An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation

MAGIC populations represent one of a new generation of crop genetic mapping resources combining high genetic recombination and diversity. We describe the creation and validation of an eight-parent MAGIC population consisting of 1091 F7 lines of winter-sown wheat (Triticum aestivum L.). Analyses based on genotypes from a 90,000-single nucleotide polymorphism (SNP) array find the population to be well-suited as a platform for fine-mapping quantitative trait loci (QTL) and gene isolation. Patterns of linkage disequilibrium (LD) show the population to be highly recombined; genetic marker diversity among the founders was 74% of that captured in a larger set of 64 wheat varieties, and 54% of SNPs segregating among the 64 lines also segregated among the eight founder lines. In contrast, a commonly used reference bi-parental population had only 54% of the diversity of the 64 varieties with 27% of SNPs segregating. We demonstrate the potential of this MAGIC resource by identifying a highly diagnostic marker for the morphological character "awn presence/absence" and independently validate it in an association-mapping panel. These analyses show this large, diverse, and highly recombined MAGIC population to be a powerful resource for the genetic dissection of target traits in wheat, and it is well-placed to efficiently exploit ongoing advances in phenomics and genomics. Genetic marker and trait data, together with instructions for access to seed, are available at http://www.niab.com/MAGIC/.

Meta-analysis of relationships between enteric methane yield and milk fatty acid profile in dairy cattle

Various studies have indicated a relationship between enteric methane (CH4) production and milk fatty acid (FA) profiles of dairy cattle. However, the number of studies investigating such a relationship is limited and the direct relationships reported are mainly obtained by variation in CH4 production and milk FA concentration induced by dietary lipid supplements. The aim of this study was to perform a meta-analysis to quantify relationships between CH4 yield (per unit of feed and unit of milk) and milk FA profile in dairy cattle and to develop equations to predict CH4 yield based on milk FA profile of cows fed a wide variety of diets. Data from 8 experiments encompassing 30 different dietary treatments and 146 observations were included. Yield of CH4 measured in these experiments was 21.5 ± 2.46 g/kg of dry matter intake (DMI) and 13.9 ± 2.30 g/ kg of fat- and protein-corrected milk (FPCM). Correlation coefficients were chosen as effect size of the relationship between CH4 yield and individual milk FA concentration (g/100 g of FA). Average true correlation coefficients were estimated by a random-effects model. Milk FA concentrations of C6:0, C8:0, C10:0, C16:0, and C16:0-iso were significantly or tended to be positively related to CH4 yield per unit of feed. Concentrations of trans-6+7+8+9 C18:1, trans-10+11 C18:1, cis- 11 C18:1, cis-12 C18:1, cis-13 C18:1, trans-16+cis-14 C18:1, and cis-9,12 C18:2 in milk fat were significantly or tended to be negatively related to CH4 yield per unit of feed. Milk FA concentrations of C10:0, C12:0, C14:0-iso, C14:0, cis-9 C14:1, C15:0, and C16:0 were significantly or tended to be positively related to CH4 yield per unit of milk. Concentrations of C4:0, C18:0, trans-10+11 C18:1, cis-9 C18:1, cis-11 C18:1, and cis- 9,12 C18:2 in milk fat were significantly or tended to be negatively related to CH4 yield per unit of milk. Mixed model multiple regression and a stepwise selection procedure of milk FA based on the Bayesian information criterion to predict CH4 yield with milk FA as input (g/100 g of FA) resulted in the following prediction equations: CH4 (g/kg of DMI) = 23.39 + 9.74 × C16:0- iso – 1.06 × trans-10+11 C18:1 – 1.75 × cis-9,12 C18:2 (R2 = 0.54), and CH4 (g/kg of FPCM) = 21.13 – 1.38 × C4:0 + 8.53 × C16:0-iso – 0.22 × cis-9 C18:1 – 0.59 × trans-10+11 C18:1 (R2 = 0.47). This indicated that milk FA profile has a moderate potential for predicting CH4 yield per unit of feed and a slightly lower potential for predicting CH4 yield per unit of milk. Key words: methane , milk fatty acid profile , metaanalysis , dairy cattle

Antibiosis in wheat interacts with crowding stress to affect Metopolophiumdirhodum development and susceptibility to malathion

We used a laboratory study to compare the performance of rose-grain aphid, Metopolophium dirhodum(Walker)(Hemiptera:Aphididae),onthewheatcultivars‘Huntsman’(susceptible)and‘Rapier’ (partiallyresistant)inbothlowdensity(uncrowded)andhighdensity(crowded)coloniesandexamined the consequences for aphid susceptibility to malathion. Adult apterae that developed on Rapier wheat had their mean relative growth rate (MRGR) reduced by 6 and 9% under uncrowded and crowded conditions, respectively, whereas the crowding treatment reduced MRGR by 3%, but only in Rapier aphids. Rapier resistance also reduced adult dry weight by 13 and 14% under crowded and uncrowded conditions, respectively, whereas crowding reduced it by 34 and 35% in Rapier and Huntsman aphids, respectively. Development on Rapier substantially reduced the topical LC50 of malathion by 37.8 and 34.8% under crowded and uncrowded conditions, suggesting that plant antibiosis increased malathion susceptibility. By comparison, crowding only reduced the LC50 by 29.5 and 26.0% on Huntsman and Rapier. The LD50 data showed that reductions on aphid body size on Rapier and through crowding did not fully explain the differences in LC50. This was particularly in the values for crowded aphids that were actually 80% higher than for uncrowded ones. Thi sapparent tolerance of crowded aphids, however, may partly be due to loss of insecticide from small aphids at dosing. Evidence of synergy between plant resistance and insecticide susceptibility raisest he possibility of using reduced concentrations of pesticides to control aphids on resistant crop cultivars, with diminished impacts on non-target and beneficial species important in integrated pest management(IPM)program

The endophytic fungus Piriformospora indica protects wheat from Fusarium crown rot disease in simulated UK autumn conditions

The root endophytic fungus Piriformospora indica (Sebacinacea) forms mutualistic symbioses with a broad range of host plants, increasing their biomass production and resistance to fungal pathogens. We evaluated the effect of P. indica on Fusarium crown rot disease of wheat, under in vitro and glasshouse conditions. Interaction of P. indica and Fusarium isolates under axenic culture conditions indicated no direct antagonistic activity of P. indica against Fusarium isolates. Seedlings of wheat were inoculated with P. indica and pathogenic Fusarium culmorum or F. graminearum and grown in sterilised soil-free medium or in a non-sterilised mix of soil and sand. Fusarium alone reduced emergence and led to visible browning and reduced root growth. Roots of seedlings in pots inoculated with both Fusarium isolates and P. indica were free of visible symptoms; seed emergence and root biomass were equivalent to the uninoculated. DNA was quantified by real-time polymerase chain reaction (qPCR). The ratio of Fusarium DNA to wheat DNA rose rapidly in the plants inoculated with Fusarium alone; isolates and species were not significantly different. P. indica inoculation reduced the ratio of Fusarium to host DNA in the root systems. The reduction increased with time. The ratio of P. indica to wheat DNA initially rose but then declined in root systems without Fusarium. With Fusarium, the ratio rose throughout the experiment. The absolute amount of Fusarium DNA in root systems increased in the absence of P. indica but was static in plants co-inoculated with P. indica.

Phosphorescence quantum yield enhanced by intermolecular hydrogen bonds in Cu4I4 clusters in the solid state

Organo-copper(I) halide complexes with a Cu4I4 cubane core and cyclic amines as ligands have been synthesized and their crystal structures have been defined. Their solid state photophysical properties have been measured and correlated with the crystal structure and packing. A unique and remarkably high luminescence quantum yield (76%) has been measured for one of the complexes having the cubane clusters arranged in a columnar structure and held together by N–HI hydrogen bonds. This high luminescence quantum yield is correlated with a slow radiationless deactivation rate of the excited state and suggests a rather strong enhancement of the cubane core rigidity bestowed by the hydrogen bond pattern. Some preliminary thin film deposition experiments show that these compounds could be considered to be good candidates for applications in electroluminescent devices because of their bright luminescence, low cost and relatively easy synthesis processes

Observed relationships between maize yield and climate in Sri Lanka

The present study evaluated the effects of climate variability on maize (Zea mays L.) yield in Sri Lanka at different spatial scales. Biophysical data from the Department of Agriculture (DOA) in Sri Lanka for six major maize-growing districts (Ampara, Anuradhapura, Badulla, Hambantota, Moneragala, and Kurunegala) from 1990 to 2010 were analyzed. Simple linear regression models were fitted to observed climate data and detrended maize yield to identify significant correlations. The correlation between first differences of maize yield and climate (r) was further investigated at 0.50° grid scale using interpolated climate data. After 2003, significantly positive (p < 0.01) yield trends varied from 154 kg ha–1 yr–1 to 360 kg ha–1 yr–1. The correlations between maize yield and climate reported that five out of six districts were significant at 10% level. Rainfall had a consistent significant (p < 0.10) positive impact on maize yield in Anuradhapura, Hambantota, and Moneragala, where seasonal total rainfall together with high temperature (“hot-dry”) are the key limitations. Further, the seasonal mean temperature had a negative impact on maize yield in Moneragala (“hot-dry”), the only district that showed high temperatures. Badulla district (“cold-dry”) reported a significant (r = 0.38) positive correlation with mean seasonal temperature, indicating higher potential toward increasing temperatures. Each 1°C rise in seasonal mean temperature reduced maize yield by about 5% from 1990 to 2010. Overall, there was a reasonable correlation between district maize yield and seasonal climate in most of the districts within the maize belt of Sri Lanka.

Climatic impacts of land-use change due to crop yield increases and a universal carbon tax from a scenario model*

Future land cover will have a significant impact on climate and is strongly influenced by the extent of agricultural land use. Differing assumptions of crop yield increase and carbon pricing mitigation strategies affect projected expansion of agricultural land in future scenarios. In the representative concentration pathway 4.5 (RCP4.5) from phase 5 of the Coupled Model Intercomparison Project (CMIP5), the carbon effects of these land cover changes are included, although the biogeophysical effects are not. The afforestation in RCP4.5 has important biogeophysical impacts on climate, in addition to the land carbon changes, which are directly related to the assumption of crop yield increase and the universal carbon tax. To investigate the biogeophysical climatic impact of combinations of agricultural crop yield increases and carbon pricing mitigation, five scenarios of land-use change based on RCP4.5 are used as inputs to an earth system model [Hadley Centre Global Environment Model, version 2-Earth System (HadGEM2-ES)]. In the scenario with the greatest increase in agricultural land (as a result of no increase in crop yield and no climate mitigation) there is a significant -0.49 K worldwide cooling by 2100 compared to a control scenario with no land-use change. Regional cooling is up to -2.2 K annually in northeastern Asia. Including carbon feedbacks from the land-use change gives a small global cooling of -0.067 K. This work shows that there are significant impacts from biogeophysical land-use changes caused by assumptions of crop yield and carbon mitigation, which mean that land carbon is not the whole story. It also elucidates the potential conflict between cooling from biogeophysical climate effects of land-use change and wider environmental aims.

JULES-crop: a parametrisation of crops in the Joint UK Land Environment Simulator

Studies of climate change impacts on the terrestrial biosphere have been completed without recognition of the integrated nature of the biosphere. Improved assessment of the impacts of climate change on food and water security requires the development and use of models not only representing each component but also their interactions. To meet this requirement the Joint UK Land Environment Simulator (JULES) land surface model has been modified to include a generic parametrisation of annual crops. The new model, JULES-crop, is described and evaluation at global and site levels for the four globally important crops; wheat, soybean, maize and rice. JULES-crop demonstrates skill in simulating the inter-annual variations of yield for maize and soybean at the global and country levels, and for wheat for major spring wheat producing countries. The impact of the new parametrisation, compared to the standard configuration, on the simulation of surface heat fluxes is largely an alteration of the partitioning between latent and sensible heat fluxes during the later part of the growing season. Further evaluation at the site level shows the model captures the seasonality of leaf area index, gross primary production and canopy height better than in the standard JULES. However, this does not lead to an improvement in the simulation of sensible and latent heat fluxes. The performance of JULES-crop from both an Earth system and crop yield model perspective is encouraging. However, more effort is needed to develop the parametrisation of the model for specific applications. Key future model developments identified include the introduction of processes such as irrigation and nitrogen limitation which will enable better representation of the spatial variability in yield.

Enantiomeric conformation controls rate and yield of photoinduced electron transfer in DNA sensitized by Ru(II) Dipyridophenazine complexes

Photosensitized oxidation of guanine is an important route to DNA damage. Ruthenium polypyridyls are very useful photosensitizers as their reactivity and DNA-binding properties are readily tunable. Here we show a strong difference in the reactivity of the two enantiomers of [Ru(TAP)2(dppz)]2+, by using time-resolved visible and IR spectroscopy. This reveals that the photosensitized one-electron oxidation of guanine in three oligonucleotide sequences proceeds with similar rates and yields for bound delta-[Ru(TAP)2(dppz)]2+, whereas those for the lambda enantiomer are very sensitive to base sequence. It is proposed that these differences are due to preferences of each enantiomer for different binding sites in the duplex.

Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability

Aims: To understand effects of tissue type, growth stage and soil fertilisers on bacterial endophyte communities of winter wheat (Triticum aestivum cv. Hereward). Methods: Endophytes were isolated from wheat grown under six fertiliser conditions in the long term Broadbalk Experiment at Rothamsted Research, UK. Samples were taken in May and July from root and leaf tissues. Results: Root and leaf communities differed in abundance and composition of endophytes. Endophytes were most abundant in roots and the Proteobacteria were most prevalent. In contrast, Firmicutes and Actinobacteria, the Gram positive phyla, were most prevalent in the leaves. Both fertiliser treatment and sample time influenced abundance and relative proportions of each phylum and genus in the endosphere. A higher density of endophytes was found in the Nil input treatment plants. Conclusions: Robust isolation techniques and stringent controls are critical for accurate recovery of endophytes. The plant tissue type, plant growth stage, and soil fertiliser treatment all contribute to the composition of the endophytic bacterial community in wheat. These results should help facilitate targeted development of endophytes for beneficial applications in agriculture.

Effect of azole fungicide mixtures, alternations and dose on azole sensitivity in the wheat pathogen Zymoseptoria tritici

The evolution of fungicide resistance in the cereal pathogen Zymoseptoria tritici, is a serious threat to the sustainability and profitability of wheat production in Europe. Application of azole fungicides has been shown to affect fitness of Z. tritici variants differentially, so it has been hypothesised that combinations of azoles could slow the evolution of resistance. This work was initiated to assess the effects of dose, mixtures and alternations of two azoles on selection for isolates with reduced sensitivity and on disease control. Naturally infected field trials were carried out at six sites across Ireland and the sensitivity of Z. tritici isolates monitored pre- and post-treatment. The azoles epoxiconazole and metconazole were applied as solo products, in alternation with each other and as a pre-formulated mixture. Full and half label doses were tested. The two azoles were partially cross-resistant, with a common azole resistance principal component accounting for 75% of the variation between isolates. Selection for isolates with reduced azole sensitivity was correlated with disease control. Decreased doses were related to decreases in sensitivity but the effect was barely significant (P = 0.1) and control was reduced. Single applications of an active ingredient (a.i.) caused smaller decreases in sensitivity than double applications. Shifts in sensitivity to the a.i. applied to a plot were greater than to the a.i. not applied, and the decrease in sensitivity was greater to the a.i. applied at the second timing. These results confirm the need to mix a.i.s with different modes of action.

Effects of agricultural management practices on earthworm populations and crop yield: validation and application of a mechanistic modelling approach

There is little consensus on how agriculture will meet future food demands sustainably. Soils and their biota play a crucial role by mediating ecosystem services that support agricultural productivity. However, a multitude of site-specific environmental factors and management practices interact to affect the ability of soil biota to perform vital functions, confounding the interpretation of results from experimental approaches. Insights can be gained through models, which integrate the physiological, biological and ecological mechanisms underpinning soil functions. We present a powerful modelling approach for predicting how agricultural management practices (pesticide applications and tillage) affect soil functioning through earthworm populations. By combining energy budgets and individual-based simulation models, and integrating key behavioural and ecological drivers, we accurately predict population responses to pesticide applications in different climatic conditions. We use the model to analyse the ecological consequences of different weed management practices. Our results demonstrate that an important link between agricultural management (herbicide applications and zero, reduced and conventional tillage) and earthworms is the maintenance of soil organic matter (SOM). We show how zero and reduced tillage practices can increase crop yields while preserving natural ecosystem functions. This demonstrates how management practices which aim to sustain agricultural productivity should account for their effects on earthworm populations, as their proliferation stimulates agricultural productivity. Synthesis and applications. Our results indicate that conventional tillage practices have longer term effects on soil biota than pesticide control, if the pesticide has a short dissipation time. The risk of earthworm populations becoming exposed to toxic pesticides will be reduced under dry soil conditions. Similarly, an increase in soil organic matter could increase the recovery rate of earthworm populations. However, effects are not necessarily additive and the impact of different management practices on earthworms depends on their timing and the prevailing environmental conditions. Our model can be used to determine which combinations of crop management practices and climatic conditions pose least overall risk to earthworm populations. Linking our model mechanistically to crop yield models would aid the optimization of crop management systems by exploring the trade-off between different ecosystem services.

Comparative in situ analyses of cell wall matrix polysaccharide dynamics in developing rice and wheat grain

Cell wall polysaccharides of wheat and rice endosperm are an important source of dietary fibre. Monoclonal antibodies specific to cell wall polysaccharides were used to determine polysaccharide dynamics during the development of both wheat and rice grain. Wheat and rice grain present near synchronous developmental processes and significantly different endosperm cell wall compositions, allowing the localisation of these polysaccharides to be related to developmental changes. Arabinoxylan (AX) and mixed-linkage glucan (MLG) have analogous cellular locations in both species, with deposition of AX and MLG coinciding with the start of grain filling. A glucuronoxylan (GUX) epitope was detected in rice, but not wheat endosperm cell walls. Callose has been reported to be associated with the formation of cell wall outgrowths during endosperm cellularisation and xyloglucan is here shown to be a component of these anticlinal extensions, occurring transiently in both species. Pectic homogalacturonan (HG) was abundant in cell walls of maternal tissues of wheat and rice grain, but only detected in endosperm cell walls of rice in an unesterified HG form. A rhamnogalacturonan-I (RG-I) backbone epitope was observed to be temporally regulated in both species, detected in endosperm cell walls from 12 DAA in rice and 20 DAA in wheat grain. Detection of the LM5 galactan epitope showed a clear distinction between wheat and rice, being detected at the earliest stages of development in rice endosperm cell walls, but not detected in wheat endosperm cell walls, only in maternal tissues. In contrast, the LM6 arabinan epitope was detected in both species around 8 DAA and was transient in wheat grain, but persisted in rice until maturity.

Influence of temperature on the composition and polymerization of gluten proteins during grain filling in spring wheat (Triticum aestivum L.)

One Norwegian and one UK spring wheat cultivar, Bjarne and Cadenza, respectively, were grown in climate chambers to investigate the effects of lower to moderate temperatures during grain filling on the gluten quality. Two experiments were carried out with weekly fertilization until anthesis, while post-anthesis fertilization was applied in a third experiment. The proportions of different gluten proteins were affected by temperature in a similar manner for both cultivars when grown without post-anthesis fertilization. However, whereas low temperature strongly decreased %UPP for Cadenza, Bjarne had high %UPP at all temperature regimes. The results indicated that the assembly of glutenin polymers in Bjarne was less sensitive to variation in temperature than in Cadenza. Thus, our results suggested that the temperature influenced the proportion of different gluten proteins in both cultivars, while its effects on the assembly of the glutenin polymers were cultivar dependent. The duration of grain filling was longer at the lower temperatures, and this was associated with increased grain weight. Temperature had little effect on the amount of protein accumulated per grain, thus the proportion of proteins was strongly decreased at lower temperatures. This was to some extent, but not fully counteracted by post-anthesis fertilization.

Jersey milk suitability for Cheddar cheese production: process, yield, quality and financial impacts

The aim of this study was to first evaluate the benefits of including Jersey milk into Holstein-Friesian milk on the Cheddar cheese making process and secondly, using the data gathered, identify the effects and relative importance of a wide range of milk components on milk coagulation properties and the cheese making process. Blending Jersey and Holstein-Friesian milk led to quadratic trends on the size of casein micelle and fat globule and on coagulation properties. However this was not found to affect the cheese making process. Including Jersey milk was found, on a pilot scale, to increase cheese yield (up to + 35 %) but it did not affect cheese quality, which was defined as compliance with the legal requirements of cheese composition, cheese texture, colour and grading scores. Profitability increased linearly with the inclusion of Jersey milk (up to 11.18 p£ L-1 of milk). The commercial trials supported the pilot plant findings, demonstrating that including Jersey milk increased cheese yield without having a negative impact on cheese quality, despite the inherent challenges of scaling up such a process commercially. The successful use of a large array of milk components to model the cheese making process challenged the commonly accepted view that fat, protein and casein content and protein to fat ratio are the main contributors to the cheese making process as other components such as the size of casein micelle and fat globule were found to also play a key role with small casein micelle and large fat globule reducing coagulation time, improving curd firmness, fat recovery and influencing cheese moisture and fat content. The findings of this thesis indicated that milk suitability for Cheddar making could be improved by the inclusion of Jersey milk and that more compositional factors need to be taken into account when judging milk suitability.