Structure of Linkage Disequilibrium and Phenotypic Associations in the Maize Genome

Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding...

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Veröffentlicht in:Proceedings of the National Academy of Sciences - PNAS 2001-09, Vol.98 (20), p.11479-11484
Hauptverfasser: Remington, David L., Thornsberry, Jeffry M., Matsuoka, Yoshihiro, Wilson, Larissa M., Whitt, Sherry R., Doebley, John, Kresovich, Stephen, Goodman, M., Buckler, Edward S.
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container_title Proceedings of the National Academy of Sciences - PNAS
container_volume 98
creator Remington, David L.
Thornsberry, Jeffry M.
Matsuoka, Yoshihiro
Wilson, Larissa M.
Whitt, Sherry R.
Doebley, John
Kresovich, Stephen
Goodman, M.
Buckler, Edward S.
description Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance (r2< 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial selection on flowering time may have played a role in generating population structure. Provided the effects of population structure are effectively controlled, this research suggests that association studies show great promise for identifying the genetic basis of important traits in maize with very high resolution.
doi_str_mv 10.1073/pnas.201394398
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subjects Alleles
Biological Sciences
Chromosome Mapping
Chromosomes
Corn
Flowers & plants
Genetic loci
Genetics
Genome, Plant
Human genetics
Linkage Disequilibrium
Molecular Sequence Data
P values
Phenotype
Phenotypic traits
Polymorphism, Genetic
Population genetics
Population parameters
Population structure
Quantitative Trait, Heritable
Simple sequence repeats
Zea mays
Zea mays - genetics
title Structure of Linkage Disequilibrium and Phenotypic Associations in the Maize Genome
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