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

Collard, B. and Mace, E. and McPhail, M. and Wenzl, P. and Cakir, M. and Fox, G. and Poulsen, D. and Jordan, D. (2009) How accurate are the marker orders in crop linkage maps generated from large marker datasets? Crop & Pasture Science, 60 (4). pp. 362-372.

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Article Link(s): http://dx.doi.org/10.1071/CP08099

Publisher URL: http://www.publish.csiro.au/


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 R-2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping

Item Type:Article
Corporate Creators:Department of Employment, Economic Development and Innovation (DEEDI), Agri-Science, Crop and Food Science, QPIF
Business groups:Agri-Science, Crop and Food Science
Additional Information:© CSIRO.
Keywords:Linkage analysis; marker ordering; accuracy; weighted accuracy of marker order scores; QTL mapping; quality; hardness.
Subjects:Science > Biology > Genetics > Quantitative genetics (esp. Quantitative Trait Loci (QTL) articles)
Science > Botany
Science > Statistics > Statistical data analysis
Science > Statistics > Statistical software
Deposited On:04 Jun 2009 02:44
Last Modified:27 Oct 2011 01:23

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