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Linkage disequilibrium in European elite maize germplasm investigated with SSRs

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Information about the extent and genomic distribution of linkage disequilibrium (LD) is of fundamental importance for association mapping. The main objectives of this study were to (1) investigate genetic diversity within germplasm groups of elite European maize (Zea mays L.) inbred lines, (2) examine the population structure of elite European maize germplasm, and (3) determine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) markers. We examined genetic diversity and LD in a cross section of European and US elite breeding material comprising 147 inbred lines genotyped with 100 SSR markers. For gene diversity within each group, significant (P<0.05) differences existed among the groups. The LD was significant (P<0.05) for 49% of the SSR marker pairs in the 80 flint lines and for 56% of the SSR marker pairs in the 57 dent lines. The ratio of linked to unlinked loci in LD was 1.1 for both germplasm groups. The high incidence of LD suggests that the extent of LD between SSR markers should allow the detection of marker-phenotype associations in a genome scan. However, our results also indicate that a high proportion of the observed LD is generated by forces, such as relatedness, population stratification, and genetic drift, which cause a high risk of detecting false positives in association mapping.

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The molecular marker analysis of this research was supported by funds from the “Gemeinschaft zur Förderung der privaten deutschen Pflanzenzüchtung” (GFP), Germany. Financial support for B. Stich was provided by a grant from the German National Academic Foundation. The authors thank the associate editor and two anonymous reviewers for their valuable suggestions.

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Correspondence to Albrecht E. Melchinger.

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Communicated by R. Bernardo

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Stich, B., Melchinger, A.E., Frisch, M. et al. Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111, 723–730 (2005).

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