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Acta Agron Sin ›› 2008, Vol. 34 ›› Issue (02): 217-223.doi: 10.3724/SP.J.1006.2008.00217

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Application Technique of Marker Grouping and Ordering in Genetic Linkage Map Construction Using Mapmaker/Exp

XING Guang-Nan,ZHAO Tuan-Jie,GAI Jun-Yi*

  

  1. Soybean Research Institute of Nanjing Agricultural University, National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing 210095, Jiangsu, China

  • Received:2007-04-05 Revised:1900-01-01 Online:2008-02-12 Published:2008-02-12
  • Contact: GAI Jun-Yi

Abstract:

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.

Key words:

Mapmaker/Exp (3.0), Genetic linkage map, Mapping technique, Marker grouping, Marker ordering

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