Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.)

Key message We have identified QTLs for stomatal characteristics on chromosome II of faba bean by applying SNPs derived from M. truncatula , and have identified candidate genes within these QTLs using synteny between the two species. Abstract Faba bean (Vicia faba L.) is a valuable food and feed crop worldwide, but drought often limits its production, and its genome is large and poorly mapped. No information is available on the effects of genomic regions and genes on drought adaptation characters such as stomatal characteristics in this species, but the synteny between the sequenced model legume, Medicago truncatula, and faba bean can be used to identify candidate genes. A mapping population of 211 F5 recombinant inbred lines (Mélodie/2 × ILB 938/2) were phenotyped to identify quantitative trait loci (QTL) affecting stomatal morphology and function, along with seed weight, under well-watered conditions in a climate-controlled glasshouse in 2013 and 2014. Canopy temperature (CT) was evaluated in 2013 under water-deficit (CTd). In total, 188 polymorphic single nucleotide polymorphisms (SNPs), developed from M. truncatula genome data, were assigned to nine linkage groups that covered ~928 cM of the faba bean genome with an average inter-marker distance of 5.8 cM. 15 putative QTLs were detected, of which eight (affecting stomatal density, length and conductance and CT) co-located on chromosome II, in the vicinity of a possible candidate gene—a receptor-like protein kinase found in the syntenic interval of M. truncatula chromosome IV. A ribose-phosphate pyrophosphokinase from M. truncatula chromosome V, postulated as a possible candidate gene for the QTL for CTd, was found some distance away in the same chromosome. These results demonstrate that genomic information from M. truncatula can successfully be translated to the faba bean genome.

A DFT study of the structures, stabilities and redox behaviour of the major surfaces of magnetite Fe3O4

The renewed interest in magnetite (Fe3O4) as a major phase in different types of catalysts has led us to study the oxidation–reduction behaviour of its most prominent surfaces. We have employed computer modelling techniques based on the density functional theory to calculate the geometries and surface free energies of a number of surfaces at different compositions, including the stoichiometric plane, and those with a deficiency or excess of oxygen atoms. The most stable surfaces are the (001) and (111), leading to a cubic Fe3O4 crystal morphology with truncated corners under equilibrium conditions. The scanning tunnelling microscopy images of the different terminations of the (001) and (111) stoichiometric surfaces were calculated and compared with previous reports. Under reducing conditions, the creation of oxygen vacancies in the surface leads to the formation of reduced Fe species in the surface in the vicinity of the vacant oxygen. The (001) surface is slightly more prone to reduction than the (111), due to the higher stabilisation upon relaxation of the atoms around the oxygen vacancy, but molecular oxygen adsorbs preferentially at the (111) surface. In both oxidized surfaces, the oxygen atoms are located on bridge positions between two surface iron atoms, from which they attract electron density. The oxidised state is thermodynamically favourable with respect to the stoichiometric surfaces under ambient conditions, although not under the conditions when bulk Fe3O4 is thermodynamically stable with respect to Fe2O3. This finding is important in the interpretation of the catalytic properties of Fe3O4 due to the presence of oxidised species under experimental conditions.

Landscape change in central Latvia since the Iron Age: multi-proxy analysis of the vegetation impact of conflict, colonization and economic expansion during the last 2000 years

This study represents the first detailed multi-proxy palaeoenvironmental investigation associated with a Late Iron Age lake-dwelling site in the eastern Baltic. The main objective was to reconstruct the environmental and vegetation dynamics associated with the establishment of the lake-dwelling and land-use during the last 2,000 years. A lacustrine sediment core located adjacent to a Late Iron Age lake-dwelling, medieval castle and Post-medieval manor was sampled in Lake Āraiši. The core was dated using spheroidal fly-ash particles and radiocarbon dating, and analysed in terms of pollen, non-pollen palynomorphs, diatoms, loss-on-ignition, magnetic susceptibility and element geochemistry. Associations between pollen and other proxies were statistically tested. During ad 1–700, the vicinity of Lake Āraiši was covered by forests and human activities were only small-scale with the first appearance of cereal pollen (Triticum and Secale cereale) after ad 400. The most significant changes in vegetation and environment occurred with the establishment of the lake-dwelling around ad 780 when the immediate surroundings of the lake were cleared for agriculture, and within the lake there were increased nutrient levels. The highest accumulation rates of coprophilous fungi coincide with the occupation of the lake-dwelling from ad 780–1050, indicating that parts of the dwelling functioned as byres for livestock. The conquest of tribal lands during the crusades resulted in changes to the ownership, administration and organisation of the land, but our results indicate that the form and type of agriculture and land-use continued much as it had during the preceding Late Iron Age.

Analysis of wall plasters and natural sediments from the Neolithic town of Çatalhöyük (Turkey) by a range of analytical techniques

Wall plaster sequences from the Neolithic town of Çatalhöyük have been analysed and compared to three types of natural sediment found in the vicinity of the site, using a range of analytical techniques. Block samples containing the plaster sequences were removed from the walls of several different buildings on the East Mound. Sub-samples were examined by IR spectroscopy, X-ray diffraction and X-ray fluorescence to determine the overall mineralogical and elemental composition, whilst thin sections were studied using optical polarising microscopy, IR Microscopy and Environmental Scanning Electron Microscopy with Energy Dispersive X-ray analysis. The results of this study have shown that there are two types of wall plaster found in the sequences and that the sediments used to produce these were obtained from at least two distinct sources. In particular, the presence of clay, calcite and magnesian calcite in the foundation plasters suggested that these were prepared predominantly from a marl source. On the other hand, the finishing plasters were found to contain dolomite with a small amount of clay and no calcite, revealing that softlime was used in their preparation. Whilst marl is located directly below and around Çatalhöyük, the nearest source of softlime is 6.5 km away, an indication that the latter was important to the Neolithic people, possibly due to the whiter colour (5Y 8/1) of this sediment. Furthermore, the same two plaster types were found on each wall of Building 49, the main building studied in this research, and in all five buildings investigated, suggesting that the use of these sources was an established practice for the inhabitants of several different households across the site.

Ground-based observations of the auroral zone and polar cap ionospheric responses to dayside transient reconnection

Observations from the EISCAT VHF incoherent scatter radar system in northern Norway, during a run of the common programme CP-4, reveal a series of polewardpropagating F-region electron density enhancements in the pre-noon sector on 23 November 1999. These plasma density features, which are observed under conditions of a strongly southward interplanetary magnetic field, exhibit a recurrence rate of under 10 min and appear to emanate from the vicinity of the open/closed field-line boundary from where they travel into the polar cap; this is suggestive of their being an ionospheric response to transient reconnection at the dayside magnetopause (flux transfer events). Simultaneous with the density structures detected by the VHF radar, polewardmoving radar auroral forms (PMRAFs) are observed by the Finland HF coherent scatter radar. It is thought that PMRAFs, which are commonly observed near local noon by HF radars, are also related to flux transfer events, although the specific mechanism for the generation of the field-aligned irregularities within such features is not well understood. The HF observations suggest, that for much of their existence, the PMRAFs trace fossil signatures of transient reconnection rather than revealing the footprint of active reconnection itself; this is evidenced not least by the fact that the PMRAFs become narrower in spectral width as they evolve away from the region of more classical, broad cusp scatter in which they originate. Interpretation of the HF observations with reference to the plasma parameters diagnosed by the incoherent scatter radar suggests that as the PMRAFs migrate away from the reconnection site and across the polar cap, entrained in the ambient antisunward flow, the irregularities therein are generated by the presence of gradients in the electron density, with these gradients having been formed through structuring of the ionosphere in the cusp region in response to transient reconnection.

Simultaneous optical and radar signatures of poleward-moving auroral forms

Dayside poleward moving auroral forms (PMAFs) were detected between 06:30 and 07:00 UT on December 16, 1998, by the meridian scanning photometer and the all-sky camera at Ny Alesund, Svalbard. Simultaneous SuperDARN HF radar measurements permitted the study of the associated ionospheric velocity pattern. A good general agreement is observed between the location and movement of velocity enhancements (flow channels) and the PMAFs. Clear signatures of equatorward flow were detected in the vicinity of PMAFs. This flow is believed to be the signature of a return flow outside the reconnected Aux tube, as predicted by the Southwood model. The simulated signatures of this model reproduce globally the measured signatures, and differences with the experimental data can be explained by the simplifications of the model. Proposed schemes of the flow modification due to the presence of several flow channels and the modification of cusp and region 1 field-aligned currents at the time of sporadic reconnection events are shown to fit well with the observations.

Coherent EISCAT Svalbard Radar spectra from the dayside cusp/cleft and their implications for transient field-aligned currents

Naturally enhanced incoherent scatter spectra from the vicinity of the dayside cusp/cleft, interpreted as being due to plasma turbulence driven by short bursts of intense field-aligned current, are compared with high-resolution narrow-angle auroral images and meridian scanning photometer data. Enhanced spectra have been observed on many occasions in association with nightside aurora, but there has been only one report of such spectra seen in the cusp/cleft region. Narrow-angle images show considerable change in the aurora on timescales shorter than the 10-s radar integration period, which could explain spectra observed with both ion lines simultaneously enhanced. Enhanced radar spectra are generally seen inside or beside regions of 630-nm auroral emission, indicative of sharp F region conductivity gradients, but there appears also to be a correlation with dynamic, small-scale auroral forms of order 100 m and less in width.

Temporal and spatial variability of auroral forms in the 10–14 MLT sector: Relationship to plasma convection and solar wind-magnetosphere coupling

Ground-based observations of dayside auroral forms and magnetic perturbations in the arctic sectors of Svalbard and Greenland, in combination with the high-resolution measurements of ionospheric ion drift and temperature by the EISCAT radar, are used to study temporal/spatial structures of cusp-type auroral forms in relation to convection. Large-scale patterns of equivalent convection in the dayside polar ionosphere are derived from the magnetic observations in Greenland and Svalbard. This information is used to estimate the ionospheric convection pattern in the vicinity of the cusp/cleft aurora. The reported observations, covering the period 0700-1130 UT, on January 11, 1993, are separated into four intervals according to the observed characteristics of the aurora and ionospheric convection. The morphology and intensity of the aurora are very different in quiet and disturbed intervals. A latitudinally narrow zone of intense and dynamical 630.0 nm emission equatorward of 75 degrees MLAT, was observed during periods of enhanced antisunward convection in the cusp region. This (type 1 cusp aurora) is considered to be the signature of plasma entry via magnetopause reconnection at low magnetopause latitudes, i.e. the low-latitude boundary layer (LLB I,). Another zone of weak 630.0 nm emission (type 2 cusp aurora) was observed to extend up to high latitudes (similar to 79 degrees MLAT) during relatively quiet magnetic conditions, when indications of reverse (sunward) convection was observed in the dayside polar cap. This is postulated to be a signature of merging between a northward directed IMF (B-z > 0) and the geomagnetic field poleward of the cusp. The coexistence of type 1 and 2 auroras was observed under intermediate circumstances. The optical observations from Svalbard and Greenland were also used to determine the temporal and spatial evolution of type 1 auroral forms, i.e. poleward-moving auroral events occurring in the vicinity of a rotational convection reversal in the early post-noon sector. Each event appeared as a local brightening at the equatorward boundary of the pre-existing type 1 cusp aurora, followed by poleward and eastward expansions of luminosity. The auroral events were associated with poleward-moving surges of enhanced ionospheric convection and F-layer ion temperature as observed by the EISCAT radar in Tromso. The EISCAT ion flow data in combination with the auroral observations show strong evidence for plasma flow across the open/closed field line boundary.

Location and characteristics of the reconnection X line deduced from low-altitude satellite and ground-based observations: 2. Defense Meteorological Satellite Program and European Incoherent Scatter data

We present an analysis of a cusp ion step, observed by the Defense Meteorological Satellite Program (DMSP) F10 spacecraft, between two poleward moving events of enhanced ionospheric electron temperature, observed by the European Incoherent Scatter (EISCAT) radar. From the ions detected by the satellite, the variation of the reconnection rate is computed for assumed distances along the open-closed field line separatrix from the satellite to the X line, do. Comparison with the onset times of the associated ionospheric events allows this distance to be estimated, but with an uncertainty due to the determination of the low-energy cutoff of the ion velocity distribution function, ƒ(ν). Nevertheless, the reconnection site is shown to be on the dayside magnetopause, consistent with the reconnection model of the cusp during southward interplanetary magnetic field (IMF). Analysis of the time series of distribution function at constant energies, ƒ(ts), shows that the best estimate of the distance do is 14.5±2 RE. This is consistent with various magnetopause observations of the signatures of reconnection for southward IMF. The ion precipitation is used to reconstruct the field-parallel part of the Cowley D ion distribution function injected into the open low-latitude boundary layer in the vicinity of the X line. From this reconstruction, the field-aligned component of the magnetosheath flow is found to be only −55±65 km s−1 near the X line, which means either that the reconnection X line is near the stagnation region at the nose of the magnetosphere, or that it is closely aligned with the magnetosheath flow streamline which is orthogonal to the magnetosheath field, or both. In addition, the sheath Alfvén speed at the X line is found to be 220±45 km s−1, and the speed with which newly opened field lines are ejected from the X line is 165±30 km s−1. We show that the inferred magnetic field, plasma density, and temperature of the sheath near the X line are consistent with a near-subsolar reconnection site and confirm that the magnetosheath field makes a large angle (>58°) with the X line.

The characteristics of the magnetopause reconnection X-line deduced from low-altitude satellite observations of cusp ions

We present an analysis of a “quasi-steady” cusp ion dispersion signature observed at low altitudes. We reconstruct the field-parallel part of the Cowley-D ion distribution function, injected into the open LLBL in the vicinity of the reconnection X-line. From this we find the field-parallel magnetosheath flow at the X-line was only 20 ± 60 km s−1, placing the reconnection site close to the flow streamline which is perpendicular to the magnetosheath field. Using interplanetary data and assuming the subsolar magnetopause is in pressure balance, we derive a wealth of information about the X-line, including: the density, flow, magnetic field and Alfvén speed of the magnetosheath; the magnetic shear across the X-line; the de-Hoffman Teller speed with which field lines emerge from the X-line; the magnetospheric field; and the ion transmission factor across the magnetopause. The results indicate that some heating takes place near the X-line as the ions cross the magnetopause, and that sheath densities may be reduced in a plasma depletion layer. We also compute the reconnection rate. Despite its quasi-steady appearance on an ion spectrogram, this cusp is found to reveal a large pulse of enhanced reconnection rate.

The excitation of ionospheric convection

This review presents recent observations of high-latitude ionospheric plasma convection, obtained using the EISCAT radar in the 'Polar' experiment mode. The paper is divided into two main parts. Firstly, the delay in the response of dayside high-latitude flows to changes in the interplanetary magnetic field is discussed. The results show the importance for the excitation of dayside convection of the transfer of magnetic flux from the dayside into the tail lobe. Consequently, ionospheric convection should be thought of as the sum of two intrinsically time-dependent flow patterns. The first of these patterns is directly driven by solar wind-magnetosphere coupling, dominates ionospheric flows on the dayside, is associated with an expanding polar cap area and is the F-region flow equivalent of the DP-2 E-region current system. The second of the two patterns is driven by the release of energy stored in the geomagnetic tail, dominates ionospheric flows on the nightside, is associated with a contracting polar cap and is equivalent to the DP-1, or substorm, current system. In the second half of the paper, various transient flow bursts observed in the vicinity of the dayside cusp are studied. These radar data, combined with simultaneous optical observations of transient dayside aurorae, strongly suggest that momentum is transferred across the magnetopause and into the ionosphere in a series of bursts, each associated with voltages of 30-80 kV. Similarities between these bursts and flux transfer events observed at the magnetopause are discussed.

Comparisons between EISCAT observations and model calculations of the high latitude ionosphere

Calculations using a numerical model of the convection dominated high latitude ionosphere are compared with observations made by EISCAT as part of the UK-POLAR Special Programme. The data used were for 24–25 October 1984, which was characterized by an unusually steady IMF, with Bz < 0 and By > 0; in the calculations it was assumed that a steady IMF implies steady convection conditions. Using the electric field models of Heppner and Maynard (1983) appropriate to By > 0 and precipitation data taken from Spiroet al. (1982), we calculated the velocities and electron densities appropriate to the EISCAT observations. Many of the general features of the velocity data were reproduced by the model. In particular, the phasing of the change from eastward to westward flow in the vicinity of the Harang discontinuity, flows near the dayside throat and a region of slow flow at higher latitudes near dusk were well reproduced. In the afternoon sector modelled velocity values were significantly less than those observed. Electron density calculations showed good agreement with EISCAT observations near the F-peak, but compared poorly with observations near 211 km. In both cases, the greatest disagreement occurred in the early part of the observations, where the convection pattern was poorly known and showed some evidence of long term temporal change. Possible causes for the disagreement between observations and calculations are discussed and shown to raise interesting and, as yet, unresolved questions concerning the interpretation of the data. For the data set used, the late afternoon dip in electron density observed near the F-peak and interpreted as the signature of the mid-latitude trough is well reproduced by the calculations. Calculations indicate that it does not arise from long residence times of plasma on the nightside, but is the signature of a gap between two major ionization sources, viz. photoionization and particle precipitation.

Ionospheric ion upwelling in the wake of flux transfer events at the dayside magnetopause

The effects of flux transfer events (FTE) on the dayside auroral ionosphere are studied, using a simple twin-vortex model of induced ionospheric plasma flow. It is shown that the predicted and observed velocities of these flows are sufficient to drive nonthermal plasma in the F region, not only within the newly opened flux tube of the FTE, but also on the closed, or "old" open, field lines around it. In fact, with the expected poleward neutral wind, the plasma is more highly nonthermal on the flanks of, but outside, the open flux tube: EISCAT observations indicate that plasma is indeed driven into nonthermal distributions in these regions. The nonthermal plasma is thereby subject to additional upforce due to the resulting ion temperature anisotropy and transient expansion due to Joule heating and also to ion accelerations associated with the FTE field aligned current system. Any upflows produced on closed field lines in the vicinity of the FTE are effectively bunched-up in the "wake" of the FTE. Observations from the AMPTE-UKS satellite at the magnetopause reveal ion upflows of energy ∼100 eV flowing out from the ionosphere on closed field lines which are only found in the wake of the FTE. Such flows are also only found shortly after two, out of all the FTEs observed by AMPTE-UKS. The outflow from the ionosphere is two orders of magnitude greater than predicted for the "classical" polar wind. It is shown that such ionospheric ion flows are only expected in association with FTEs on the magnetopause which are well removed from the sub-solar point-either towards dusk or, as in the UKS example discussed here, towards dawn. It is suggested that such ionospheric ions will only be observed if the center of the FTE open flux tube passes very close to the satellite. Consequently, we conclude the ion upflows presented here are probably driven by the second of two possible source FTEs and are observed at the satellite with a lag after the FTE which is less than their time-of-flight.

Upwelling O+ ion source characteristics

Recent observations from the Dynamics Explorer 1 (DE-1) spacecraft have shown that the dayside auroral zone is an important source of very low-energy superthermal O^+ ions for the polar magnetosphere. When observed at 2000- to 5000-km altitude, the core of the O^+ distribution exhibits transverse heating to energies on the order of 10 eV, significant upward heat flux, and subsonic upward flow at significant flux levels exceeding 10^8 cm^{-2}s^{-1}. The term "upwelling ions" has been adopted to label these flows, which stand out in sharp contrast to the light ion polar wind flows observed in the same altitude range in the polar cap and subauroral magnetosphere. We have chosen a typical upwelling ion event for detailed study, correlating retarding ion mass spectrometer observations of the low-energy plasma with energetic ion observations and local electromagnetic field observations. The upwelling ion signature is colocated with the magnetospheric cleft as marked by precipitating energetic magnetosheath ions. The apparent ionospheric heating is clearly linked with the magnetic field signatures of strong field-aligned currents in the vicinity of the dayside polar cap boundary. Electric field and ion plasma measurements indicate that a very strong and localized convection channel or jet exists coincident with the other signatures of this event. These observations indicate that transverse ion heating to temperatures on the order of 10^5 K in the 2000- to 5000-km ionosphere is an important factor in producing heavy ion outflows into the polar magnetosphere. This result contrasts with recent suggestions that electron heating to temperatures of order 10^4 K is the most important parameter with regard to O^+ outflow.

The effects of springtime mid-latitude storms on trace gas composition determined from the MACC reanalysis

The relationship between springtime air pollution transport of ozone (O3) and carbon monoxide (CO) and mid-latitude cyclones is explored for the first time using the Monitoring Atmospheric Composition and Climate (MACC) reanalysis for the period 2003–2012. In this study, the most intense spring storms (95th percentile) are selected for two regions, the North Pacific (NP) and the North Atlantic (NA). These storms (∼60 storms over each region) often track over the major emission sources of East Asia and eastern North America. By compositing the storms, the distributions of O3 and CO within a "typical" intense storm are examined. We compare the storm-centered composite to background composites of "average conditions" created by sampling the reanalysis data of the previous year to the storm locations. Mid-latitude storms are found to redistribute concentrations of O3 and CO horizontally and vertically throughout the storm. This is clearly shown to occur through two main mechanisms: (1) vertical lifting of CO-rich and O3-poor air isentropically, from near the surface to the mid- to upper-troposphere in the region of the warm conveyor belt; and (2) descent of O3-rich and CO-poor air isentropically in the vicinity of the dry intrusion, from the stratosphere toward the mid-troposphere. This can be seen in the composite storm's life cycle as the storm intensifies, with area-averaged O3 (CO) increasing (decreasing) between 200 and 500 hPa. The influence of the storm dynamics compared to the background environment on the composition within an area around the storm center at the time of maximum intensity is as follows. Area-averaged O3 at 300 hPa is enhanced by 50 and 36% and by 11 and 7.6% at 500 hPa for the NP and NA regions, respectively. In contrast, area-averaged CO at 300 hPa decreases by 12% for NP and 5.5% for NA, and area-averaged CO at 500 hPa decreases by 2.4% for NP while there is little change over the NA region. From the mid-troposphere, O3-rich air is clearly seen to be transported toward the surface, but the downward transport of CO-poor air is not discernible due to the high levels of CO in the lower troposphere. Area-averaged O3 is slightly higher at 1000 hPa (3.5 and 1.8% for the NP and NA regions, respectively). There is an increase of CO at 1000 hPa for the NP region (3.3%) relative to the background composite and a~slight decrease in area-averaged CO for the NA region at 1000 hPa (-2.7%).