AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs.
AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs.
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DOI：
10.1093/bioinformatics/bty375
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发表时间：
2018-10-01
期刊：
影响因子：
--
通讯作者：
Hickey JM
中科院分区：
文献类型：
--
作者：
Gorjanc G;Hickey JM
AlphaMate 是一个灵活的程序，可优化育种计划中的选择、遗传多样性的维护和配偶分配。它可用于动物和异花授粉和自花授粉植物群体。这些种群可以接受选择性育种或保护管理。该问题被表述为有效交配计划的多目标优化，并通过进化算法解决。有效的交配计划是由特定性别或通用的交配约束（交配次数、父母的最大数量、每个父母的最小/相等/最大贡献数量或自交允许）的组合来定义的。优化可以最大化遗传增益，最小化群体共谱，最小化个体交配的近交，或者最大化群体共谱或近交的给定增加的遗传增益。用户提供候选者列表以及相关的性别和选择标准信息（如果适用）以及祖先矩阵。选择标准和共源矩阵可以基于谱系或全基因组标记。可以包括额外的个体或交配特定信息以丰富优化目标。小麦快速循环基因组选择的一个例子表明，与截断选择相比，AlphaMate 如何将遗传多样性转化为遗传增益的效率提高一倍。另一个例子展示了使用基因组编辑来扩大增益多样性前沿。适用于 Windows、Mac 和 Linux 平台的 AlphaMate 的可执行版本可从 http://www.AlphaGenes.roslin.ed.ac.uk/AlphaMate 获取。
AlphaMate 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. Executable versions of AlphaMate for Windows, Mac and Linux platforms are available at http://www.AlphaGenes.roslin.ed.ac.uk/AlphaMate.
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影响因子：
4.1
作者：
TORO, M;PEREZENCISO, M
通讯作者：
PEREZENCISO, M
DOI：
10.1186/s12711-015-0135-3
发表时间：
2015-07-02
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Jenko J;Gorjanc G;Cleveland MA;Varshney RK;Whitelaw CB;Woolliams JA;Hickey JM
通讯作者：
Hickey JM
影响因子：
3.7
作者：
Akdemir D;Sánchez JI
通讯作者：
Sánchez JI
影响因子：
1.8
作者：
Storn, R;Price, K
通讯作者：
Price, K
影响因子：
4.1
作者：
Pong-Wong, Ricardo;Woolliams, John A.
通讯作者：
Woolliams, John A.