Liu Fenxiang, Tong Chunfa, Tao Shentong, Wu Jiyan, Chen Yuhua, Yao Dan, Li Huogen, Shi Jisen
The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
College of Department of Computer Science and Engineering, Sanjiang University, Nanjing, 210012, China.
BMC Bioinformatics. 2017 Nov 23;18(1):515. doi: 10.1186/s12859-017-1908-1.
With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F population. However, based on such genetic maps, quantitative trait loci (QTL) mapping cannot be directly conducted with traditional statistical methods or tools because the linkage phase and segregation pattern of molecular markers are not always fixed as in inbred lines.
We implemented the traditional composite interval mapping (CIM) method to multivariate trait data in forest trees and developed the corresponding software, mvqtlcim. Our method not only incorporated the various segregations and linkage phases of molecular markers, but also applied Takeuchi's information criterion (TIC) to discriminate the QTL segregation type among several possible alternatives. QTL mapping was performed in a hybrid F population of Populus deltoides and P. simonii, and 12 QTLs were detected for tree height over 6 time points. The software package allowed many options for parameters as well as parallel computing for permutation tests. The features of the software were demonstrated with the real data analysis and a large number of Monte Carlo simulations.
We provided a powerful tool for QTL mapping of multiple or longitudinal traits in an outbred F population, in which the traditional software for QTL mapping cannot be used. This tool will facilitate studying of QTL mapping and thus will accelerate molecular breeding programs especially in forest trees. The tool package is freely available from https://github.com/tongchf /mvqtlcim.
随着新一代测序技术成本的大幅下降，可以在林木杂交F群体中构建高密度遗传连锁图谱。然而，基于此类遗传图谱，由于分子标记的连锁相和分离模式并不总是像近交系那样固定，因此无法直接使用传统统计方法或工具进行数量性状位点（QTL）定位。
我们将传统的复合区间作图（CIM）方法应用于林木的多变量性状数据，并开发了相应的软件mvqtlcim。我们的方法不仅纳入了分子标记的各种分离和连锁相，还应用了竹内信息准则（TIC）在几种可能的选择中区分QTL分离类型。在美洲黑杨和小叶杨的杂交F群体中进行了QTL定位，在6个时间点检测到12个与树高相关的QTL。该软件包允许对参数进行多种设置，并支持对置换检验进行并行计算。通过实际数据分析和大量蒙特卡罗模拟展示了该软件的功能。
我们为异交F群体中多个或纵向性状的QTL定位提供了一个强大的工具，而传统的QTL定位软件无法在此群体中使用。该工具将有助于QTL定位研究，从而加速分子育种计划，特别是在林木育种中。该工具包可从https://github.com/tongchf /mvqtlcim免费获取。
