72 research outputs found
A function accounting for training set size and marker density to model the average accuracy of genomic prediction.
No full textPrediction of genomic breeding values is of major practical relevance in dairy cattle breeding. Deterministic equations have been suggested to predict the accuracy of genomic breeding values in a given design which are based on training set size, reliability of phenotypes, and the number of independent chromosome segments ([Formula: see text]). The aim of our study was to find a general deterministic equation for the average accuracy of genomic breeding values that also accounts for marker density and can be fitted empirically. Two data sets of 5'698 Holstein Friesian bulls genotyped with 50 K SNPs and 1'332 Brown Swiss bulls genotyped with 50 K SNPs and imputed to ∼600 K SNPs were available. Different k-fold (k = 2-10, 15, 20) cross-validation scenarios (50 replicates, random assignment) were performed using a genomic BLUP approach. A maximum likelihood approach was used to estimate the parameters of different prediction equations. The highest likelihood was obtained when using a modified form of the deterministic equation of Daetwyler et al. (2010), augmented by a weighting factor (w) based on the assumption that the maximum achievable accuracy is [Formula: see text]. The proportion of genetic variance captured by the complete SNP sets ([Formula: see text]) was 0.76 to 0.82 for Holstein Friesian and 0.72 to 0.75 for Brown Swiss. When modifying the number of SNPs, w was found to be proportional to the log of the marker density up to a limit which is population and trait specific and was found to be reached with ∼20'000 SNPs in the Brown Swiss population studied
Accuracy of direct genomic values for functional traits in Brown Swiss cattle
No full textIn this study, direct genomic values for the functional traits general temperament, milking temperament, aggressiveness, rank order in herd, milking speed, udder depth, position of labia, and days to first heat in Brown Swiss dairy cattle were estimated based on ∼777,000 (777k) single nucleotide polymorphism (SNP) information from 1,126 animals. Accuracy of direct genomic values was assessed by a 5-fold cross-validation with 10 replicates. Correlations between deregressed proofs and direct genomic values were 0.63 for general temperament, 0.73 for milking temperament, 0.69 for aggressiveness, 0.65 for rank order in herd, 0.69 for milking speed, 0.71 for udder depth, 0.66 for position of labia, and 0.74 for days to first heat. Using the information of ∼54,000 (54k) SNP led to only marginal deviations in the observed accuracy. Trying to predict the 20% youngest bulls led to correlations of 0.55, 0.77, 0.73, 0.55, 0.64, 0.59, 0.67, and 0.77, respectively, for the traits listed above. Using a novel method to estimate the accuracy of a direct genomic value (defined as correlation between direct genomic value and true breeding value and accounting for the correlation between direct genomic values and conventional breeding values) revealed accuracies of 0.37, 0.20, 0.19, 0.27, 0.48, 0.45, 0.36, and 0.12, respectively, for the traits listed above. These values are much smaller but probably also more realistic than accuracies based on correlations, given the heritabilities and samples sizes in this study. Annotation of the largest estimated SNP effects revealed 2 candidate genes affecting the traits general temperament and days to first heat
How to Use Fewer Markers in Admixture Studies
No full textSwiss Fleckvieh has been established from 1970 as a composite of Simmental and Red Holstein Friesian cattle. Breed composition is currently reported based on pedigree information. Information on ancestry informative molecular markers potentially provides more accurate information. For the analysis Illumina Bovine SNP50 Beadchip data for 495 bulls were used. Markers were selected based on difference in allele frequencies in the pure populations, using FST as an indicator. Performance of sets with decreasing number of markers was compared. The scope of the study was to see how much we can reduce the number of markers based on FST to get a reliability that is close to that with the full set of markers. On these sets of markers hidden Markov models (HMM) and methods used in genomic selection (BayesB, partial least squares regression, LASSO variable selection) were applied. Correlations of admixture levels were estimated and compared with admixture levels based on pedigree information. FST chosen SNP gave very high correlations with pedigree based admixture. Only when using 96 and 48 SNP with the highest FST, correlations dropped to 0.92 and 0.90, respectively
Developing communities of practice and research through research informed teaching and learning in cross-cultural groups.
No full textThis conceptual research aims to answer three questions:
• What is the process for learning where teachers and learners research together?
• How can this process be enriched and enhanced, specifically working within an international
and cross-cultural student population?
• How can a co-existence of a pedagogic research informed learning and teaching environment
be embedded with staff and students?
This research looks into the way staff research informs pedagogic practice, and how staff work as
’joint partners’ with students to deliver more ’iterative’ education learning models. The research is aimed at the development of inclusive scholarly knowledge-building communities of practice (see Brew, 2006). The research highlights how staff work with students in an iterative communal process through project-based research activity and collaborative teamwork within cross-cultural groups. It also describes the processes of working with students and how it has helped to directly reinforce the curricula and informed the author’s own learning and teaching strategies. Significantly, this type of open engagement with cultural groups has alerted the author to howtraditional linear ’Western’ forms of academic research within art and design can be influenced by Eastern models of research enquiry. The research describes a coexistence of practice where research and enquiry can be fluidly exchanged between teacher and student.
Changes were made to curricula to develop a more social constructivist form of working (Gredler,
1997) where both the context in which learning occurs and the social contexts that learners bring
to their learning environment were put centre stage. A short film entitled Event digestion, a
pedagogic filmic picnic, where students came together to form a community event, highlighted
this process. This process was also one of cross-disciplinary staff team-working within art and
design where research work is enhanced through creating a more open social experiential learning
environment.
The research methodology is a predominantly qualitative one through problem solving and action
research. It is also situated within a pedagogic research-informed teaching approach where
teaching draws upon enquiry into the teaching and learning process itself (Jenkins & Healey,
2005). Methods incorporated have been cross-cultural international focus groups attended by
students, ’unstructured’ interviews, student case studies and, importantly, practice-based work.
The paper highlights how an active educational model can be developed through learning by
doing (Gibbs, 1998) and thinking (Ramsden, 2003), however, coming from a perspective which
addresses creativity across cultures (Lubart), is cross-disciplinary, and, importantly, by a practicebase collaborative international team project approach. The practical pedagogic findings will be of use to anyone working in design education wishing to develop cross-cultural curricula through practice-based learning and research
Encouraging beneficial insects in your garden
No full textTitle from PDF caption (viewed on June 28, 2018)."Originally published as part of Sustainable gardening: the Oregon-Washington master gardener handbook, EM 8742, ©1999."This archived document is maintained by the State Library of Oregon as part of the Oregon Documents Depository Program. It is for informational purposes and may not be suitable for legal purposes.Includes bibliographical references (page 2).Mode of access: Internet from the Oregon Government Publications Collection.Text in English
Pentatomomorpha I
No full textSpecies of the superfamilies Aradoidea, Lygaeoidea and Pyrrhocoroidea occurring in Slovenia are listed and data on the examined specimens presented. Six species or subspecies are reported for Slovenia for the first time: Aradus pallescens frigidus Kiritshenko, 1913, Ischnocoris hemipterus (Schilling, 1829), Stygnocoris cimbricus (Gredler, 1870), Stygnocoris fuligineus (Geoffroy, 1785), Stygnocoris matocqi Péricart, 1993 and Rhyparochromus sanguineus (Douglas & Scott, 1868). As far as the last species is concerned, however, the author believes that it is only a synonym for Rh. phoeniceus. 9 species, previously reported for Slovenia, have been omitted from the list due to misidentifications or misinterpreted localities
Runs of Homozygosity Reveal Genome-wide Autozygosity in the Austrian Fleckvieh Cattle
No full textRuns of homozygosity (ROH) are recognized as potential inbreeding measure in studies on humans. Inbreeding coefficients derived from ROH (FROH) measure proportion of the genome arranged in long homozygous segments and highly correlate with those derived from pedigree (Fped). From that we assumed that ROH represent an alternative to pedigree inbreeding levels in studies on animals too, because pedigree can be incorrect, incomplete and can not fully explain what happened in meiosis. To confirm our premise we used pedigree and genotype data from 500 Austrian dual purpose Simmental bulls to determine correlation between FROH and Fped. ROH were obtainedusing Fortran 90 soft ware created by the authors. Proportions of genome in ROH were calculated for lengths of ROH of >1, >2, >4, >8 and >16 Mb. Pedigree data were analyzed and inbreeding coefficients for complete pedigree (FpedT) and five generations (Fped5) were calculated using ENDOG soft ware. We found low FpedT and Fped5 (means of 1.5% and 0.9%) while FROH for segments >1Mb suggested much higher values (9.0%) indicating old inbreeding that can not be traced using pedigree. The highest correlations were found between FROH calculated from ROH of length >4Mb and FpedT (0.68) that is consistent with studies on humans. We conclude that inbreeding coefficients derived from ROH are useful for measuring levels of inbreeding in cattle, because ROH are not subject to mistakes as pedigrees and calculations made from those
Optimizing selection of the reference population for genotype imputation from array to sequence variants
No full textImputation of high-density genotypes to whole-genome sequences (WGS) is a cost-effective method to increase the density of available markers within a population. Imputed genotypes have been successfully used for genomic selection and discovery of variants associated with traits of interest for the population. To allow for the use of imputed genotypes for genomic analyses, accuracy of imputation must be high. Accuracy of imputation is influenced by multiple factors, such as size and composition of the reference group, and the allele frequency of variants included. Understanding the use of imputed WGSs prior to the generation of the reference population is important, as accurate imputation might be more focused, for instance, on common or on rare variants. The aim of this study was to present and evaluate new methods to select animals for sequencing relying on a previously genotyped population. The Genetic Diversity Index method optimizes the number of unique haplotypes in the future reference population, while the Highly Segregating Haplotype selection method targets haplotype alleles found throughout the majority of the population of interest. First the WGSs of a dairy cattle population were simulated. The simulated sequences mimicked the linkage disequilibrium level and the variants' frequency distribution observed in currently available Holstein sequences. Then, reference populations of different sizes, in which animals were selected using both novel methods proposed here as well as two other methods presented in previous studies, were created. Finally, accuracies of imputation obtained with different reference populations were compared against each other. The novel methods were found to have overall accuracies of imputation of more than 0.85. Accuracies of imputation of rare variants reached values above 0.50. In conclusion, if imputed sequences are to be used for discovery of novel associations between variants and traits of interest in the population, animals carrying novel information should be selected and, consequently, the Genetic Diversity Index method proposed here may be used. If sequences are to be used to impute the overall genotyped population, a reference population consisting of common haplotypes carriers selected using the proposed Highly Segregating Haplotype method is recommended
Estimating age of admixture in a cattle population based on SNP chip data
No full textThe aim of this study was to predict individual age of admixture in the crossbred Swiss Fleckvieh population. We checked how well the method is dealing with recent admixture with high throughput single nucleotide polymorphism data from the bovine 50K SNP Chip. A total of 101 Red Holstein, 91 Simmental, and 308 crossed animals were available for analysis. Age of admixture was derived from the complete pedigree and molecular markers. The method applied (using SABER software) based on Markov-hidden Markov model was able to derive age of admixture similar to estimates of pedigree data, however the values were often overestimated. Of 21 investigated cases, results from SNP data reflected paternal and maternal age of admixture well for 9 cases but provided results out of range for the other 12 cases. Alternative methods based on breed-specific haplotype blocks need to be evaluated in the future
Short communication : Genomic prediction using imputed whole-genome sequence variants in Brown Swiss Cattle
No full textThe accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle. The extreme scenarios were 50K SNP chip data and whole-genome sequence data with intermediate scenarios using linkage disequilibrium-pruned whole-genome sequence variants, only variants predicted to be missense, or the top 50K variants from genome-wide association studies. We estimated genomic breeding values for 3 traits (somatic cell score, nonreturn rate in heifers, and stature) and found differences in accuracy levels between traits. However, among different SNP sets, accuracy was very similar. In our analyses, sequence data led to a marginal increase in accuracy for 1 trait and was lower than 50K for the other traits. We concluded that the inclusion of imputed whole-genome sequence data does not lead to increased accuracy of genomic prediction with the methods
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