摘要
Mapmaker/Exp(3.0)是国内外广泛使用的遗传连锁数据分析软件,在分子标记数量大时(多于500个)往往出现所绘制连锁图谱图距偏大的现象。本文从标记分群和标记排序两个遗传作图环节分析原因并概括出以下两个实施要点:(1)标记分群不应强求同一LOD值,对特殊的连锁群可试用不同LOD值;(2)在标记排序时,一次order命令后用ripple命令反复梳理有时并不能获得最佳排列顺序,而应多次使用order,每次order后用ripple反复梳理,经反复比较才能得出最佳排列顺序,必要时还须结合人工调整。通过大豆遗传作图实例比较了软件推荐思路2的通常用法和作者建议的新用法所构建的遗传图谱及相应QTL定位的差异,认为新用法具有更好的效果。
Mapmaker/Exp （3.0） is one of the most often used computer software packages for constructing genetic linkage map worldwide. It was found that the distances of the map constructed with the software were often exaggerated when large number of markers was involved. The present paper is to introduce our technical experiences in using Method 2 （marker number more than 500） of the software for a more reasonable linkage map. In Method 2 of Mapmaker/Exp （3.0）, markers were usually grouped into linkage groups under an identical LOD value for all linkage groups; and then an ＂order＂ command followed by multiple ＂ripple＂ command was used to test the order with a window size of 5. The causes for the exaggerated map distances were found probably in two aspects in Method 2, i.e. the way of assignment of LOD value and utilization of ＂order＂ and ＂ripple＂ commands in marker grouping and marker ordering. Therefore, two innovations were taken in the application of Method 2 as： （1） different LOD values used for some specific linkage groups in addition to a common LOD value for the others; and （2） multiple ＂order＂ commands each followed with multiple ＂ripple＂ commands used for ordering markers in linkage groups, combined with some artificial adjustments when needed, for relatively higher likelihoods of the linkage groups. The innovations were used to construct a soybean genetic linkage map which showed more reasonable than that constructed with the old procedure with a better consistency to the soybean consensus map.
出处
《作物学报》
CAS
CSCD
北大核心
2008年第2期217-223,共7页
Acta Agronomica Sinica
基金
国家自然科学基金项目(30490250)
国家重点基础研究发展计划(973计划)项目(2002CB111304
2004CB7206
2006CB101708)
国家高技术研究发展计划(863计划)项目(2002AA211052
2006AA100104)
教育部长江学者和创新团队发展计划项目(PCSIRT)
