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AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs.

Gregor Gorjanc¹, John M Hickey¹

¹The Roslin Institute, Royal Dick School of Veterinary Studies, The University of Edinburgh, Scotland, UK.

Bioinformatics (Oxford, England)

|May 4, 2018

Summary

AlphaMate optimizes breeding programs by balancing genetic gain and diversity. This program enhances selection and mate allocation, doubling efficiency in genomic selection for wheat.

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Area of Science:

* Animal and plant breeding
* Evolutionary algorithms
* Conservation genetics

Background:

* Breeding programs require optimization of genetic gain and diversity.
* Existing methods may not adequately balance these objectives.
* Flexible tools are needed for diverse breeding and conservation scenarios.

Purpose of the Study:

* To introduce AlphaMate, a novel program for optimizing breeding programs.
* To enable simultaneous optimization of genetic gain and diversity maintenance.
* To provide a flexible platform for various breeding and conservation applications.

Main Methods:

* Formulates mating plan optimization as a multi-objective problem.
* Employs an evolutionary algorithm to solve complex mating constraints.
* Integrates pedigree or genomic marker data for coancestry and selection.

Main Results:

* AlphaMate can maximize genetic gain while minimizing coancestry and inbreeding.
* Demonstrated a doubling of efficiency in genomic selection for wheat.
* Showcased potential for genome editing to expand gain-diversity trade-offs.

Conclusions:

* AlphaMate offers a powerful, flexible solution for breeding program optimization.
* The program effectively balances genetic gain with the preservation of genetic diversity.
* Applicable to both selective breeding and conservation management across species.