Akond Zobaer, Alam Md Jahangir, Hasan Mohammad Nazmol, Uddin Md Shalim, Alam Munirul, Mollah Md Nurul Haque
Bioinformatics Lab,Department of Statistics,University of Rajshahi,Rajshahi-6205,Bangladesh.
Institute of Environmental Science,University of Rajshahi-6205,Bangladesh.
Bioinformation. 2019 Feb 28;15(2):90-94. doi: 10.6026/97320630015090. eCollection 2019.
Quantitative trait locus (QTL) analysis is a statistical method that links two types of information such as phenotypic data (trait measurements) and genotypic data (usually molecular markers). There a number of QTL tools have been developed for gene linkage mapping. Standard Interval Mapping (SIM) or Simple Interval Mapping or Interval Mapping (IM), Haley Knott, Extended Haley Knott and Multiple Imputation (IMP) method when the single-QTL is unlinked and Composite Interval Mapping (CIM) is designed to map the genetic linkage for both linked and unlinked genes in the chromosome. Performance of these methods is measured based on calculated LOD score. The QTLs are considered significant above the threshold LOD score 3.0. For backcross-simulated data, the CIM method performs significantly in detecting QTLs compare to other SIM mapping methods. CIM detected three QTLs in chromosome 1 and 4 whereas the other methods were unable to detect any significant marker positions for simulated data. For a real rice dataset, CIM also showed performance considerably in detecting marker positions compared to other four interval mapping methods. CIM finally detected 12 QTL positions while each of the other four SIM methods detected only six positions.
数量性状位点（QTL）分析是一种将两种信息联系起来的统计方法，比如表型数据（性状测量值）和基因型数据（通常是分子标记）。已经开发了许多用于基因连锁图谱绘制的QTL工具。当单QTL不连锁时，有标准区间作图（SIM）或简单区间作图或区间作图（IM）、哈利·诺特法、扩展哈利·诺特法和多重填补（IMP）方法，而复合区间作图（CIM）则用于绘制染色体上连锁和不连锁基因的遗传连锁图谱。这些方法的性能是根据计算出的LOD分数来衡量的。当LOD分数高于阈值3.0时，QTL被认为是显著的。对于回交模拟数据，与其他SIM作图方法相比，CIM方法在检测QTL方面表现显著。CIM在第1和第4染色体上检测到3个QTL，而其他方法无法检测到模拟数据的任何显著标记位置。对于一个真实的水稻数据集，与其他四种区间作图方法相比，CIM在检测标记位置方面也表现出色。CIM最终检测到12个QTL位置，而其他四种SIM方法每种仅检测到6个位置。
