Curation of wheat maps to improve map accuracy and QTL detection
A. Lehmensiek A D , P. J. Eckermann B , A. P. Verbyla B , R. Appels C , M. W. Sutherland A and G. E. Daggard AA Centre for Systems Biology, Faculty of Sciences, University of Southern Queensland, Toowoomba, Qld 4350, Australia.
B BiometricsSA, University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia.
C Molecular Plant Breeding CRC, Department of Agriculture, Murdoch University, Western Australia Locked Bag 4, Bentley Delivery Centre, WA 6983, Australia.
D Corresponding author. Email: lehmensi@usq.edu.au
Australian Journal of Agricultural Research 56(12) 1347-1354 https://doi.org/10.1071/AR05126
Submitted: 15 April 2005 Accepted: 2 September 2005 Published: 15 December 2005
Abstract
Three Australian doubled haploid populations were used to illustrate the importance of map curation in order to improve the quality of linkage maps and quantative trait locus (QTL) detection. The maps were refined and improved by re-examining the order of markers, inspection of the genetic maps in relation to a consensus map, editing the marker data for double crossovers, and determining estimated recombination fractions for all pairs of markers. The re-ordering of markers and replacing genotypes at double crossovers with missing values resulted in an overall decrease in the length of the maps. Fewer apparent genotyping errors, associated with the presence of double recombinants, were identified with restriction fragment length polymorphisms (RFLPs) than with other types of markers used in this study. The complications that translocations may cause in the ordering of markers and subsequent QTL analysis were investigated. QTL analysis using both the original and revised maps indicated that QTL peaks were more sharply located or had improved log-likelihood (LOD) scores in the revised maps. An accurate indication of the QTL peak and a significant LOD score are both essential for the identification of markers suitable for marker-assisted selection. Recommendations are provided for the improvement of the quality of linkage maps.
Additional keywords: linkage map revision, locus order, double recombinants, recombination fractions, translocation, doubled haploid lines.
Acknowledgments
The authors thank the Grain Research and Development Corporation for funding of this project through the Australian Winter Cereals Molecular Marker Program. We also thank all the research groups that have contributed towards the maps, and Lynette Rampling (CSIRO Plant Industry, Canberra) for providing us with DNA for the populations.
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