Mapmarker/Exp3.0遗传图谱构建中重要参数设置初步探讨

Selection Techniques of Some Important Parameters in Genetic Linkage Map Construction Using Mapmarker/Exp 3.0

Mapmarker/Exp(3.0)是目前分子作图中应用最广的软件之一,但由于许多重要参数的默认值并非是作图的最佳值,影响提高作图的精确性。本文以川麦42×川农16重组近交系(F8)作图群体为实例,对Mapmarker/Exp 3.0软件在遗传作图中不同LOD值、max distance值以及用compare and try、compare和order 3种排序方式对遗传图谱的影响进行了初步比较,结果表明,作图过程中,不应强求采取统一LOD值,对于特殊的连锁群可采取不同的LOD值;max distance值在20至50为宜,值过小容易遗漏大量本来正确连锁的标记;小于等于7个标记的连锁群可直接用compare命令排序。

Mapmarker/Exp（3.0） is one of the most widely used software for linkage map constructing. However, the results of linkage map constructing would be affected by the optimum of the important and indispensable parameters. In present paper, the linkage maps using different LOD value, max distance and ordering commands were compared by using recombinant inbred lines of Chuanmai 42 and Chuannong 16. The result indicated that different LOD values should be used in different linkage groups, especially for some special linkage groups. The optimization value of max distance should range from 20 to 50, otherwise, many markers that original linkage together would be missing if the value is too low. The linkage group can directly use ＇ compare＇ command to get the marker sequence, when the used markers equal to or less than seven.