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Bioinformation. 2019 Feb 28;15(2):90-94. doi: 10.6026/97320630015090. eCollection 2019.

A Comparison on Some Interval Mapping Approaches for QTL Detection.

Author information

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

Abstract

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.

KEYWORDS:

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

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