| QTL mapping research has been a prominent study in the field of quantitative genetics. The choice of tools for QTL mapping plays a significant role in the study of QTL mapping. As a free programming language, the two packages R/qtl and R/qtlbim of R language can be used for the QTL mapping analysis of F2population. In this study, R/qtl and R/qtlbim were used for the QTL mapping of12traits of the F2population derived from maize inbred lines JB and Y53, and the results were compared with those of the several commonly used mapping softwares QTL Cartograph, QTLnetwork and ICIMapping. The results were as follows.(1) The CIM method of QTL Cartograph software owned the most powerful capability to find QTL, which mapped161QTLs underlying the12traits. However, lots of QTLs found by the CIM of QTL Cartograph located nearby, which suggested the existence of a lot of ghost QTLs. The weakest capability to find QTL was the multi-QTL fitting method of R/qtlbim, which just mapped18QTLs for12traits. This suggested that the multi-QTL fitting method of R/qtlbim might miss lots of QTLs.(2) According to the analysis results, both different methods of the same software and the same method of different softwares were not identical in QTL mapping. The four methods of R/qtl mapped56,67,38and41QTLs, respectively. But only16QTLs among which were all detected by different methods in the same sofeware.The two methods of R/qtlbim mapped24and18QTLs respectively, among which repeat detected QTLs just had5. The maker analysis method of R/qtl, QTL Cartograph and ICIMapping separately mapped57,84and116QTL, among which repeat detected QTLs were only17. The IM method of the five tools R/qtl, R/qtlbim, QTL Cartograph, ICIMapping and QTLnetwork separately mapped68,23,92,51and101QTLs respectively, but only one QTL was repeat detected. The CIM method of the three tools R/qtl, QTL Cartograph and ICIMapping separately mapped38,161and35QTLs, and only2QTLs were repeat found. In epistasis QTL mapping, just one pair of interaction was found the same in R/qtl and R/qtlbim. (3) As to the analysis efficiency, all the softwares were quick at one-dimensional scanning. And all the softwares took long time when the pemutation test was run. It was suggested that the empirical LOD threshold could be adopted directly to declare QTL.According to the results of this study, no method or software could be ensured to have the best QTL mapping. Multiple methods and softwares should be recommended in the real QTL mapping. |
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