Abstract
SummaryAlphaMate is a flexible program that optimizes selection, maintenance of genetic diversity and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimization of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic. The optimization can maximize genetic gain, minimize group coancestry, minimize inbreeding of individual matings, or maximize genetic gain for a given increase in group coancestry or inbreeding. Users provide a list of candidate individuals with associated gender and selection criteria information (if applicable) and coancestry matrix. Selection criteria and coancestry matrix can be based on pedigree or genome-wide markers. Additional individual or mating specific information can be included to enrich optimization objectives. An example of rapid recurrent genomic selection in wheat demonstrates how AlphaMate can double the efficiency of converting genetic diversity into genetic gain compared to truncation selection. Another example demonstrates the use of genome editing to expand the gain-diversity frontier.Availability and implementationExecutable versions of AlphaMate for Windows, Mac and Linux platforms are available at http://www.AlphaGenes.roslin.ed.ac.uk/AlphaMate.
Highlights
This paper describes the AlphaMate program that optimises selection, maintenance of genetic diversity, and mate allocation in breeding programs
While elite individuals increase the mean of generations, their excessive use significantly reduces the amount of genetic diversity
We describe its methodology and show its application in two examples i) maximising efficiency of converting genetic diversity into genetic gain in a rapid recurrent genomic selection program for wheat and ii) expanding the gain-diversity frontier with genome editing
Summary
This paper describes the AlphaMate program that optimises selection, maintenance of genetic diversity, and mate allocation in breeding programs. Breeding programs that select for improved performance must balance short and long-term genetic gain by avoiding excessive use of elite individuals. While elite individuals increase the mean of generations, their excessive use significantly reduces the amount of genetic diversity This reduction limits the potential for long-term improvement. The optimal contribution theory formulates balancing selection and maintenance of genetic diversity as optimisation of individuals’ contributions to the generation under constrained rate of group coancestry; see Woolliams et al (2015) for review. Optimisation of contributions can be followed by mate allocation to minimize inbreeding of individual matings This second optimisation prevents excessive inbreeding depression in resulting progeny. We describe its methodology and show its application in two examples i) maximising efficiency of converting genetic diversity into genetic gain in a rapid recurrent genomic selection program for wheat and ii) expanding the gain-diversity frontier with genome editing
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