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46 Estimation of recombination frequency in bi-parental genetic populations

Hits： | Time：2013-03-26

Summary Linkage analysis plays an important role in genetic studies. In linkage analysis, accurate estimation ofrecombination frequency is essential. Many bi-parental populations have been used, and determining anappropriate population is of great importance in preciserecombination frequency. In this study, we investigatedthe estimation efficiency of recombination frequency in 12 bi-parental populations. The criteria that we used forcomparison were LOD score in testing linkage relationship, deviation between estimated and real recombinationfrequency, standard error (SE) of estimates and the least theoretical population size (PS) required toobserve atleast one recombinant and to declare the statistically significant linkage relationship. Theoretical and simulationresults indicated that larger PS and smaller recombination frequency resulted in higher LOD score and smallerdeviation. Lower LOD score, higher deviation and higher SE for estimating the recombination frequency inthe advanced backcrossing and selfing populations are larger than those in backcross and F2 populations,respectively. For advanced backcrossing and selfing populations, larger populations were needed in order toobserve at least one recombinant and to declare significant linkage. In comparison, in F2 and F3 populationshigher LOD score, lower deviation and SE were observed for co-dominant markers. A muchlarger populationwas needed to observe at least one recombinant and to detect loose linkage for dominant and recessive markers.Therefore, advanced backcrossing and selfing populations had lower precision in estimating the recombinationfrequency. F2 and F3 populations together with co-dominant markers represent the ideal situation for linkageanalysis and linkage map construction.

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46 Estimation of recombination frequency in bi-parental genetic populations

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