genecont

Calculates the genetic contributions each individual has from specified ancestors.

A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees. The methods are described in:\n Wellmann, R., and Pfeiffer, I. (2009) <doi:10.1017/S0016672309000202>.\n Wellmann, R., and Bennewitz, J. (2011) <doi:10.2527/jas.2010-3709>.\n Wellmann, R., Hartwig, S., Bennewitz, J. (2012) <doi:10.1186/1297-9686-44-34>.\n de Cara, M. A. R., Villanueva, B., Toro, M. A., Fernandez, J. (2013) <doi:10.1111/mec.12560>.\n Wellmann, R., Bennewitz, J., Meuwissen, T.H.E. (2014) <doi:10.1017/S0016672314000196>.\n Wellmann, R. (2019) <doi:10.1186/s12859-018-2450-5>.

Robin Wellmann

optiSel

Optimum Contribution Selection and Population Genetics

genecont function

<dl><dt>Pedig</dt>
<dd>Data frame containing the pedigree, where the first columns are <code>Indiv</code> (Individual ID), <code>Sire</code>, and <code>Dam</code>.</dd><dt>from</dt>
<dd>Vector with ancestors whose contributions to the individuals should be calculated. By default, the contributions from all individuals will be calculated.</dd><dt>to</dt>
<dd>Vector with individuals for which the contributions from ancestors should be calculated. By default, the contributions are calculated for all individuals.</dd></dl>

Arguments

Author

Calculates Genetic Contributions using Pedigrees. — genecont

<dl>

<dt>Pedig</dt>
<dd>Data frame containing the pedigree, where the first columns are <code>Indiv</code> (Individual ID), <code>Sire</code>, and <code>Dam</code>.</dd>

<dt>from</dt>
<dd>Vector with ancestors whose contributions to the individuals should be calculated. By default, the contributions from all individuals will be calculated.</dd>

<dt>to</dt>
<dd>Vector with individuals for which the contributions from ancestors should be calculated. By default, the contributions are calculated for all individuals.</dd>

</dl>

genecont: Calculates Genetic Contributions using Pedigrees.

Description

Usage

Value

Arguments

Author

Details

Examples