Complementary Phenotyping of Maize Root System Architecture by Root Pulling Force and X-Ray Imaging.

The root system is critical for the survival of nearly all land plants and a key target for improving abiotic stress tolerance, nutrient accumulation, and yield in crop species. Although many methods of root phenotyping exist, within field studies, one of the most popular methods is the extraction and measurement of the upper portion of the root system, known as the root crown, followed by trait quantification based on manual measurements or 2D imaging. However, 2D techniques are inherently limited by the information available from single points of view. Here, we used X-ray computed tomography to generate highly accurate 3D models of maize root crowns and created computational pipelines capable of measuring 71 features from each sample. This approach improves estimates of the genetic contribution to root system architecture and is refined enough to detect various changes in global root system architecture over developmental time as well as more subtle changes in root distributions as a result of environmental differences. We demonstrate that root pulling force, a high-throughput method of root extraction that provides an estimate of root mass, is associated with multiple 3D traits from our pipeline. Our combined methodology can therefore be used to calibrate and interpret root pulling force measurements across a range of experimental contexts or scaled up as a stand-alone approach in large genetic studies of root system architecture.

Calibration and validation of the DNDC model to estimate nitrous oxide emissions and crop productivity for a summer maize-winter wheat double cropping system in Hebei, China.

The main aim of this paper was to calibrate and evaluate the DeNitrification-DeComposition (DNDC) model for estimating N2O emissions and crop productivity for a summer maize-winter wheat double cropping system with different N fertilizer rates in Hebei, China. The model's performance was assessed before and after calibration and model sensitivity was investigated. The calibrated and validated DNDC performed effectively in estimating cumulative N2O emissions (coefficient of determination (1:1 relationship; r2) = 0.91; relative deviation (RD) = -13 to 16%) and grain yields for both crops (r2 = 0.91; RD = -21 to 7%) from all fertilized treatments, but poorly estimated daily N2O patterns. Observed and simulated results showed that optimal N fertilizer treatment decreased cumulative N2O flux, compared to conventional N fertilizer, without a significant impact on grain yields of the summer maize-winter wheat double cropping system. The high sensitivity of the DNDC model to rainfall, soil organic carbon and temperature resulted in significant overestimation of N2O peaks during the warm wet season. The model also satisfactorily estimated daily patterns/average soil temperature (o C; 0-5 cm depth) (r2 = 0.88 to 0.89; root mean square error (RMSE) = 4 °C; normalized RMSE (nRMSE) = 25% and index of agreement (d) = 0.89-0.97) but under-predicted water filled pore space (WFPS; %; 0-20 cm depth) (r2 = 0.3 to 0.4) and soil ammonium and nitrate (exchangeable NH4+ & NO3-; kg N ha-1; r2 = 0.97). With reference to the control treatment (no N fertilizer), DNDC was weak in simulating both N2O emissions and crop productivity. To be further improved for use under pedo-climatic conditions of the summer maize-winter wheat double cropping system we suggest future studies to identify and resolve the existing problems with the DNDC, especially with the control treatment.

To what extent is climate change adaptation a novel challenge for agricultural modellers?

Modelling is key to adapting agriculture to climate change (CC), facilitating evaluation of the impacts and efficacy of adaptation measures, and the design of optimal strategies. Although there are many challenges to modelling agricultural CC adaptation, it is unclear whether these are novel or, whether adaptation merely adds new motivations to old challenges. Here, qualitative analysis of modellers' views revealed three categories of challenge: Content, Use, and Capacity. Triangulation of findings with reviews of agricultural modelling and Climate Change Risk Assessment was then used to highlight challenges specific to modelling adaptation. These were refined through literature review, focussing attention on how the progressive nature of CC affects the role and impact of modelling. Specific challenges identified were: Scope of adaptations modelled, Information on future adaptation, Collaboration to tackle novel challenges, Optimisation under progressive change with thresholds, and Responsibility given the sensitivity of future outcomes to initial choices under progressive change.

Husk to caryopsis adhesion in barley is influenced by pre- and post-anthesis temperatures through changes in a cuticular cementing layer on the caryopsis.

BACKGROUND: At ripeness, the outer husk of "covered" barley grains firmly adheres to the underlying caryopsis. A cuticular cementing layer on the caryopsis is required for husk adhesion, however the quality of adhesion varies significantly among cultivars which produce the cementing layer, resulting in the economically important malting defect, grain skinning. The composition of the cementing layer, and grain organ development have been hypothesised to influence the quality of husk adhesion. Plants of Hordeum vulgare 'Concerto' were grown at different temperatures pre- and post-anthesis to effect changes in the development of the husk, caryopsis and cuticular cementing layer, to determine how these variables influence the quality of husk-to-caryopsis adhesion. RESULTS: Warm conditions pre-anthesis decreased the quality of husk adhesion, and consequently increased the incidence of grain skinning. Cool post-anthesis conditions further decreased the quality of husk adhesion. The composition of the cementing layer, rather than its structure, differed with respect to husk adhesion quality. This cementing layer was produced at the late milk stage, occurring between nine and 29 days post-anthesis, conditional on the temperature-dependent growth rate. The compounds octadecanol, tritriacontane, campesterol and ß-sitosterol were most abundant in caryopses with high-quality husk adhesion. The differences in adhesion quality were not due to incompatible husk and caryopsis dimensions affecting organ contact. CONCLUSIONS: This study shows that husk-to-caryopsis adhesion is dependent on cementing layer composition, and implies that this composition is regulated by temperature before, and during grain development. Understanding this regulation will be key to improving husk-to-caryopsis adhesion.

Relative emissions intensity of dairy production systems: employing different functional units in life-cycle assessment.

This study aimed to assess the merit and suitability of individual functional units (FU) in expressing greenhouse gas emissions intensity in different dairy production systems. An FU provides a clearly defined and measurable reference to which input and output data are normalised. This enables the results from life-cycle assessment (LCA) of different systems to be treated as functionally equivalent. Although the methodological framework of LCA has been standardised, selection of an appropriate FU remains ultimately at the discretion of the individual study. The aim of the present analysis was to examine the effect of different FU on the emissions intensities of different dairy production systems. Analysis was based on 7 years of data (2004 to 2010) from four Holstein-Friesian dairy systems at Scotland's Rural College's long-term genetic and management systems project, the Langhill herd. Implementation of LCA accounted for the environmental impacts of the whole-farm systems and their production of milk from 'cradle to farm gate'. Emissions intensity was determined as kilograms of carbon dioxide equivalents referenced to six FU: UK livestock units, energy-corrected milk yield, total combined milk solids yield, on-farm land used for production, total combined on- and off-farm land used for production, and the proposed new FU-energy-corrected milk yield per hectare of total land used. Energy-corrected milk was the FU most effective for reflecting differences between the systems. Functional unit that incorporated a land-related aspect did not find difference between systems which were managed under the same forage regime, despite their comprising different genetic lines. Employing on-farm land as the FU favoured grazing systems. The proposed dual FU combining both productivity and land use did not differentiate between emissions intensity of systems as effectively as the productivity-based units. However, this dual unit displayed potential to quantify in a simple way the positive or negative outcome of trade-offs between land and production efficiencies, in which improvement in emissions intensity using one FU may be accompanied by deterioration using another FU. The perceived environmental efficiencies of different dairy production systems in terms of their emissions intensities were susceptible to change based upon the FU employed, and hence the FU used in any study needs to be taken into account in the interpretation of results.

Nitrous oxide emissions from cattle excreta applied to a Scottish grassland: effects of soil and climatic conditions and a nitrification inhibitor.

Dung and urine excreted onto grasslands are a major source of nitrous oxide (N2O). These N2O emissions stem from inefficient utilisation of nitrogen (N) ingested by ruminants, and the inability of pasture to utilise the deposited N. Predicted growth in dairy and meat consumption means that there is a requirement to quantify N2O emissions, and investigate emission reduction mechanisms. Three 12 month 'seasonal' experiments were undertaken at Crichton, SW Scotland, where N2O emissions were measured from applications of cattle urine, dung, artificial urine and urine+a nitrification inhibitor (NI), dicyandiamide (DCD). The three application timings were 'spring', 'summer' and 'autumn', representative of early-, mid- and late grazing seasons. N2O emissions were measured from static chambers for 12 months. The aim was to quantify emissions from cattle excreta, and determine their dependence on the season of application, and the respective contribution of dung and urine to total excreta emissions. Measurement from NI amended urine was made to assess DCD's potential as an emission mitigation tool. Emissions were compared to the IPCC's default emission factor (EF) of 2% for cattle excreted N. Mean annual cumulative emissions from urine were the highest when applied in summer (5034 g N2O-N ha(-1)), with lower emissions from spring (1903 g N2O-N ha(-1)) and autumn (2014 g N2O-N ha(-1)) application, most likely due to higher temperatures and soil moisture conducive to both nitrification and denitrification in the summer months. Calculated EFs were significantly greater from urine (1.1%) than dung (0.2%) when excreta was applied in summer, and EFs varied with season of application, but in all experiments were lower than the IPCC default of 2%. These results support both lowering and disaggregating this EF into individual EFs for dung and urine. Addition of DCD to urine caused no significant reduction in emissions, suggesting that more research is required into its use as a mitigation option.

Review and analysis of global agricultural N2O emissions relevant to the UK.

As part of a UK government funded research project to update the UK N2O inventory methodology, a systematic review of published nitrous oxide (N2O) emission factors was carried out of non-UK research, for future comparison and synthesis with the UK measurement based evidence base. The aim of the study is to assess how the UK IPCC default emission factor for N2O emissions derived from synthetic or organic fertiliser inputs (EF1) compares to international values reported in published literature. The availability of data for comparing and/or refining the UK IPCC default value and the possibility of analysing sufficient auxiliary data to propose a Tier 2 EF1 reporting strategy is evaluated. The review demonstrated a lack of consistency in reporting error bounds for fertiliser-derived EFs and N2O flux data with 8% and 44% of publications reporting EF and N2O flux error bounds respectively. There was also poor description of environmental (climate and soil) and experimental design auxiliary data. This is likely to be due to differences in study objectives, however potential improvements to soil parameter reporting are proposed. The review demonstrates that emission factors for agricultural-derived N2O emissions ranged -0.34% to 37% showing high variation compared to the UK Tier 1 IPCC EF1 default values of 1.25% (IPCC 1996) and 1% (IPPC 2006). However, the majority (83%) of EFs reported for UK-relevant soils fell within the UK IPCC EF1 uncertainty range of 0.03% to 3%. Residual maximum likelihood (REML) analysis of the data collated in the review showed that the type and rate of fertiliser N applied and soil type were significant factors influencing EFs reported. Country of emission, the length of the measurement period, the number of splits, the crop type, pH and SOC did not have a significant impact on N2O emissions. A subset of publications where sufficient data was reported for meta-analysis to be conducted was identified. Meta-analysis of effect sizes of 41 treatments demonstrated that the application of fertiliser has a significant effect on N2O emissions in comparison to control plots and that emission factors were significantly different to zero. However no significant relationships between the quantity of fertiliser applied and the effect size of the amount of N2O emitted from fertilised plots compared to control plots were found. Annual addition of fertiliser of 35 to 557 kg N/ha gave a mean increase in emissions of 2.02 ± 0.28 g N2O/ha/day compared to control treatments (p<0.01). Emission factors were significantly different from zero, with a mean emission factor estimated directly from the meta analysis of 0.17 ± 0.02%. This is lower than the IPCC 2006 Tier 1 EF1 value of 1% but falling within the uncertainty bound for the IPCC 2006 Tier 1 EF1 (0.03% to 3%). As only a small number of papers were viable for meta analysis to be conducted due to lack of reporting of the key controlling factors, the estimates of EF in this paper cannot include the true variability under conditions similar to the UK. Review-derived EFs of 0.34% to 37% and mean EF from meta-analysis of 0.17 ± 0.02% highlight variability in reporting EFs depending on the method applied and sample size. A protocol of systematic reporting of N2O emissions and key auxiliary parameters in publications across disciplines is proposed. If adopted this would strengthen the community to inform IPCC Tier 2 reporting development and reduce the uncertainty surrounding reported UK N2O emissions.

A novel mechanism of abscission in fronds of Lemna minor L. and the effect of silver ions.

Lemna minor L. (duckweed) forms colonies through vegetative propagation because mother fronds remain connected for some time with their daughter fronds by stipes. The colony size is controlled by abscission of stipes at a specific preformed abscission zone. Application of silver ions (Ag(+) ) enhances the rate of frond abscission, thus resulting in smaller colonies. The mechanism behind this process has not yet been identified. Silver caused an abscission response that saturated after 7 h of treatment. The half-maximal effective concentration was 0.72 µm Ag(+) for the standard clone, L. minor St. Other clones of the same species show sensitivities that differ by one order of magnitude. Transmission electron microscopy revealed: (i) large numbers of vesicles close to the plasmalemma in cells adjacent to the abscission zone, which proves a vesicular type secretory activity; and (ii) a moderately electron-dense secretion accumulated in the enlarging intercellular spaces, and seemed to flow from the adjacent cells towards the abscission zone. We assume that increasing pressure causes this material to push apart the cells, thereby causing the break in the abscission zone of the stipe. This is a novel mechanism of abscission that has not previously been described. The same mechanism occurs in stipes of both control and Ag(+) -treated samples. Silver ions only accelerate the process leading to abscission of stipes, without affecting the mechanism involved.

Identification of a maize neocentromere in an oat-maize addition line.

We report a neocentromere event on maize chromosome 3 that occurred due to chromosome breakage. The neocentromere lies on a fragment of the short arm that lacks the primary centromere DNA elements, CentC and CRM. It is transmitted in the genomic background of oat via a new centromere (and kinetochore), as shown by immunolocalization of the oat CENH3 protein. Despite normal transmission of the maize fragment in most progeny, neocentromeres appear to vary in size within the same tissue, as shown by fluorescent measurements. A secondary truncation in one line lowered mitotic transmission to 3% and precipitously reduced the size of the chromosome. The results support the view that neocentromere formation is generally associated with major genomic disturbances such as wide species crosses or deletion of an existing centromere. The data further suggest that new centromeres may undergo a period of instability that is corrected over a period of several generations.

Caseinomacropeptide self-association is dependent on whether the peptide is free or restricted in kappa-casein.

There is a general agreement that the experimentally determined molecular weight (MW) of caseinomacropeptide (CMP) is greater than the theoretical MW. Some studies suggest that this is due to a pH-dependent aggregation of monomeric CMP. How this aggregation is influenced by pH is not understood. This study was carried out to study the nature of CMP aggregates and to clarify which conditions affect aggregation of CMP. The apparent MW of CMP at different pH values was determined using size-exclusion chromatography. Caseinomacropeptide was further characterized by immunochemical analysis, sodium dodecyl sulfate-PAGE, N-terminal sequencing, and mass spectrometry. The hydrophobicity of CMP was studied by means of 1-anilino-naphthalene-8-sulfonic acid binding experiments. Four CMP products prepared by different methods were studied: CMP produced by enzymatic (chymosin or pepsin) hydrolysis of kappa-casein (CN), and 2 commercial CMP products. Both commercial products and CMP resulting from chymosin-hydrolysis of kappa-CN (at pH 6.6) had elution volumes with a MW corresponding to 35 kDA at pH 8.0 and 3.4. Caseinomacropeptide prepared from pepsin-hydrolysis of kappa-CN (at pH 2.5) eluted as multiple peaks with apparent MW of 35, 18, and 9 kDa, again independently of pH. Hydrolysis of kappa-CN with chymosin or pepsin at different pH values (pH 2.5, 3.4, and 6.6) produced differently sized aggregates of CMP, largely depending on the pH of the hydrolysis. These results indicate that, whereas CMP molecules are irreversibly associated, CMP in kappa-CN may associate reversibly in a pH-dependent manner. We suggest that interactions between para-kappa-CN parts of the kappa-CN molecules may be a requisite for the pH-dependent dissociation/association.

Influence of local airflow on the pollutant emission from indoor building surfaces.

This article reports the results of an investigation, based on fundamental fluid dynamics and mass transfer theory, carried out to obtain a general understanding of the mechanisms involved in the emissions from building materials in ventilated rooms. In addition, a generally applicable method for the prediction of surface emissions is proposed. The work focused on the emission of vapours and gases and no particulate emissions were considered. The methods used were numerical calculations by computational fluid dynamics (CFD) and full-scale laboratory experiments. It was found that the emissions are a strong function of air-change rate, local air velocity and local turbulence, as the mass transfer coefficient increases in proportion to these parameters. The findings further show that the mass transfer coefficient increases in proportion to the velocity when the emission is controlled by evaporation from the surface. With regard to diffusion-controlled emissions, the mass transfer coefficient is unaffected by the velocity.