268 research outputs found
Assessment of the dynamics of microparasite infections in genetically homogeneous and heterogeneous populations using a stochastic epidemic model
Genetic variation of metabolite and hormone concentration in UK Holstein-Friesian calves and the genetic relationship with economically important traits
Impact of single nucleotide polymorphisms in leptin, leptin receptor, growth hormone receptor, and diacylglycerol acyltransferase (DGAT1) gene loci on milk production, feed, and body energy traits of UK dairy cows
Breeding schemes in reindeer husbandry
The objective of the paper was to investigate annual genetic gain from selection (G), and the influence of selection on the inbreeding effective population size (Ne), for different possible breeding schemes within a reindeer herding district. The breeding schemes were analysed for different proportions of the population within a herding district included in the selection programme. Two different breeding schemes were analysed: an open nucleus scheme where males mix and mate between owner flocks, and a closed nucleus scheme where the males in non-selected owner flocks are culled to maximise G in the whole population. The theory of expected long-term genetic contributions was used and maternal effects were included in the analyses. Realistic parameter values were used for the population, modelled with 5000 reindeer in the population and a sex ratio of 14 adult females per male. The standard deviation of calf weights was 4.1 kg. Four different situations were explored and the results showed: 1. When the population was randomly culled, Ne equalled 2400. 2. When the whole population was selected on calf weights, Ne equalled 1700 and the total annual genetic gain (direct + maternal) in calf weight was 0.42 kg. 3. For the open nucleus scheme, G increased monotonically from 0 to 0.42 kg as the proportion of the population included in the selection programme increased from 0 to 1.0, and Ne decreased correspondingly from 2400 to 1700. 4. In the closed nucleus scheme the lowest value of Ne was 1300. For a given proportion of the population included in the selection programme, the difference in G between a closed nucleus scheme and an open one was up to 0.13 kg. We conclude that for mass selection based on calf weights in herding districts with 2000 animals or more, there are no risks of inbreeding effects caused by selection
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Applying principles of metrology to historical Earth observations from satellites
Approaches from metrology can assist Earth Observation (EO) practitioners to develop quantitative characterisation of uncertainty in EO data. This is necessary for the credibility of statements based on Earth observations in relation to topics of public concern, particularly climate and environmental change. This paper presents the application of metrological uncertainty analysis to historical Earth observations from satellites, and is intended to aid mutual understanding of metrology and EO. The nature of satellite observations is summarised for different EO data processing levels, and key metrological nomenclature and principles for uncertainty characterisation are reviewed. We then address metrological approaches to developing estimates of uncertainty that are traceable from the satellite sensor, through levels of data processing, to products describing the evolution of the geophysical state of the Earth. EO radiances have errors with complex error correlation structures that are significant when performing common higher-level transformations of EO imagery. Principles of measurement-function-centred uncertainty analysis are described that apply sequentially to each EO data processing level. Practical tools for organising and traceably documenting uncertainty analysis are presented. We illustrate these principles and tools with examples including some specific sources of error seen in EO satellite data as well as with an example of the estimation of sea surface temperature from satellite infra-red imagery. This includes a simulation-based estimate for the error distribution of clear-sky infra-red brightness temperature (BT) in which calibration uncertainty and digitisation are found to dominate. The propagation of these errors to sea surface temperature is then presented, illustrating the relevance of the approach to derivation of EO-based climate datasets. We conclude with a discussion arguing that there is broad scope and need for improvement in EO practice as a measurement science. EO practitioners and metrologists willing to extend and adapt their disciplinary knowledge to meet this need can make valuable contributions to EO
Genomic selection requires genomic control of inbreeding
BACKGROUND: In the past, pedigree relationships were used to control and monitor inbreeding because genomic relationships among selection candidates were not available until recently. The aim of this study was to understand the consequences for genetic variability across the genome when genomic information is used to estimate breeding values and in managing the inbreeding generated in the course of selection on genome-enhanced estimated breeding values. METHODS: These consequences were measured by genetic gain, pedigree- and genome-based rates of inbreeding, and local inbreeding across the genome. Breeding schemes were compared by simulating truncation selection or optimum contribution selection with a restriction on pedigree- or genome-based inbreeding, and with selection using estimated breeding values based on genome- or pedigree-based BLUP. Trait information was recorded on full-sibs of the candidates. RESULTS: When the information used to estimate breeding values and to constrain rates of inbreeding were either both pedigree-based or both genome-based, rates of genomic inbreeding were close to the desired values and the identical-by-descent profiles were reasonably uniform across the genome. However, with a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding were much higher than expected. With pedigree-instead of genome-based estimated breeding values, the impact of the largest QTL on the breeding values was much smaller, resulting in a more uniform genome-wide identical-by-descent profile but genomic rates of inbreeding were still higher than expected based on pedigree relationships, because they measure the inbreeding at a neutral locus not linked to any QTL. Neutral loci did not exist here, where there were 100 QTL on each chromosome. With a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding substantially exceeded the value of its constraint. In contrast, with a genome-based inbreeding constraint and genome-based estimated breeding values, marker frequencies changed, but this change was limited by the inbreeding constraint at the marker position. CONCLUSIONS: To control inbreeding, it is necessary to account for it on the same basis as what is used to estimate breeding values, i.e. pedigree-based inbreeding control with traditional pedigree-based BLUP estimated breeding values and genome-based inbreeding control with genome-based estimated breeding values
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Radiance uncertainty characterisation to facilitate climate data record creation
The uncertainty in a climate data records (CDRs) derived from Earth observations in part derives from the propagated uncertainty in the radiance record (the fundamental climate data record, FCDR) from which the geophysical estimates in the CDR are derived. A common barrier to providing uncertainty-quantified CDRs is the inaccessibility to CDR creators of appropriate radiance uncertainty information in the FCDR. Here, we propose radiance uncertainty information designed directly to facilitate estimation of propagated uncertainty in derived CDRs at full resolution and in gridded products. Errors in Earth observations are typically highly structured and complex, and the uncertainty information we propose is of intermediate complexity, sufficient to capture the main variability in propagated uncertainty in a CDR, while avoiding unfeasible complexity or data volume. The uncertainty and error correlation characteristics of uncertainty are quantified for three classes of error with different propagation properties: independent, structured and common radiance errors. The meaning, mathematical derivations, practical evaluation and example applications of this set of uncertainty information are presented
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