Selective Mapping: A Strategy for Optimizing the Construction of High-Density Linkage Maps

Author:

Vision Todd J1,Brown Daniel G2,Shmoys David B23,Durrett Richard T4,Tanksley Steven D1

Affiliation:

1. Department of Plant Breeding, Cornell University, Ithaca, New York 14853

2. Department of Computer Science, Cornell University, Ithaca, New York 14853

3. School of Operations Research and Industrial Engineering, Cornell University, Ithaca, New York 14853

4. Department of Mathematics, Cornell University, Ithaca, New York 14853

Abstract

Abstract Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps.

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference34 articles.

1. On constructing radiation hybrid maps;Ben-Dor;J. Comput. Biol.,1997

2. The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse;Blake;Nucleic Acids Res.,1999

3. Recombinant inbreds for molecular mapping in maize;Burr;Trends Genet.,1991

4. Positional cloning moves from perditional to traditional;Collins;Nat. Genet.,1995

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