Comparisons of four approximation algorithms for large-scale linkage map construction |
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| Authors: | Jixiang Wu Johnie N Jenkins Jack C McCarty Xiang-Yang Lou |
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| Institution: | (1) Department of Plant Sciences, Mississippi State University, Mississippi State, MS 39762, USA;(2) Plant Science Department, South Dakota State University, Box 2140C, Brookings, SD 57007, USA;(3) Crop Science Research Laboratory, USDA-ARS, P.O. Box 5367, Mississippi State, MS 39762, USA;(4) Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA |
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| Abstract: | Efficient construction of large-scale linkage maps is highly desired in current gene mapping projects. To evaluate the performance
of available approaches in the literature, four published methods, the insertion (IN), seriation (SER), neighbor mapping (NM),
and unidirectional growth (UG) were compared on the basis of simulated F2 data with various population sizes, interferences, missing genotype rates, and mis-genotyping rates. Simulation results showed
that the IN method outperformed, or at least was comparable to, the other three methods. These algorithms were also applied
to a real data set and results showed that the linkage order obtained by the IN algorithm was superior to the other methods.
Thus, this study suggests that the IN method should be used when constructing large-scale linkage maps. |
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