A complete solution for dissecting pure main and epistatic effects of QTL in triple testcross design.
A complete solution for dissecting pure main and epistatic effects of QTL in triple testcross design.
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在三重测交设计中剖析 QTL 的纯主效应和上位效应的完整解决方案
DOI：
10.1371/journal.pone.0024575
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Zhang YM
中科院分区：
文献类型：
--
作者：
He XH;Zhang YM
上位性在遗传、进化和作物育种中起着重要作用。为了检测上位性，几十年前开发了三重测交（TTC）设计。TTC设计的经典程序仅使用线性变换Z1、Z2和Z3（从TTC家族数量性状平均值计算）来推断所有基因的集体加性、显性和上位性效应的性质。虽然已经开发了几种TTC设计中的数量性状基因座（QTL）定位方法，但这些方法并没有提供一个完整的解决方案来剖析纯主效应和上位效应。因此，在本研究中，我们开发了一种两步法来估计F2和F∞度量模型下基于F2的TTC设计中的所有纯主效应和上位效应。在第一步中，Z1和Z2的扩增的主效应和上位效应的全基因组上的所有假定的QTL同时考虑使用经验贝叶斯方法估计，和Z3的三个纯上位效应使用二维基因组扫描。在第二步中，将第一步中获得的三个纯上位效应与增广上位效应和主效应整合，以进一步估计所有其他纯效应。一系列的蒙特卡罗模拟实验已经进行了验证所提出的方法。模拟试验结果表明：（1）新定义的遗传参数能正确识别，具有满意的统计功效和精度，（2）TTC设计的F2比F2和F2：3设计的效果好上级，（3）在Z1和Z2设计中，纯上位效应的符号显著影响检测增广上位效应的统计功效，（4）纯上位效应的符号显著影响检测增广上位效应的统计功效。4）用Z3估计纯上位效应需要较大的样本量和家系重复数。进一步讨论了本研究中所提出的方法在其他基础人群中的推广。
Epistasis plays an important role in genetics, evolution and crop breeding. To detect the epistasis, triple test cross (TTC) design had been developed several decades ago. Classical procedures for the TTC design use only linear transformations Z1, Z2 and Z3, calculated from the TTC family means of quantitative trait, to infer the nature of the collective additive, dominance and epistatic effects of all the genes. Although several quantitative trait loci (QTL) mapping approaches in the TTC design have been developed, these approaches do not provide a complete solution for dissecting pure main and epistatic effects. In this study, therefore, we developed a two-step approach to estimate all pure main and epistatic effects in the F2-based TTC design under the F2 and F∞ metric models. In the first step, with Z1 and Z2 the augmented main and epistatic effects in the full genetic model that simultaneously considered all putative QTL on the whole genome were estimated using empirical Bayes approach, and with Z3 three pure epistatic effects were obtained using two-dimensional genome scans. In the second step, the three pure epistatic effects obtained in the first step were integrated with the augmented epistatic and main effects for the further estimation of all other pure effects. A series of Monte Carlo simulation experiments has been carried out to confirm the proposed method. The results from simulation experiments show that: 1) the newly defined genetic parameters could be rightly identified with satisfactory statistical power and precision; 2) the F2-based TTC design was superior to the F2 and F2:3 designs; 3) with Z1 and Z2 the statistical powers for the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects; and 4) with Z3 the estimation of pure epistatic effects required large sample size and family replication number. The extension of the proposed method in this study to other base populations was further discussed.
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影响因子：
3.3
作者：
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通讯作者：
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