, macerated in alkali and subsequently neutralized. The method was used routinely with barley and wheat leaf samples and the extracted material was used to screen for specific traits of interests, including barley yellow dwarf virus resistance and β-amylase activity in barley and stem rust resistance in wheat. This system allows complete PCR analysis of 384 seedlings or more by one person in a day.     

Influence of soil water deficits on root growth of cotton seedlings

Summary Cotton (Gossypium hirsutum L. cv. H14) seedlings were raised in soil of differing soil water content in specially designed pots in which the roots had access to freely available water and nutrients located 2.5 cm below the base of the soil core. The time for root emergence from the soil core and the rate of root growth were measured daily from sowing to harvest. The root and shoot dry weight and leaf water potential were measured at the final harvest 16 days after sowing. As soil water content decreased, the root emerged from the soil earlier and the initial rate of root elongation was faster. In spite of the availability of freely available water, the plants in the soil at low water contents had significantly lower leaf water potentials than those in soil at high water contents. The root: shoot ratio increased as the soil water content decreased. This arose from an absolute increase in root weight, with shoot weight not being significantly affected.     

Multichannel plating unit for high-throughput plating of cell cultures

High-throughput genomic approaches to gene function or target identification have led to the development and implementation of the 96-well format for many standard molecular biology manipulations. The apparatus described here, a Multichannel Plating Unit, is designed to plate out individual cultures efficientlyfrom standard 96-well culture blocks. Following transformation, aliquots of culture are loaded onto sterile beads that are rolled along individual channels of agar media. After the beads traverse the channel, they drop into the exit alley for disposal via an exit pore. The apparatus presented has 12 individual lanes, and the spacing is compatible with a standard 12-channel pipettor Thus, the unit allows for the rapid plating of 12 individual cultures at a time. For one 96-well block of transformants, this method reduces the labeling and plating effort from 96 culture dishes that are spread individually to eight multichannel plates. The savings in time, materials, and storage space is significant     

Population Dynamics,Root Penetration,and Feeding Behavior of Pratylenchus agilis in Monoxenic Root Cultures of Corn,Tomato, and Soybean

Population dynamics, rate of root penetration, and external root feeding behavior of Pratylenchus agilis (Pa) in monoxenic cultures of intact corn seedlings and root explants of corn, tomato, and soybean were studied. In descending order of suitability as hosts were I. O. Chief corn, Rutgers tomato, and Williams soybean. Soybean entries Kent, Pickett 71, PI 90763, and Essex were poor hosts. Numbers of eggs and vermiform Pa in the agar medium indicated total fecundity and host suitability. Agar, sand, or soil as support media did not appear to affect Pa root penetration, but the rate of corn root growth did. Whereas most vermiform Pa and eggs were in roots, substantial numbers appeared able to feed and complete their life cycle as ectoparasites on root epidermal cells and root hairs.     

Mycorrhizal inoculant alleviates salt stress in<Emphasis Type="Italic"> Sesbania aegyptiaca</Emphasis> and<Emphasis Type="Italic"> Sesbania grandiflora</Emphasis> under field conditions: evidence for reduced sodium and improved magnesium uptake

A field experiment was conducted to examine the effect of the arbuscular mycorrhizal fungus Glomus macrocarpum and salinity on growth of Sesbania aegyptiaca and S. grandiflora. In the salt-stressed soil, mycorrhizal root colonisation and sporulation was significantly higher in AM-inoculated than in uninoculated plants. Mycorrhizal seedlings had significantly higher root and shoot dry biomass production than non-mycorrhizal seedlings grown in saline soil. The content of chlorophyll was greater in the leaves of mycorrhiza-inoculated as compared to uninoculated seedlings. The number of nodules was significantly higher in mycorrhizal than non-mycorrhizal plants. Mycorrhizal seedling tissue had significantly increased concentrations of P, N and Mg but lower Na concentration than non-mycorrhizal seedlings. Under salinity stress conditions both Sesbania sp. showed a high degree of dependence on mycorrhizae, increasing with the age of the plants. The reduction in Na uptake together with a concomitant increase in P, N and Mg absorption and high chlorophyll content in mycorrhizal plants may be important salt-alleviating mechanisms for plants growing in saline soil.     

Efficacy of a Novel Nematicidal Seed Treatment against Meloidogyne incognita on Cotton

The efficacy of abamectin as a seed treatment for control of Meloidogyne incognita on cotton was evaluated in greenhouse, microplot, and field trials in 2002 and 2003. Treatments ranging from 0 to 100 g abamectin/100 kg seed were evaluated. In greenhouse tests 35 d after planting (DAP), plants from seed treated with abamectin were taller than plants from nontreated seed, and root galling severity and nematode reproduction were lower where treated seed were used. The number of second stage juveniles that had entered the roots of plants from seed treated with 100 g abamectin/kg seed was lower during the first 14 DAP than with nontreated seed. In microplots tests, seed treatment with abamectin and soil application of aldicarb at 840 g/kg of soil reduced the number of juveniles penetrating seedling roots during the first 14 DAP compared to the nontreated seedlings. In field plots, population densities of M. incognita were lower 14 DAP in plots that received seed treated with abamectin at 100 g/kg seed than where aldicarb (5.6 kg/ha) was applied at planting. Population densities were comparable for all treatments, including the nontreated controls, at both 21 DAP and harvest. Root galling severity did not differ among treatments at harvest.     

Simple Tests to Detect Errors in High-Throughput Genotype Data in the Molecular Laboratory

With the advent of high-density DNA marker data sets for the mouse and other model systems, 100 or more genotypes are routinely generated from large groups of mice. Issues of the accuracy and reliability of the genotyping are extremely important but often not addressed until genetic analysis is conducted. Simple tests that rely on the robust predictions arising from Mendelian genetics can be made quickly in the molecular laboratory as the data are generated, and require only a spreadsheet program. In this report, genotype data from 392 mice tested at 96 marker sites were analyzed for errors that are typical when handling large volumes of data generated in a repetitive process. The testing consisted of: (1) repeating the genotyping of approximately 1% of the samples; (2) examining the deviation from the expected segregation ratio (1:2:1) on a marker-by-marker basis; and (3) testing the correlation of the genotype at one marker with that at neighboring genetic markers on a chromosome. These three steps allowed analysis at the level of the microtiter plate, where errors are most likely to occur. A set of 96 dinucleotide repeat markers that are polymorphic between the C57BL/6J and DBA/2J mouse strains and can be multiplexed is reported for use in other genotyping projects.