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Last updated: 2021-01-03

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Knit directory: PredictOutbredCrossVar/

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    Modified:   output/crossPredictions/predictedUntestedCrossMeansBV.rds
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    Modified:   output/crossPredictions/predictedUntestedCrossMeansTGV.rds
    Modified:   output/crossPredictions/predictedUntestedCrossMeans_SelIndices.rds
    Modified:   output/crossPredictions/predictedUntestedCrossMeans_tidy_traits.rds
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    Modified:   output/crossRealizations/realizedCrossMeans.rds
    Modified:   output/crossRealizations/realizedCrossMeans_BLUPs.rds
    Modified:   output/crossRealizations/realizedCrossMetrics.rds
    Modified:   output/crossRealizations/realizedCrossVars.rds
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    Modified:   output/crossRealizations/realized_cross_means_and_covs_traits.rds
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    Modified:   output/gblups_DirectionalDom_parentwise_crossVal_folds.rds
    Modified:   output/gblups_geneticgroups.rds
    Modified:   output/gblups_parentwise_crossVal_folds.rds
    Modified:   output/gebvs_ModelA_GroupAll_stdSI.rds
    Modified:   output/mtMarkerEffects/mt_All_A.rds
    Modified:   output/mtMarkerEffects/mt_All_AD.rds
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    Modified:   output/mtMarkerEffects/mt_GG_A.rds
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    Modified:   output/mtMarkerEffects/mt_GG_DirectionalDom.rds
    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold1_testset_A.rds
    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold1_testset_AD.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold2_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold2_trainset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold3_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold3_trainset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold4_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold4_trainset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold5_testset_A.rds
    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold5_testset_AD.rds
    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold5_testset_DirectionalDom.rds
    Modified:   output/mtMarkerEffects/mt_Repeat1_Fold5_trainset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold1_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold1_trainset_A.rds
    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold1_trainset_AD.rds
    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold1_trainset_DirectionalDom.rds
    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold2_testset_A.rds
    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold2_testset_AD.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold2_trainset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold3_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold3_trainset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold4_testset_A.rds
    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold4_testset_AD.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold4_trainset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold5_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat2_Fold5_trainset_DirectionalDom.rds
    Modified:   output/mtMarkerEffects/mt_Repeat3_Fold1_testset_A.rds
    Modified:   output/mtMarkerEffects/mt_Repeat3_Fold1_testset_AD.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat3_Fold1_trainset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat3_Fold2_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat3_Fold2_trainset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat3_Fold3_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat3_Fold3_trainset_DirectionalDom.rds
    Modified:   output/mtMarkerEffects/mt_Repeat3_Fold4_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat4_Fold1_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat4_Fold3_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_Repeat5_Fold5_testset_A.rds
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    Modified:   output/mtMarkerEffects/mt_TMS13_A.rds
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    Modified:   output/mtMarkerEffects/mt_TMS13_DirectionalDom.rds
    Modified:   output/mtMarkerEffects/mt_TMS14_A.rds
    Modified:   output/mtMarkerEffects/mt_TMS14_AD.rds
    Modified:   output/mtMarkerEffects/mt_TMS14_DirectionalDom.rds
    Modified:   output/mtMarkerEffects/mt_TMS15_A.rds
    Modified:   output/mtMarkerEffects/mt_TMS15_AD.rds
    Modified:   output/mtMarkerEffects/mt_TMS15_DirectionalDom.rds
    Modified:   output/obsVSpredMeans.rds
    Modified:   output/obsVSpredUC.rds
    Modified:   output/obsVSpredVars.rds
    Modified:   output/pmv_DirectionalDom_varcomps_geneticgroups.rds
    Modified:   output/pmv_varcomps_geneticgroups.rds
    Modified:   output/pmv_varcomps_geneticgroups_tidy_includingSIvars.rds
    Modified:   workflowr_log.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/about.Rmd) and HTML (docs/about.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	22e6c87	wolfemd	2021-01-03	Build site.
html	34c84f3	wolfemd	2020-10-27	Build site.
Rmd	b4edd2c	wolfemd	2020-10-27	Start workflowr project.
html	3dbb1e8	wolfemd	2020-10-08	Site built for first COMPLETE draft, shared with co-authors.
html	b06eee7	wolfemd	2020-08-31	Build site.
html	7a4e168	wolfemd	2020-07-31	Build site.
html	a5ac99f	wolfemd	2020-07-31	Build site.
html	ff4fc8b	wolfemd	2020-07-31	Build site.
html	e6f8fe8	wolfemd	2020-07-31	Build site.
Rmd	07509a8	wolfemd	2020-07-31	Organized and ready to be published as a workflowr HTML page.
Rmd	f9e7617	wolfemd	2019-11-23	Start workflowr project.

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Abstract, acknowledgements and funding sources for the project here.

Abstract

Diverse crops ranging from staples (e.g., cassava) to cash crops (e.g., cacao) are both outbred and clonally propagated. In these crops, exceptional genotypes can be immortalized and commercialized as clonal varieties. To take advantage of this, genomic prediction can incorporate both additive and non-additive effects in clonal crops to select candidates with high breeding value as parents for crossing and candidates with high total genetic merit as varieties for release to farmers. It is possible to predict not only the mean breeding value but also the additive genetic variance and trait covariance in a cross using genome-wide phased parental haplotypes, marker effects estimates, and a recombination map. Several recent studies in both animal and plant breeding have demonstrated improved short and long term genetic gain using optimized parent selection and mate allocation, enabled by predictions of cross variances. In this study, we extend cross (co)variance prediction to include non-additive (namely dominance) effects. We present an empirical study of cassava (Manihot esculenta), a staple root crop essential to food security throughout the tropics. We analyze 462 outbred cassava families (209 parents total) derived from a genomic selection program, part of the Next Generation Cassava Breeding Project (www.nextgencassava.org). We assess the practical potential to predict the multivariate genetic distribution (means, variances and trait covariances) in untested cassava crosses in terms of both general and specific combining ability using cross-validation. Ultimately, we hope to enable breeders of outbred clonal crops to consider the potential of crosses to produce future parents (progeny with excellent breeding values) as well as potential varieties (progeny with top performance) on a multi-trait selection index.

Acknowledgements

Funding