High-throughput Phenotyping of Wheat Seminal Root Traits in a Breeding Context

Water availability is a major limiting factor for wheat (Triticum aestivum L.) in rain-fed agricultural systems worldwide. Root architecture has important functional implications for the timing and extent of soil water extraction, yet selection for root traits in wheat breeding programs has been largely limited due to the lack of suitable phenotyping methods. The aim of this research was to develop a low-cost high-throughput phenotyping method to facilitate selection for desirable root traits. We developed a method to assess ‘seminal root angle’ and ‘seminal root number’ in seedlings – two proxy traits associated to root architecture of mature wheat plants (1). The method involves measuring the angle between the first pair of seminal roots and the number of roots of wheat seedlings grown in transparent pots (Figure 1). Images captured at 5 to 10 days after sowing are analyzed to calculate seminal root angle and number. Performing this technique under “speed breeding” conditions (plants grown at a density of 600 plants / m2, under controlled temperature and constant light) allows the selection based on the desired root traits of up to 5 consecutive generations within 12 months. Alternatively, when focusing only on germplasm screening, up to 52 successive phenotypic assays can be conducted within 12 months. This approach has been shown to be highly reproducible, it requires little resource (time, space, and labour) and can be used to rapidly enrich breeding populations with desirable alleles for narrow root angle and a high number of seminal roots to indirectly target the selection of deeper root system with higher branching at depth. Such root characteristics are highly desirable in wheat to cope with the climate model projections, especially in summer rainfall dominant regions including some Australian, Indian, South American and African cropping regions, where winter crops mainly rely on deep stored water.

Integrating Rapid Phenotyping and Speed Breeding to Improve Stay-Green and Root Adaptation of Wheat in Changing, Water-Limited, Australian Environments

Temperatures have increased and in-crop rainfall decreased over recent decades in many parts of the Australian wheat cropping region. With these trends set to continue or intensify, improving crop adaptation in the face of climate change is particularly urgent in this, already drought-prone, cropping region. Importantly, improved performance under water-limitation must be achieved while retaining yield potential during more favourable seasons. A multi-trait-based approach to improve wheat yield and yield stability in the face of water-limitation and heat has been instigated in northern Australia using novel phenotyping techniques and a nested association mapping (NAM) approach. An innovative laboratory technique allows rapid root trait screening of hundreds of lines. Using soil grown seedlings, the method offers significant advantages over many other lab-based techniques. Another recently developed method allows novel stay-green traits to be quantified objectively for hundreds of genotypes in standard field trial plots. Field trials in multiple locations and seasons allow evaluation of targeted trait values and identification of superior germplasm. Traits, including yield and yield components are measured for hundreds of NAM lines in rain fed environments under various levels of water-limitation. To rapidly generate lines of interest, the University of Queensland “speed breeding” method is being employed, allowing up to 7 plant generations per annum. A NAM population of over 1000 wheat recombinant inbred lines has been progressed to the F5 generation within 18 months. Genotyping the NAM lines with the genome-wide DArTseq molecular marker system provides up to 40,000 markers. They are now being used for association mapping to validate QTL previously identified in bi-parental populations and to identify novel QTL for stay-green and root traits. We believe that combining the latest techniques in physiology, phenotyping, genetics and breeding will increase genetic progress toward improved adaptation to water-limited environments.

Does Fumigation of Durum Wheat and Semolina with Sulfuryl Fluoride affect Quality of the Grain, Semolina and derived Spaghetti and Bread?

There is no information on the effect of sulfuryl fluoride (SF) on durum wheat technological properties and products made from fumigated durum wheat. Durum wheat and semolina were exposed to a range of SF applications under conditions that might be typically encountered in bulk storage facilities used in many countries. SF greatly reduced the germination percentage of fumigated durum wheat with increasing impact under higher SF concentration, grain moisture content, and fumigation temperature. SF greatly reduced seed germination percentage impacting more the higher the SF concentration. SF had little to no effects on grain test weight, 1000 grain weight, hardness, protein content, semolina ash content and mixograph properties. At the highest SF concentration (31.25 mg/L for 48 h) there was a tendency for pasta cooking loss to be increased but still acceptable while other pasta properties were largely unaffected. Fumigation with SF did not have any impact on the baking properties of a wholemeal durum flour-commercial flour mix. Therefore, SF is not recommended if the grains are to be used as seeds for agricultural production but for the production of semolina, pasta and bread, SF used under typical fumigation conditions has little to no impact on technological properties of durum wheat.

Expansion of high pressure gas into air - A more realistic blast wave model

In this paper, we consider a more realistic model of a spherical blast wave of moderate strength. An arbitrary number of terms for the series solution in each of the regions behind the main shock - the expansion region, the nearly uniform region outside the main expansion and the region between the contact surface and the main shock, have been generated and matched across the boundaries. We then study the convergence of the solution by using Pade approximation. It constitutes a genuine analytic solution for a moderately strong explosion, which, however, does not involve a secondary shock. The pressure distribution behind the shock however shows some significant changes in the location of the tail of the rarefaction and the interface, in comparison to the planar problem. The theory developed for the spherical blasts is also extended to cylindrical blasts. The results are compared with the numerical solution.

Improved k-t BLAST for fast fMR imaging

A popular dynamic imaging technique, k-t BLAST (ktB) is studied here for BAR imaging. ktB utilizes correlations in k-space and time, to reconstruct the image time series with only a fraction of the data. The algorithm works by unwrapping the aliased Fourier conjugate space of k-t (y-f-space). The unwrapping process utilizes the estimate of the true y-f-space, by acquiring densely sampled low k-space data. The drawbacks of this method include separate training scan, blurred training estimates and aliased phase maps. The proposed changes are incorporation of phase information from the training map and using generalized-series-extrapolated training map. The proposed technique is compared with ktB on real fMRI data. The proposed changes allow for ktB to operate at an acceleration factor of 6. Performance is evaluated by comparing activation maps obtained using reconstructed images. An improvement of up to 10 dB is observed in thePSNR of activation maps. Besides, a 10% reduction in RMSE is obtained over the entire time series of fMRI images. Peak improvement of the proposed method over ktB is 35%, averaged over five data sets. (C)2010 Elsevier Inc. All rights reserved.

Plastic response of orthotropic spherical shells under blast loading

The plastic response of a segment of a simply supported orthotropic spherical shell under a uniform blast loading applied on the convex surface of the shell is presented. The blast is assumed to impart a uniform velocity to the shell surface initially. The material of the shell is orthotropic obeying a modified Tresca yield hypersurface conditions and the associated flow rules. The deformation of the shell is determined during all phases of its motion by considering the motion of plastic hinges in different regimes of flow. Numerical results presented include the permanent deformed configuration of the shell and the total time of shell response for different degrees of orthotropy. Conclusions regarding the plastic behaviour of spherical shells with circumferential and meridional stiffening under uniform blast load are presented.

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

Owing to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. Intermediate sequences possess sequence features of more than one protein and facilitate detection of remotely related proteins. We have demonstrated recently the employment of Cascade PSI-BLAST where we perform PSI-BLAST for many 'generations', initiating searches from new homologues as well. Such a rigorous propagation through generations of PSI-BLAST employs effectively the role of intermediates in detecting distant similarities between proteins. This approach has been tested on a large number of folds and its performance in detecting superfamily level relationships is similar to 35% better than simple PSI-BLAST searches. We present a web server for this search method that permits users to perform Cascade PSI-BLAST searches against the Pfam, SCOP and SwissProt databases. The URL for this server is http://crick.mbu.iisc.ernet.in/similar to CASCADE/CascadeBlast.html.

Self-similar solutions of laser produced blast waves

The aerodynamics of the blast wave produced by laser ablation is studied using the piston analogy. The unsteady one-dimensional gasdynamic equations governing the flow an solved under assumption of self-similarity. The solutions are utilized to obtain analytical expressions for the velocity, density, pressure and temperature distributions. The results predict. all the experimentally observed features of the laser produced blast waves.

BSSB: BLAST Server for Structural Biologists

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processing BLAST output, but none of them provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed tool BLAST Server for Structural Biologists (BSSB), which maps a BLAST output onto the three-dimensional structure of the subject protein. The three-dimensional structure of the subject protein is represented using a three-color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three-dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence-structure correlation. Furthermore, the additional structure-level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.

Influence of metalaxyl on Glomus fasciculatum associated with wheat (Triticum aestivum L)

Soil incorporation of metalaxyl [methyl N-(2-methoxyacetyl)-N-(2,6,xylyl)-DL-alaninate] significantly enhanced root colonization of the vesicular-arbuscular (VA) mycorrhizal fungi Glomus fasciculatum associated with wheat. The stimulatory response of VA mycorrhizal fungi to low concentration of metalaxyl resulted in increased plant biomass production, nutrient uptake and grain yield of wheat. However, higher concentrations of metalaxyl, particularly 2.5 ppm of metalaxyl affected the mycorrhizal infection and seed yield of wheat, Addition of urban compost to an extent ameliorated the toxic effect of fungicide on VA mycorrhizal colonization, plant growth and yield of wheat when compared to unamended soil.

Mathematical modelling of divided blast cupola

A pseudo 2-D mathematical model has been developed to simulate a cupola with one row and two rows of tuyere. The simulation results predicted higher spout temperature and combustion ratio for cupola with two rows of tuyere compared to that with one row. Further, the model has been used to study the effect of the distance of separation between the two rows of tuyere on cupola performance. The computed results shows that the spout temperature increases with tuyere level separation and attains the maximum at an optimum distance of separation between two rows of tuyere. Above the optimum, the spout temperature starts decreasing. The exit gas temperature and combustion ratio increases monotonously with the increase in tuyere level separation. These results agree well with the reported experimental observations. The mechanism behind the improved cupola performance with two rows of tuyere has been deduced from the computed temperature and composition profiles inside the cupola.