English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Background  Bayesian approaches for predicting genomic breeding values (GEBV) have been proposed that allow for different variances for individual markers resulting in a shrinkage procedure that uses prior information to coerce negligible effects towards zero. These approaches have generally assumed application to high-density genotype data on all individuals, which may not be the case in practice. In this study, three approaches were compared for their predictive power in computing GEBV when training at high SNP marker density and predicting at high or low densities: the well- known  Bayes-A,  a generalization of  Bayes-A  where scale and degrees of freedom are estimated from the data ( Student-t ) and a Bayesian implementation of the  Lasso  method. Twelve scenarios were evaluated for predicting GEBV using low-density marker subsets, including selection of SNP based on genome spacing or size of additive effect and the inclusion of unknown genotype information in the form of genotype probabilities from pedigree and genotyped ancestors.    Results  The GEBV accuracy (calculated as correlation between GEBV and traditional breeding values) was highest for  Lasso,  followed by  Student-t  and then  Bayes-A.  When comparing GEBV to true breeding values,  Student-t  was most accurate, though differences were small. In general the shrinkage applied by the  Lasso  approach was less conservative than  Bayes-A  or  Student-t,  indicating that  Lasso  may be more sensitive to QTL with small effects. In the reduced-density marker subsets the ranking of the methods was generally consistent. Overall, low-density, evenly-spaced SNPs did a poor job of predicting GEBV, but SNPs selected based on additive effect size yielded accuracies similar to those at high density, even when coverage was low. The inclusion of genotype probabilities to the evenly-spaced subsets showed promising increases in accuracy and may be more useful in cases where many QTL of small effect are expected.    Conclusions  In this dataset the  Student-t  approach slightly outperformed the other methods when predicting GEBV at both high and low density, but the  Lasso  method may have particular advantages in situations where many small QTL are expected. When markers were selected at low density based on genome spacing, the inclusion of genotype probabilities increased GEBV accuracy which would allow a single low- density marker panel to be used across traits.

Genomic breeding value prediction using three Bayesian methods and application to reduced density marker panels