Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

status: publishe

Development and Commercialization of Software for Genetic Improvement Programmes: a Case Study

The development of computers within the last 20 years has been dramatic. Whilst computer scientists may have been making predictions of such changes, it would have been hard for livestock breeders to appreciate fully that, within a short space of time, populations of millions would have individual breeding values calculated using complex and demanding statistical techniques. Examination of pre-1990 research indicates the extent of computational development since. Many techniques that are common and accepted in research today were rare, e.g. simple stochastic simulation of populations and Bayesian analysis of complex data using Monte-Carlo Markov Chains. Even providing a standard error for a variance component was a challenge! This surge in computing power has prompted the development of concepts to remove important areas of ignorance in our understanding of genetic improvement schemes, and it is not surprising that this same surge has had a profound impact on their operational management

Climate Data Records from Meteosat First Generation Part III: Recalibration and Uncertainty Tracing of the Visible Channel on Meteosat-2–7 Using Reconstructed, Spectrally Changing Response Functions

This paper presents a new Fundamental Climate Data Record (FCDR) for the visible (VIS) channel of the Meteosat Visible and Infrared Imager (MVIRI), with pixel-level metrologically traceable uncertainties and error covariance estimates. MVIRI has flown onboard Meteosat First Generation (MFG) satellites between 1982 and 2017. It has served the weather forecasting community with measurements of “visible„, “infra-red„ and “water vapour„ radiance in near real-time. The precision of the pre-launch sensor spectral response function (SRF) characterisation, particularly of the visible band of this sensor type, improved considerably with time, resulting in higher quality radiances towards the end of the MFG program. Despite these improvements, the correction of the degradation of this sensor has remained a challenging task and previous studies have found the SRF degradation to be faster in the blue than in the near-infrared part of the spectrum. With these limitations, the dataset cannot be immediately applied in climate science. In order to provide a data record that is suited for climate studies, the Horizon 2020 project “FIDelity and Uncertainty in Climate-data records from Earth Observation„ (FIDUCEO) conducted (1) a thorough metrological uncertainty analysis for each instrument, and (2) a recalibration using enhanced input data such as reconstructed SRFs. In this paper, we present the metrological analysis, the recalibration results and the resulting consolidated FCDR. In the course of this study we were able to trace-back the remaining uncertainties in the calibrated MVIRI reflectances to underlying effects that have distinct physical root-causes and spatial/temporal correlation patterns. SEVIRI and SCIAMACHY reflectances have been used for a validation of the harmonised dataset. The resulting new FCDR is publicly available for climate studies and for the production of climate data records (CDRs) spanning about 35 years

Characterization of OAR1 and OAR18 QTL associated with muscle depth in British commercial terminal sire sheep

This study aimed at verifying previously identified QTL affecting growth and carcass traits on ovine chromosome 18 (OAR18) in Texel sheep (n = 1844), and on OAR1 in Charollais (n = 851) and Suffolk (n = 998) sheep. The QTL were investigated using regression and variance component mapping (VCA) of body weight, muscle and fat depth measurements. In addition, the mode of inheritance of the Texel OAR18 QTL was explored, using data from 4376 Texel sheep, fitting VCA models testing for additive and imprinting effects. We also simulated a 480-sheep population with different QTL imprinting models and various available levels of marker information to understand the behaviour of the VCA results under different assumed genetic models. In summary, the previously identified QTL were successfully verified using both interval mapping and VCA in the three breeds. We propose a polar overdominance mode of inheritance for the OAR18 QTL in Texel sheep, and we present methods to dissect the QTL mode of inheritance, using the Texel OAR18 QTL as an example