Using semidefinite programming to optimize unequal deployment of genotypes to a clonal seed orchard
Using semidefinite programming to optimize unequal deployment of genotypes to a clonal seed orchard
复制标题
使用半定规划优化克隆种子果园的基因型不平等部署
DOI：
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复制
发表时间：
2014
影响因子：
2.4
通讯作者：
Makoto Yamashita
中科院分区：
文献类型：
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作者：
J. Ahlinder;Tim J. Mullin;Makoto Yamashita
树育种者必须经常考虑遗传多样性的保护，同时最大程度地提高对选择的反应。就种子果园而言，种子的买家希望对部署到森林的多样性的限制（有时是立法），同时需要最高的绩效。最佳选择不会完全避免亲属关系，而是最大程度地提高增益，同时对平均相关性施加限制。在这里，我们介绍了半决赛编程（SDP）的应用，作为一种优化基因型在克隆种子果园中部署的灵活方法。我们将选择问题提出为SDP，在这种情况下，平均繁殖值将最大化，同时对相关性施加限制，以及每个候选人的最大和最小贡献。将开源求解器SDPA嵌入了一种工具中，该工具旨在通过SDP简单而灵活地通过SDP优化种子果园。案例研究优化了苏格兰松树和洛伯利松树的种子果园，这说明了如何使用这种灵活性对某些候选基因型可用的scion材料施加其他约束，即使相关候选者之间具有不同程度的辅助手段，它们之间也可以优化选择。讨论了可以使用SDP的其他情况。
Tree breeders must often consider the conservation of genetic diversity, while at the same time, maximizing response to selection. In the case of seed orchards, the buyer of seed wants maximum performance, while satisfying a restriction, sometimes legislated, on the diversity deployed to the forest. Optimal selection will not completely avoid kinship but rather maximize gain while imposing a constraint on average relatedness. Here, we present the application of semidefinite programming (SDP) as a flexible approach to optimize the deployment of genotypes to a clonal seed orchard. We formulate the selection problem as an SDP, where average breeding value is to be maximized, while imposing constraints on relatedness, as well as maximum and minimum contributions from each candidate. An open-source solver, SDPA, was embedded into a tool designed to make the optimization of seed orchards by SDP simple and flexible. Case studies optimizing seed orchards for Scots pine and loblolly pine illustrate how this flexibility can be used to impose additional constraints on the scion material available from some candidate genotypes and optimize selection even when related candidates have varying degrees of coancestry among them. Additional situations where SDP can be employed are discussed.
DOI：
10.3920/978-90-8686-592-5
发表时间：
--
期刊：
影响因子：
--
作者：
Eding H;Bennewitz J.
通讯作者：
Bennewitz J.