How accurate are the marker orders in crop linkage maps generated from large marker datasets?
Bertrand Collard A , Emma Mace A E , Mark McPhail A , Peter Wenzl B , Mehmet Cakir C , Glen Fox D , David Poulsen A and David Jordan AA Department of Primary Industries and Fisheries (DPI&F), Hermitage Research Station, 604 Yangan Road, Warwick, Qld 4370, Australia.
B Diversity Arrays Technology P/L and Triticarte P/L, Both at PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia.
C WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia.
D DPI&F, Queensland Grains Research Centre, 13 Holberton Street, Toowoomba, Qld 4350, Australia.
E Corresponding author. Email: emma.mace@dpi.qld.gov.au
Crop and Pasture Science 60(4) 362-372 https://doi.org/10.1071/CP08099
Submitted: 17 March 2008 Accepted: 9 January 2009 Published: 21 April 2009
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.
Additional keywords: linkage analysis, marker ordering, accuracy, weighted accuracy of marker order scores, QTL mapping, quality, hardness.
Acknowledgments
The generation of simulated data using QU-GENE by Kevin McCallef is gratefully acknowledged. We sincerely thank Dr Herman Van Eck for numerous correspondences regarding the interpretation of RECORD results. We also thank members of the Australian Wheat and Barley Map Curation team (Rudi Appels, Anke Lehmensiek, Kerry Willsmore and Bill Bovill) for valuable discussion and an independent analysis of the Patty/Tallon mapping population. The funding provided by the Grains Research and Development Corporation (GRDC) is also gratefully acknowledged.
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