Comparison of Linkage Disequilibrium in Elite European Maize Inbred Lines using AFLP and SSR Markers |
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Authors: | Benjamin Stich Hans P Maurer Albrecht E Melchinger Matthias Frisch Martin Heckenberger Jeroen Rouppe van der Voort Johan Peleman Anker P Sørensen Jochen C Reif |
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Institution: | (1) Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany;(2) Keygene, P.O. Box 216, Wageningen, 6700, AE, The Netherlands |
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Abstract: | Application of association mapping to plant breeding populations has the potential to revolutionize plant genetics. The main
objectives of this study were to (i) investigate the extent and genomic distribution of linkage disequilibrium (LD) between
pairs of amplified fragment length polymorphism (AFLP) markers, (ii) compare these results with those obtained with simple
sequence repeat (SSR) markers, and (iii) compare the usefulness of AFLP and SSR markers for genomewide association mapping
in plant breeding populations. We examined LD in a cross-section of 72 European elite inbred lines genotyped with 452 AFLP
and 93 SSR markers. LD was significant (p < 0.05) for about 15% of the AFLP marker pairs and for about 49% of the SSR marker pairs in each of the two germplasm groups,
flint and dent. In both germplasm groups the ratio of linked to unlinked loci pairs in LD was higher for AFLPs than for SSRs.
The observation of LD due to linkage for both marker types suggested that genome-wide association mapping should be possible
using either AFLPs or SSRs. The results of our study indicated that SSRs should be favored over AFLPs but the opposite applies
to populations with a long history of recombination. |
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Keywords: | AFLPs Association mapping European elite maize inbred lines Linkage disequilibrium SSRs |
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