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A Comparison on Some Interval Mapping Approaches for QTL Detection



Zobaer Akond1, 2, 3,*, Md. Jahangir Alam1, Mohammad Nazmol Hasan1,5 , Md. Shalim Uddin6, Munirul Alam4, Md. Nurul Haque Mollah5



1Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh; 2Institute of Environmental Science, University of Rajshahi-6205, Bangladesh; 3Agricultural Statistics and Information & Communication Technology (ASICT) Division, Bangladesh Agricultural Research Institute (BARI), Joydebpur, Gazipur-1701, Bangladesh; 4Emerging Infections, Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b); 5Bangabandhu Sheikh Mujibur Rahaman Agricultural University,Joydebpur,Gazipur-1706, Bangladesh. 6Plant Genetic Resources Center, Bangladesh Agricultural Research Institute, Joydebpur, Gazipur-1701



Zobaer Akond E-mail:; *Corresponding Author


Article Type

Research Article



Received January 17, 2019; Revised February 2, 2019; Accepted February 2, 2019; Published February 28, 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.



Quantitative trait locus (QTL), Simple Interval Mapping, Composite Interval Mapping, Logarithm-Of-Odds (LOD)



Akond et al. Bioinformation 15(2): 90-94 (2019)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.