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Large population with low marker density verse small population with high marker density for QTL mapping: A case study for mapping QTL controlling barley net blotch resistance
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Large population with low marker density verse small population with high marker density for QTL mapping: A case study for mapping QTL controlling barley net blotch resistance

J. Yang, C. Li, X. Gong, S. Gupta, R. Lance, G. Zhang, R. Loughman and J. Zhu
Advance in Barley Sciences. Proceedings of 11th International Barley Genetics Symposium, pp.301-315
Springer
2012
DOI: https://doi.org/10.1007/978-94-007-4682-4_25
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Abstract

The development of array-based high-throughput genotyping methods created significant opportunities to increase the number of genetic populations for linkage analysis. In the present study, a strategy was proposed for mapping QTLs (quantitative trait loci) based on DArT (diversity arrays technology) genotyping system. A consensus linkage map was constructed with both DArT and SSR markers by utilizing a subgroup DH population, and a second linkage map was constructed with SSR markers alone and a more extensive full DH population. Resistance to barley net-type net blotch disease was analyzed using the subpopulation data with the high-density consensus linkage map and the full-population data with the low-density SSR linkage map, respectively. Two interactive QTLs were detected either by the sub- or full population. Simulation studies were conducted to validate the strategy presented in this chapter. In addition, a computer program written in C++ is freely available on the web to deal with the data files. Based on both real data analysis and simulation studies, we concluded that high-density molecular markers, small population size, and precise phenotyping can improve the precision of mapping major-effect QTL and the efficiency of conducting QTL mapping experiment.

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