A strategy for finding the optimal scale of plant core collection based on Monte Carlo simulation.
A strategy for finding the optimal scale of plant core collection based on Monte Carlo simulation.
复制标题
基于蒙特卡罗模拟寻找植物核心采集最佳规模的策略
DOI：
10.1155/2014/503473
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发表时间：
2014
影响因子：
--
通讯作者：
Hu J
中科院分区：
文献类型：
--
作者：
Wang J;Guan Y;Wang Y;Zhu L;Wang Q;Hu Q;Hu J
核心集合是全基因组关联研究（GWAS）的理想资源。子核心集合是核心集合的子集。提出了一种基于蒙特卡罗模拟的植物亚核采集的最佳采样百分比求解策略。以棉花种质组168份，20个数量性状为材料，构建亚核心种质。采用混合线性模型法消除环境效应和基因型×环境效应。采用最小距离逐步抽样（LDSS）方法，结合6种常用的遗传距离和UPGMA聚类方法构建亚核集合。采用同质群体评价法对亚核心采集的7个评价参数的效度进行评价。对采样百分比、性状个数和评价参数进行了蒙特卡罗模拟。采用“从实验数据中提取自由形式自然规律”的新方法，寻找确定最优抽样百分比的最佳公式。结果表明，范围符合率（CR）是最有效的评价参数，适合作为寻找最佳抽样百分比的阈值。主成分分析表明，该策略计算的最优抽样百分比构建的子核集合具有较好的代表性。
Core collection is an ideal resource for genome-wide association studies (GWAS). A subcore collection is a subset of a core collection. A strategy was proposed for finding the optimal sampling percentage on plant subcore collection based on Monte Carlo simulation. A cotton germplasm group of 168 accessions with 20 quantitative traits was used to construct subcore collections. Mixed linear model approach was used to eliminate environment effect and GE (genotype × environment) effect. Least distance stepwise sampling (LDSS) method combining 6 commonly used genetic distances and unweighted pair-group average (UPGMA) cluster method was adopted to construct subcore collections. Homogeneous population assessing method was adopted to assess the validity of 7 evaluating parameters of subcore collection. Monte Carlo simulation was conducted on the sampling percentage, the number of traits, and the evaluating parameters. A new method for “distilling free-form natural laws from experimental data” was adopted to find the best formula to determine the optimal sampling percentages. The results showed that coincidence rate of range (CR) was the most valid evaluating parameter and was suitable to serve as a threshold to find the optimal sampling percentage. The principal component analysis showed that subcore collections constructed by the optimal sampling percentages calculated by present strategy were well representative.