How accurate are the marker orders in crop linkage maps generated from large marker datasets?

Collard, Bertrand, Mace, Emma, McPhail, Mark, Wenzl, Peter, Cakir, Mehmet, Fox, Glen, Poulsen, David and Jordan, David (2009) How accurate are the marker orders in crop linkage maps generated from large marker datasets?. Crop and Pasture Science, 60 4: 362-372.


Author Collard, Bertrand
Mace, Emma
McPhail, Mark
Wenzl, Peter
Cakir, Mehmet
Fox, Glen
Poulsen, David
Jordan, David
Title How accurate are the marker orders in crop linkage maps generated from large marker datasets?
Journal name Crop and Pasture Science   Check publisher's open access policy
ISSN 1836-5795
1836-5795
Publication date 2009
Sub-type Article (original research)
DOI 10.1071/CP08099
Volume 60
Issue 4
Start page 362
End page 372
Total pages 11
Place of publication Collingwood, Vic., Australia
Publisher CSIRO Publishing
Language eng
Formatted abstract Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930–932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30–40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping.
Keyword Linkage analysis
Marker ordering
Accuracy
Weighted accuracy of marker order scores
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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