The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
To make progress in breeding, populations should have a favorable mean and high genetic variance (Bernardo 2010). These two parameters can be combined into a single measure called the usefulness criterion (Schnell and Utz 1975), visualized in Figure 1.
Ideally, breeders would identify the set of parent combinations that, when realized in a cross, would give rise to populations meeting these requirements. PopVar is a package that uses phenotypic and genomewide marker data on a set of candidate parents to predict the mean, genetic variance, and superior progeny mean in bi-parental or multi-parental populations. Thre package also contains functionality for performing cross-validation to determine the suitability of different statistical models. More details are available in Mohammadi, Tiede, and Smith (2015) A dataset think_barley is included for reference and examples.
You can install the released version of PopVar from CRAN with:
And the development version from GitHub with:
Below is a description of the functions provided in PopVar:
| Function | Description |
|---|---|
pop.predict |
Uses simulations to make predictions in recombinant inbred line populations; can internally perform cross-validation for model selections; can be quite slow. |
pop.predict2 |
Uses deterministic equations to make predictions in populations of complete or partial selfing and with or without the induction of doubled haploids; is much faster than pop.predict; does not perform cross-validation or model selection internally. |
pop_predict2 |
Has the same functionality as pop.predict2, but accepts genomewide marker data in a simpler matrix format. |
x.val |
Performs cross-validation to estimate model performance. |
mppop.predict |
Uses deterministic equations to make predictions in 2- or 4-way populations of complete or partial selfing and with or without the induction of doubled haploids; does not perform cross-validation or model selection internally. |
mpop_predict2 |
Has the same functionality as mppop.predict, but accepts genomewide marker data in a simpler matrix format. |
Examples are outlined in the package vignette.
Bernardo, Rex. 2010. Breeding for Quantitative Traits in Plants. Woodbury, Minnesota: Stemma Press.
Mohammadi, Mohsen, Tyler Tiede, and Kevin P Smith. 2015. “PopVar: A Genome-Wide Procedure for Predicting Genetic Variance and Correlated Response in Biparental Breeding Populations.” Crop Sci. 55 (5): 2068–77. https://doi.org/10.2135/cropsci2015.01.0030.
Schnell, F W, and H F Utz. 1975. “F1-Leistung Und Elternwahl Euphyder züchtung von Selbstbefruchtern.” In Bericht über Die Arbeitstagung Der Vereinigung Österreichischer Pflanzenzüchter, 243–48. Gumpenstein, Austria: BAL Gumpenstein.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.