Managing the rate of inbreeding (ΔF) provides a general framework for managing genetic resources in farmed breeding populations. Methods for managing ΔF have been developed over the last five years and they allow the attainment of the greatest expected genetic progress while restricting at the same time the increase in inbreeding. This is achieved by optimising the contribution that each candidate for selection must have to produce the next generation. The methods take into account all available performance and pedigree information and use Best Linear Unbiased Prediction (BLUP) estimates as a predictor of merit. Importantly, these tools give at least equal, but more often more gain than traditional selection based on truncation of BLUP estimated breeding values when compared at the same ΔF. Deterministic predictions for the expected gain obtained with optimised selection with ΔF restricted are now available. The optimisation tool can be also applied in a conservation context to minimise ΔF with restrictions to avoid loss in performance in valuable traits. Information on known quantitative trait loci or on markers linked to them can be incorporated into the optimisation process to further increase selection response. Molecular genetic information can also be incorporated into these tools to increase the precision of genetic relationships between individuals and to manage ΔF at specific positions or genome regions.

Best Linear Unbiased Prediction (BLUP) estimates of breeding values (EBVs) for economically relevant traits have been used for selection decisions in the UK Aberdeen Angus (AA) population since the early nineteen nineties. Selection exclusively based on BLUP-EBVs is expected to give higher gains than less accurate selection but can also lead to increased rates of inbreeding (ΔF). Dynamic rules using BLUP-EBVs to maximise genetic merit while DF is constrained to a pre-defined level are currently available (e.g. Grundy et al 1998). They showed that the use of these rules gives higher gains than standard BLUP selection at the same level of ΔF. The objective of this study was to investigate the potential of these procedures for optimising selection decisions in the UK AA population.

Widespread international use of AI and best linear unbiased prediction (BLUP) breeding values for milk yield has increased genetic gain in many dairy populations, including the UK. The proliferation of few sires through AI and the coselection of relatives favoured by BLUP has however increased the relatedness and inbreeding of the UK population. Inbreeding is undesirable for a number of reasons and it is important to monitor the rate at which it accumulates. Currently, the level and rates of inbreeding (∆F) are not routinely reported for UK dairy cattle. Optimised selection procedures that maximise genetic gain while constraining ∆F to a pre-defined level have been shown to control ∆F and increase genetic gain over truncation selection at the same ∆F (e.g. Avendaño et al. 2003). The objective of this study was to determine the current rates of inbreeding and to assess the potential of using optimised selection procedures in the UK dairy population.

Studies investigating the value of Marker Assisted Selection (MAS) for increasing genetic gain have compared responses from MAS and conventional schemes obtained with standard truncation selection and have ignored rates of inbreeding, DF (e.g. Ruane and Colleau, 1995). On the other hand, research comparing schemes at the same ΔF using optimised selection (Villanueva et al. 1999) has assumed that the effect of the QTL is known without error. This study extends the optimisation methods to include selection on genetic markers rather than on the QTL itself.

Dynamic selection algorithms using quadratic indices to optimise the contributions of selection candidates for maximising rates of genetic gain (ΔG) while constraining the rate of inbreeding (ΔF) in the long-term to pre-defined values, are available (Grundy et al, 1998). Avendaño et al (2001 a,b) applied these optimal selection algorithms on the UK Meatlinc (sheep) and Aberdeen Angus (beef cattle) pedigree breeds and found substantial expected increases (of at least 17%) in the average index score at the observed ΔF. Although these algorithms constitute powerful operational tools for breeding schemes, the framework for deterministically predicting ΔG under optimal selection with restricted ΔF is not yet available. This study presents a novel approach to this problem.

Best Linear Unbiased Prediction (BLUP) estimates of breeding values (EBVs) have been routinely used for selection decisions in the UK Meatlinc (ML) population since the early nineteen nineties. This has enabled accurate selection and has allowed higher genetic gains for traits of economic relevance than in other terminal sheep breeds (MLC, 1999). However, concerns regarding increased rates of inbreeding (ΔF) by selecting exclusively on BLUP-EBVs have arisen in this small population. Dynamic rules to maximise genetic merit while ΔF is constrained to a pre-defined level using BLUP EBVs are currently available (e.g. Grundy et al 1998). They found higher gains than standard BLUP selection at the same ΔF by using these rules. The objective of this study was to investigate the potential of these procedures for optimising selection decisions under constrained inbreeding in the UK ML sheep population.

The high yields obtained in agriculture rely heavily on the use of domesticated and genetically improved breeds and varieties. Until quite recently this has not been the case for most farmed aquaculture species that, in the genetic sense, are still much closer to the wild state than are the major terrestrial animals and food crops. Less than 10 % of the total world aquaculture production is based on improved strains. Due to a growing human population and a decline in production from capture fisheries, there is therefore a great disparity between the need for increased aquaculture production and the genetic quality of the strains available to meet that need. Moreover, full benefits of investments in management improvements (feed and feeding practices, control of diseases, etc.) can only be obtained through the use of genetically improved animals.

The Atacama Large Millimeter/submillimeter Array (ALMA) was used to obtain measurements of spatially and spectrally resolved CH3OH emission from comet C/2012 K1 (PanSTARRS) on 28-29 June 2014. Detection of 12-14 emission lines of CH3OH on each day permitted the derivation of spatially-resolved rotational temperature profiles (averaged along the line of sight), for the innermost 5000 km of the coma. On each day, the CH3OH distribution was centrally peaked and approximately consistent with spherically symmetric, uniform outflow. The azimuthally-averaged CH3OH rotational temperature (T rot) as a function of sky-projected nucleocentric distance (ρ), fell by about 40 K between ρ= 0 and 2500 km on 28 June, whereas on 29 June, T rot fell by about 50 K between ρ =0 km and 1500 km. A remarkable (~50 K) rise in T rot at ρ = 1500-2500 km on 29 June was not present on 28 June. The observed variations in CH3OH rotational temperature are interpreted primarily as a result of variations in the coma kinetic temperature due to adiabatic cooling, and heating through Solar irradiation, but collisional and radiative non-LTE excitation processes also play a role.

This study presents the use of atomistic process simulations to optimize p+/n ultra-shallow junctions fabrication process. We first bring to the fore that a high injection of interstitials close to the boron profile decreases the sensibility of boron diffusion to thermal budget. Preamorphization of the substrate is thus necessary to decrease boron diffusion by thermal budget reduction, the latter being obtained by the use of the thermal conduction tool (Levitor) instead of the classical lamp-type rapid thermal annealing. At the same time we show that the use of Levitor does not enhance boron activation, the substrate being preamorphize or not. So Levitor anneal can improve sheet resistance/junction depth trade-off only with preamorphization implant. Experiments are performed that confirm the predictions of our simulations. Further discussions explain activation path of boron during temperature cycle, as a function of amorphous depth, and for both lamp-type and Levitor anneal.

The eastern English Channel, the narrow channel of water separating northern France and southeast England is an area of intense human use of the array of resources concentrated into its relative small area. The vulnerability of living resources and their habitats brought together French and British maritime experts within a common project (called CHARM): to create an atlas of marine resource habitats in the eastern English Channel so as to provide planners and decision-makers with the necessary information to help managing the use of its living and non-living resources. This multidisciplinary and richly illustrated atlas provides abundant information on the legal framework and physical environment; benthic invertebrates, fish and their habitats; fishing activities; and a first attempt at developing a trophic network model (using ECOPATH software) and a marine conservation planning exercise (using MARXAN software, at a spatial resolution of 25 km $^{2})$ . Although most of the data used were collected elsewhere, some were collected especially for the project. Similarly, most of the analyses performed on the data where entirely original for this geographical area. The CHARM atlas has significantly improved the knowledge about the eastern Channel while contributing to the recognition that such holistic or multidisciplinary approaches to exploited marine systems are necessary to efficiently and durably manage their resources use.

Susceptibility to scrapie is known to be associated with polymorphisms at the prion protein (PrP) gene, and this association is the basis of current selective programmes implemented to control scrapie in many countries. However, these programmes might have unintended consequences for other traits that might be associated with PrP genotype. The objective of this study was to investigate the relationship between PrP genotype and coat colour characteristics in two UK native sheep breeds valued for their distinctive coat colour patterns. Coat colour pattern, darkness and spotting and PrP genotype records were available for 11 674 Badgerfaced Welsh Mountain and 2338 Shetland sheep. The data were analysed with a log–linear model using maximum likelihood. Results showed a strong significant association of PrP genotype with coat colour pattern in Badgerfaced Welsh Mountain and Shetland sheep and with the presence of white spotting in Shetland sheep. Animals with the ARR/ARR genotype (the most scrapie resistant) had higher odds of having a light dorsum and a dark abdomen than the reverse pattern. The implication of these associations is that selection to increase resistance to scrapie based only on PrP genotype could result in change in morphological diversity and affect other associated traits such as fitness.

Over recent years, selection methodologies have been developed to allow the maximization of genetic gain whilst constraining the rate of inbreeding. The desired rate of inbreeding is achieved by constraining the group coancestry using the numerator relationship matrix computed from pedigree. It is shown that when the method is applied to mixed inheritance models, where a QTL is segregating together with polygenes, the rate of inbreeding achieved in the region around a QTL is greater than the desired level. The constraint on group coancestry at specific positions around the QTL is achieved by using a relationship matrix computed from pedigree and genetic markers. However, the rate of inbreeding realized at the position of constraint is lower than that expected given the assumed relationship between group coancestry and the subsequent rate of inbreeding. The use of markers in the calculation of the relationship matrix allows the selection of candidates with very low or zero relationships because they are homozygous for alternative alleles, which results in a heterozygosity amongst their offspring higher than would be expected given their allele frequencies. A generation of random selection restored the expected relationship between group coancestry and inbreeding.

Scottish Blackface lamb viability records at birth, and postnatal survival from 1 day to 14 days, from 15 days to 120 days and from 121 days to 180 days were used to determine influential factors and to estimate variance components of lamb survival traits. The binary trait viability at birth was analysed using a linear model whereas the postnatal survival traits were analysed as continuous traits using a Weibull model. The data consisted of about 15 000 survival records of lambs born from 1996 to 2005 on two farms in Scotland. The models included fixed factors that had significant effects and random direct and maternal additive genetic effects and maternal litter effects for viability at birth, and sire and maternal litter effects for the postnatal survival traits. The possible effect of maternal behaviour measured around lambing on lamb survival was investigated in separate analyses. Male lambs were found to be at a higher risk of mortality than females during all periods considered. The effect of type of birth and age of dam was more important during the preweaning period than at later ages. The postnatal hazard rate was not significantly affected by the behaviour score of the dams. The genetic merit of dams had more influence on viability at birth than the genetic merit of lambs themselves. Estimates of heritability for postnatal survival traits were in the range of 0.18 to 0.33 and were significantly greater than zero. These results indicate that lamb survival can be improved through farm management practices and genetic selection. Both animal and maternal genetic effects should be considered in breeding programmes for improving viability at birth.

Gene banks are usually used for storing general genetic variability of endangered living populations but can be also used for storing alleles of a particular locus that are being eradicated through artificial selection programmes. In such scenarios gene banks would allow future re-introduction of one or more of the alleles being eradicated (and the associated diversity) into living populations. Frequencies within the bank for the locus of interest should have pre-determined target values. In this study, an algorithm is derived to obtain the optimal contributions of all candidate donors to achieve the target frequencies of the removed alleles in the bank while maintaining at the same time genetic variability in other loci unlinked to those targeted in the eradication programme. The efficiency of the algorithm is tested using the case of gene banks storing prion protein alleles currently disfavoured in scrapie eradication programmes (i.e., the AHQ, ARH, ARQ and VRQ alleles). Results showed that the algorithm was able to find the combinations of candidate contributions fulfilling different objectives regarding target frequencies and restrictions on coancestry. The most important factors influencing the optimal contributions were the allelic frequencies and the levels of diversity (coancestry) of the living population. Heterozygotes were favoured over homozygous individuals as, for a given number of animals contributing to the bank, the use of heterozygotes leads to lower levels of coancestry. Notwithstanding, almost all donors were sampled when restrictions on the global genetic diversity to be stored were severe.

Polymorphisms at codons 136, 154 and 171 of the gene encoding the prion protein (PrP) are associated with susceptibility to classical scrapie in sheep. Genetic selection for scrapie resistance based on PrP genotypes is central to the scrapie eradication programme in Great Britain but there are concerns about how this may affect other economically important traits. The objective of this study was to evaluate associations of PrP genotypes with live weight and slaughter traits in a hill sheep breed in Great Britain. Data used were from an experimental flock of Swaledale sheep in which the alleles ARR, ARQ, AHQ and VRQ were present. About 1450 genotyped lambs with birth, marking and weaning weights, and 620 with slaughter records were used for the study. Mixed models with various fixed effects and random direct genetic and maternal effects were tested to determine the appropriate model to use for each trait. None of the differences in lamb performance between PrP genotypes consistently reached significance. Therefore, this study does not support existence of significant relationships between PrP genotype and lamb performance traits in this breed.

Several studies investigating associations between prion protein (PrP) genotypes and performance traits in several sheep breeds have recently been published. Most of these studies have failed to give conclusive results due to small numbers of animals used or a potential genotyping bias as those animals selected for PrP genotyping were chosen based on their performance (e.g. De Vries et al., 2005). Polymorphisms of the PrP gene has been linked with susceptibility to scrapie with the ARR allele generally associated with resistance and the VRQ with susceptibility. This study investigates the associations with PrP genotype for a wide range of lamb performance traits in experimental flocks of Scottish Blackface in which all animals have been PrP genotyped.

Genetic selection based on polymorphisms identified at codons 136, 154 and 171 of the prion protein (PrP) gene is being implemented in scrapie eradication programs (e.g. Defra, 2005). These programs aim to remove the VRQ allele (associated with the highest incidence of classical scrapie) and increase the frequency of the ARR allele (which confers the highest level of resistance). However, concerns remain about how selection on the PrP gene would affect other economically important traits. The objective of this study was to investigate potential associations between the PrP alleles and lamb traits in an experimental flock of Swaledale sheep, a hill sheep breed.

Quadratic indices are a general approach for the joint management of genetic gain and inbreeding in artificial selection programmes. They provide the optimal contributions that selection candidates should have to obtain the maximum gain when the rate of inbreeding is constrained to a predefined value. This study shows that, when using quadratic indices, the selective advantage is a function of the Mendelian sampling terms. That is, at all times, contributions of selected candidates are allocated according to the best available information about their Mendelian sampling terms (i.e. about their superiority over their parental average) and not on their breeding values. By contrast, under standard truncation selection, both estimated breeding values and Mendelian sampling terms play a major role in determining contributions. A measure of the effectiveness of using genetic variation to achieve genetic gain is presented and benchmark values of 0·92 for quadratic optimisation and 0·5 for truncation selection are found for a rate of inbreeding of 0·01 and a heritability of 0·25.

A dynamic selection algorithm for maximizing annual genetic response while constraining the rate of inbreeding per generation in populations with overlapping generations is presented. The procedure gives the optimum number of individuals to be selected and the progeny they each produce. The solution to the problem was obtained by using BLUP estimated breeding values, the augmented numerator relationship matrix and lifetime breeding profiles. The procedure was able to constrain the rate of inbreeding per generation to a predefined level across generations of selection by considering all gene flow pathways. The optimization procedure represents an improvement on standard truncation BLUP selection, as it yielded substantially more genetic response (up to 35%) at the same rate of inbreeding.