Study of strategies for selecting quantitative trait locus mapping procedures by computer simulation

Along with the development and integration of molecular genetics and quantitative genetics, many quantitative trait locus (QTL) mapping studies have been conducted using different mapping populations in various crop species. Existing QTLs can be used for marker-assisted breeding and map-based clonin...

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Bibliographic Details
Published in:Molecular breeding 2013-04, Vol.31 (4), p.947-956
Main Authors: Su, Chengfu, Qiu, Xinmian, Ji, Zhixian
Format: Article
Language:English
Subjects:
Biomedical and Life Sciences
Biotechnology
Cartography
Cloning
Computer simulation
computer software
Epistasis
Gene mapping
Genetics
inbred lines
Inbreeding
Life Sciences
Mapping
marker-assisted selection
Molecular biology
molecular cloning
Plant biology
Plant Genetics and Genomics
Plant Pathology
Plant Physiology
Plant Sciences
Quantitative genetics
Quantitative trait loci
Scanning
screening
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Summary:Along with the development and integration of molecular genetics and quantitative genetics, many quantitative trait locus (QTL) mapping studies have been conducted using different mapping populations in various crop species. Existing QTLs can be used for marker-assisted breeding and map-based cloning, whereas the false-positive QTLs are no use. The purpose of this study is to evaluate the suitability of different mapping procedures for data from different genetic models. In this study, four types of recombinant inbred lines (RILs) with different genetic models, viz. additive QTLs (Model I), additive and epistatic QTLs (Model II), additive QTLs and QTL × environment interaction (Model III), additive, epistatic QTLs and QTL × environment interaction (Model IV), were simulated by computer. Six types of QTL mapping procedures, viz. CIM, MIMF, MIMR, ICIM, MQM and NWIM, on four kinds of QTL mapping software, viz. WinQTL Cartographer Version 2.5, IciMapping Version 2.0, MapQTL Version 5.0 and QTLnetwork Version 2.0, were used for screening QTLs of the simulated RILs. The results showed that different mapping procedures have different suitability for different genetic models. CIM and MQM can only screen Model I data. MIMR, MIMF and ICIM can only screen Model I and Model II data. NWIM can screen all four models’ data. It can be concluded that different genetic models’ data have different most suitable mapping procedures. In practical experiments where the genetic model of the data is unknown, a multiple model mapping strategy should be used, that is a full model scanning with complex model procedure followed by verification with other procedures corresponding to the scanning results.
ISSN:1380-3743
1572-9788
DOI:10.1007/s11032-013-9848-6