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Comadran J.,Scottish Crop Research Institute | Ramsay L.,Scottish Crop Research Institute | MacKenzie K.,BIOSS | Hayes P.,Oregon State University | And 4 more authors.
Theoretical and Applied Genetics | Year: 2011

We carried out a genome-wide analysis of polymorphism (4,596 SNP loci across 190 elite cultivated accessions) chosen to represent the available genetic variation in current elite North West European and North American barley germplasm. Population sub-structure, patterns of diversity and linkage disequilibrium varied considerably across the seven barley chromosomes. Gene-rich and rarely recombining haplotype blocks that may represent up to 60% of the physical length of barley chromosomes extended across the 'genetic centromeres'. By positioning 2,132 bi-parentally mapped SNP markers with minimum allele frequencies higher than 0.10 by association mapping, 87.3% were located to within 5 cM of their original genetic map position. We show that at this current marker density genetically diverse populations of relatively small size are sufficient to fine map simple traits, providing they are not strongly stratified within the sample, fall outside the genetic centromeres and population sub-structure is effectively controlled in the analysis. Our results have important implications for association mapping, positional cloning, physical mapping and practical plant breeding in barley and other major world cereals including wheat and rye that exhibit comparable genome and genetic features. © 2010 The Author(s).

Van Der Heijden G.,Wageningen University | Song Y.,BioSS | Horgan G.,Rowett Institute | Polder G.,Wageningen University | And 5 more authors.
Functional Plant Biology | Year: 2012

Most high-throughput systems for automated plant phenotyping involve a fixed recording cabinet to which plants are transported. However, important greenhouse plants like pepper are too tall to be transported. In this research we developed a system to automatically measure plant characteristics of tall pepper plants in the greenhouse. With a device equipped with multiple cameras, images of plants are recorded at a 5cm interval over a height of 3m. Two types of features are extracted: (1) features from a 3D reconstruction of the plant canopy; and (2) statistical features derived directly from RGB images. The experiment comprised 151 genotypes of a recombinant inbred population of pepper, to examine the heritability and quantitative trait loci (QTL) of the features. Features extracted from the 3D reconstruction of the canopy were leaf size and leaf angle, with heritabilities of 0.70 and 0.56 respectively. Three QTL were found for leaf size, and one for leaf angle. From the statistical features, plant height showed a good correlation (0.93) with manual measurements, and QTL were in accordance with QTL of manual measurements. For total leaf area, the heritability was 0.55, and two of the three QTL found by manual measurement were found by image analysis. © 2012 CSIRO.

Umstatter C.,Scotland’s Rural College | Brocklehurst S.,BioSS | Ross D.W.,Scotland’s Rural College | Haskell M.J.,Scotland’s Rural College
Applied Animal Behaviour Science | Year: 2013

Fences are crucial for successful grazing management of livestock. However, conventional fencing is expensive and lacks spatial flexibility. To date, this flexibility has been provided by electric fences, but these are not always efficient to erect and move and are not suitable for all locations. The development of virtual fencing could improve flexibility, but implementations often incorporate electric shock as a means to deter animals from crossing a defined line. Alternative deterrent methods may be required due to legal requirements in some countries. Therefore, the aim of the study was to test "irritating" sounds from the sonic range (8. kHz and a mix of 8-10. kHz) in order to establish if they could discourage beef cows from spending time in a specific area. A third treatment using "acute alarming" sounds as a comparison was also tested. In our study, we created a virtual fence by placing loudspeakers at 10. m intervals across a small paddock. There were six groups of test cows: three groups were tested in a first observation session and three groups in a second session each day. Testing took place over three consecutive weeks, with two control days and two test days per week. In each week each group was tested with one of the three sounds in one of three paddocks. The results indicated that irritating sounds are as effective as acute alarming sounds at discouraging animals, but not sufficiently effective for commercial application when played from loudspeakers mounted on posts. However, a highly significant effect of the use of sounds was identified, showing that sounds can be used as adverse stimuli. Moreover, reduction in use of zones closest to the loudspeakers and increased use of zones furthest away from the loudspeakers during the sound tests strongly indicates that the use of sound can influence cattle location. In synthesis, the study has shown that the use of irritating sounds as aversive stimuli is a valid and potential option for the development of virtual fencing. Although, it does not have exactly the same effect as a conventional fence in terms of stock-proofing, this technology can open up new possibilities in grazing management, especially when low grazing pressure is favourable. However, for commercial applications, further research is needed to investigate the use of animal-borne devices to broadcast sounds so that the dB level for the sound is kept at a consistent level. © 2013 Elsevier B.V.

Tolkamp B.J.,Animal Health Group | Allcroft D.J.,BioSS | Barrio J.P.,University of León | Bley T.A.G.,University of Hohenheim | And 7 more authors.
American Journal of Physiology - Regulatory Integrative and Comparative Physiology | Year: 2011

Meals have long been considered relevant units of feeding behavior. Large data sets of feeding behavior of cattle, pigs, chickens, ducks, turkeys, dolphins, and rats were analyzed with the aims of 1) describing the temporal structure of feeding behavior and 2) developing appropriate methods for estimating meal criteria. Longer (between-meal) intervals were never distributed as the negative exponential assumed by traditional methods, such as log-survivorship analysis, but as a skewed Gaussian, which can be (almost) normalized by log-transformation of interval lengths. Log-transformation can also normalize frequency distributions of within-meal intervals. Meal criteria, i.e., the longest interval considered to occur within meals, can be estimated after fitting models consisting of Gaussian functions alone or of one Weibull and one or more Gaussian functions to the distribution of log-transformed interval lengths. Nonuniform data sets may require disaggregation before this can be achieved. Observations from all species were in conflict with assumptions of random behavior that underlie traditional methods for criteria estimation. Instead, the observed structure of feeding behavior is consistent with 1) a decrease in satiety associated with an increase in the probability of animals starting a meal with time since the last meal and 2) an increase in satiation associated with an increase in the probability of animals ending a meal with the amount of food already consumed. The novel methodology proposed here will avoid biased conclusions from analyses of feeding behavior associated with previous methods and, as demonstrated, can be applied across a range of species to address questions relevant to the control of food intake. © 2011 the American Physiological Society.

Alexander P.D.,Royal Horticultural Society Wisley | Williams R.H.,Royal Horticultural Society Wisley | Nevison I.M.,BioSS
Acta Horticulturae | Year: 2013

UK gardeners need sound, evidence-based advice regarding water management of peat-free growing media. However, our understanding of water relations in peat alternatives is relatively poor compared to our knowledge of peat, which has been acquired over many years of practice and research. This experiment aimed to address this knowledge gap and examined the performance of fuchsia 'Snowcap' when grown in four different commercially available products based either on peat, coir, wood fibre or green compost. Five different irrigation regimes, determined by regulated deficit irrigation over the preceding 24 hour period, were adopted. The control treatment replaced water lost in this period while the other application rates increased or decreased that amount by 25% and 50%. Growth index, flower counts, upper plant biomass (dry) and two forms of visual plant assessment were undertaken. Growth index of peat- and coir-grown plants were generally comparable across all irrigation regimes and significantly larger (P<0.001) than plants grown in wood fibre- and green compost-based media. Flower number in both peat- and coir-based media declined significantly (P<0.01) when under-watered. Flower number in wood fibre- and green compost- grown plants declined in both over- and under-watered plants compared to the control watering regime but this was not always statistically significant (P<0.05). There was no evidence (P>0.1) of inferiority of coir-grown to peat-grown plants across any of the irrigation regimes for either marketable size or quality. For wood fibregrown plants, only the control regime produced plants close to marketable quality but these were not considered as good as the peat- and coir-grown plants. No green compost-grown plants were considered marketable.

McVittie A.,SAC | Moran D.,SAC | Elston D.,BioSS
Regional Studies | Year: 2010

MCVITTIE A., MORAN D. and ELSTON D. Public preferences for rural policy reform: evidence from Scottish surveys, Regional Studies. Agricultural reform across the European Union has focused debate on how agriculture delivers wider rural objectives. The authors undertook economic valuation and multicriteria studies to explore public preferences for rural policy. The results suggest simultaneous preferences for both environmental and social benefits, notably locally grown food, water quality, wildlife habitats, and maintaining rural communities. The public assigned greatest weight to locally grown food, which is closely linked to them as a direct use and is also routinely transacted for. The multicriteria study yielded a different preference ordering potentially arising from the differing elicitation methods indicating a possible drawback of the approach employed. © 2010 Regional Studies Association.

Dittrich R.,Environment and Society Research Group | Wreford A.,Environment and Society Research Group | Butler A.,BioSS | Moran D.,Environment and Society Research Group
Climatic Change | Year: 2016

Household flood management measures can significantly reduce the risk from flooding. Understanding the factors that influence the uptake of measures has important implications for the design of measures to induce people to take charge of risk mitigation. We investigate the impact of flood action groups in communities in Scotland on the uptake of four measures: insurance, flood warnings, sandbags and floodgates applying regression analysis using a cross-sectional survey (n = 124). The groups were formed in response to the threat from flooding in those communities, and offer information and training on household flood management measures. We use the theoretical framework of Protection Motivation Theory, and compare uptake of the measures before and after the foundation of the flood action groups, as well as in the near future. The models show positive adoption effects for flood warnings, floodgates and to an extent for insurance, and a positive correlation with increased confidence of implementing and belief in the effectiveness of the measures. The effect is significant if specific information on the measures was provided, indicating the importance of tailored content. We conclude that appropriately designed flood action groups can be a cost-effective way of increasing the uptake of household flood management measures. © 2016 The Author(s)

MacKenzie K.,BioSS | Hackett C.A.,BioSS
Euphytica | Year: 2012

The analysis of association mapping populations is frequently complicated by substructure within the population. If this is unaccounted for, it generally results in many false positive marker-trait associations. In this study, we simulate a large barley population, modelling inbreeding and selection, and compare five models for analysing marker-trait associations. One of these includes no population substructure, one includes information about geographical origin and type of barley to represent structure within the population and three use different approaches that have been proposed for estimating marker-based kinship. Kinship methods reduced the number of false positives substantially compared to the other models but none of these approaches had a clear advantage over the others. One solution is to fit more than one model and to consider as candidate associations those markers that are significant by all models. None of the approaches were very successful at detecting true associations at the lowest level of heritability considered (25%), suggesting it is important to consider power in association mapping studies to avoid missing some true associations and overestimating others. © 2011 Springer Science+Business Media B.V.

Orcic D.Z.,University of Novi Sad | Mimica-Dukic N.M.,University of Novi Sad | Franciskovic M.M.,University of Novi Sad | Petrovic S.S.,BIOSS | Jovin E.T.,University of Novi Sad
Chemistry Central Journal | Year: 2011

Background: The St John's Wort (Hypericum perforatum; Clusiaceae) has been used in traditional and modern medicine for a long time due to its high content of biologically active phenolics. The purpose of this work was to develop a method for their fractionation and identification, and to determine the most active antioxidant compounds in plant extract.Results: An LC-MS method which enables fast qualitative and semiquantitative analysis was developed. The composition determined is in agreement with the previous results, where 6 flavonoids, 4 naphthodianthrones and 4 phloroglucinols have been identified. Significant antioxidant activity was determined for most of the fractions by DPPH assay (the lowest IC50of 0.52 μg/ml), NO scavenging (6.11 μg/ml), superoxide scavenging (1.86 μg/ml), lipid peroxidation (0.0079 μg/ml) and FRAP (the highest reduction capacity of 104 mg Fe equivalents/g) assays.Conclusion: LC-MS technique has been successfully applied for a quick separation and identification of the major components of H. perforatum fractions. Majority of the fractions analyzed have expressed a very high antioxidative activity when compared to synthetic antioxidants. The antioxidant activity could be attributed to flavonoids and phenolic acids, while phloroglucinols and naphthodianthrones showed no significant activity. It is demonstrated that it is possible to obtain, by fractionation, H. perforatum preparations with significantly increased phloroglucinols-to-naphthodianthrones ratio (up to 95:5). © 2011 Orčić et al.

Poggio L.,James Hutton Institute | Gimona A.,James Hutton Institute | Brewer M.J.,BioSS
Geoderma | Year: 2013

Knowledge of soil properties with complete area coverage is needed for policy-making, land resource management, and monitoring environmental impacts. Remote sensing offers possibilities to support Digital Soil Mapping, especially in data-poor regions. The aim of this work was to test the potential of time-series of MODIS (Moderate Resolution Imaging Spectroradiometer) vegetation and drought indices to provide relevant information to model topsoil properties in a Boreal-Atlantic region (Scotland) focussing on differentiation between soils with high and soils with low organic matter contents. For each of the three considered years, 345 MODIS data sets were included in the exploratory analysis; 15 data products for 23 dates (bi-weekly) per year. Terrain parameters derived from Shuttle Radar Topography Mission were also included. A methodology was implemented to exploit fully the high number of covariates, to identify the band, index or product that best correlates with the soil property of interest. In particular the proposed approach i. relies on freely globally available data-sets; ii. uses statistical criteria to select the combination of covariates providing the highest predictive capability, among the data considered and available; iii. deals with both continuous (using Generalized Additive Models, GAMs) and multinomial categorical (using Random Trees) types of variables; iv. takes into account fully the spatial autocorrelation of the data; v. provides estimates of the spatial uncertainty for each pixel; and vi. is computationally efficient when compared with methods such as forward stepwise. The models fitted show a fairly good agreement with existing data sets, presenting a consistent spatial pattern. The use of MODIS data as covariates increased the predictive capabilities of GAMs using only terrain parameters. The misclassification error for organic matter classes was between 25 and 35%. The assessment provided of the spatial uncertainty of the modelled values can be used in further modelling and in the assessment of consequences of climate-change and trade-off in land use changes. This approach can contribute to improving our understanding and modelling of soil processes and function over large, and relatively sparsely sampled, areas of the world. © 2013 Elsevier B.V.

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