Optimizing mating schemes in fish breeding

The optimal contribution selection method and the simulated annealing algorithm were used to maximize the genetic gain and reduce inbreeding in fish breeding populations. This study considered the following mating designs: full factorial (3 x 3); full factorial (6 x 6) and nested (6 males x 18 females). A quantitative trait based on a strictly additive and polygenic model was simulated. Two levels for the number of genotyped offspring (360 or 720) and three levels of heritability (0.1; 0.3; 0.5) were assumed. The best results in terms of DF and DG were obtained with the full factorial design (6 x 6) and considering a trait with a high heritability. The optimal family size was found at 20 fish per mating

An Evolutionary Perspective on Epistasis and the Missing Heritability

<div><p>The relative importance between additive and non-additive genetic variance has been widely argued in quantitative genetics. By approaching this question from an evolutionary perspective we show that, while additive variance can be maintained under selection at a low level for some patterns of epistasis, the majority of the genetic variance that will persist is actually non-additive. We propose that one reason that the problem of the “missing heritability” arises is because the additive genetic variation that is estimated to be contributing to the variance of a trait will most likely be an artefact of the non-additive variance that can be maintained over evolutionary time. In addition, it can be shown that even a small reduction in linkage disequilibrium between causal variants and observed SNPs rapidly erodes estimates of epistatic variance, leading to an inflation in the perceived importance of additive effects. We demonstrate that the perception of independent additive effects comprising the majority of the genetic architecture of complex traits is biased upwards and that the search for causal variants in complex traits under selection is potentially underpowered by parameterising for additive effects alone. Given dense SNP panels the detection of causal variants through genome-wide association studies may be improved by searching for epistatic effects explicitly.</p> </div

Intensive Archeological Survey for Proposed Wastewater Improvements City of Anton, Hockley County, Texas

In October 2015, an intensive archeological survey was completed in order to inventory and evaluate archeological resources within a parcel of land where wastewater improvements are planned for the City of Anton, Hockley County, Texas. The planned improvements include a new wastewater plant/pump station, facultative lagoon, holding pond, and effluent application area. The archeological area of potential effects (APE) is a triangular parcel of land that measures approximately 0.45 by 0.47 by 0.62 miles (0.72 by 0.76 by 1.0 kilometers) and covers approximately 72 acres (29 hectares). The APE is on a level upland adjacent to Yellowhouse Draw. The work was carried out under Texas Antiquities Permit 7442 by Virginia Hatfield of Cox|McLain Environmental Consulting, Inc. (CMEC), a subcontractor to Parkhill, Smith and Cooper, Inc. (PSC). Ground surfaces within the APE were highly visible (100 percent across the entire APE) as the parcel of land has been utilized for agricultural activities, most recently hay. Six shovel tests were excavated, with a focus on southern edge due to the proximity of Yellowhouse Draw. All shovel tests were negative and revealed relatively shallow soils with the B horizon occurring at around 30 to 35 centimeters below the surface (cmbs). All materials (notes, photographs, administrative documents, and other project data) generated from this work will be housed at the Center for Archaeological Studies (CAS) at Texas State University, where they will be made permanently available to future researchers per 13 Texas Administrative Code (TAC) 26.16-17. If any unanticipated cultural materials or deposits are found at any stage of clearing, preparation, or construction, the work should cease and Texas Historical Commission (THC) personnel should be notified immediately. The Texas Historical Commission (THC) concurred with the findings and recommendations of this report on November 30, 2015 (see Appendix A)

Research: knowledge and method: reflections on Helen Mayer Harrison, Newton Harrison and David Haley's practice.

This paper is by way of an initial attempt to articulate a set of thoughts that are still emergent. These thoughts are concerned with artists working in public life. They are concerned with the form of research that artists do. They are concerned with the uses of knowledge. Greenhouse Britain: Losing Ground, Gaining Wisdom (2005-2008) was undertaken by Helen Mayer Harrison, Newton Harrison (the Harrisons) and David Haley, and which I joined as producer. More generally I tend to describe myself as a producer and researcher. The research word has a number of uses and I am going to try and make a little sense of them first by identifying the various individual relationships with research. Helen Mayer Harrison and Newton Harrison are Professors Emeritus of the University of California at San Diego, and have been involved in research on at least two levels for much of their career. Greenhouse Britain is typical of their work (as well as the work of David Haley) in that it involved working with scientists and others: people working on the ground with environmental issues such as farmers and water engineers

Stellarator Optimization with Poloidal Field Coils

Stellarators are devices that use magnetic fields to optimize the conditions needed for plasmas to undergo fusion. Unlike tokamaks, stellarators do not rely on a plasma current but can produce a helical magnetic field using only external coils. In a stellarator, the coils surrounding the plasma are called modular coils and those that follow the plasma are called poloidal field coils. Modular coils can be difficult to build if they are too complex. An effort is underway to develop coil conditions that meet both physics and engineering constraints. The FOCUS code was developed to flexibly optimize stellarator coil configurations [C. Zhu, et al., Plasma Phys. Contr. Fusion 60, 065008 (2018)]. In this work, we will use the FOCUS code to develop and analyze coil configurations for a plasma boundary that is optimized for particle confinement. We will examine modular coil configurations with and without a set of poloidal field coils

QTL detection and allelic effects for growth and fat traits in outbred pig populations

Quantitative trait loci (QTL) for growth and fatness traits have previously been identified on chromosomes 4 and 7 in several experimental pig populations. The segregation of these QTL in commercial pigs was studied in a sample of 2713 animals from five different populations. Variance component analysis (VCA) using a marker-based identity by descent (IBD) matrix was applied. The IBD coefficient was estimated with simple deterministic (SMD) and Markov chain Monte Carlo (MCMC) methods. Data for two growth traits, average daily gain on test and whole life daily gain, and back fat thickness were analysed. With both methods, seven out of 26 combinations of population, chromosome and trait, were significant. Additionally, QTL genotypic and allelic effects were estimated when the QTL effect was significant. The range of QTL genotypic effects in a population varied from 4.8% to 10.9% of the phenotypic mean for growth traits and 7.9% to 19.5% for back fat trait. Heritabilities of the QTL genotypic values ranged from 8.6% to 18.2% for growth traits, and 14.5% to 19.2% for back fat. Very similar results were obtained with both SMD and MCMC. However, the MCMC method required a large number of iterations, and hence computation time, especially when the QTL test position was close to the marker

Ten years of the Genomics of Common Diseases: “The end of the beginning”

The 10th anniversary ‘Genomics of Common Diseases’ meeting was held in Baltimore, September 25-28, 2016. Professor Chris Haley reports from the meeting on progress and challenges in the field

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBDL are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM