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United States Department of Agriculture

Agricultural Research Service

Title: Structure of Linkage Disequilibrium and Phenotypic Associations in the Maize Genome.

Authors
item Buckler, Edward
item Remington, David - NORTH CAROLINA STATE UNIV
item Thornsberry, Jeffry - NORTH CAROLINA STATE UNIV
item Matsuoka, Yoshi - UNIVERSITY OF WISCONSIN
item Wilson, Larissa - NORTH CAROLINA STATE UNIV
item Whitt, Sherry
item Kresovich, Stephen - CORNELL UNIVERSITY
item Goodman, Major - NORTH CAROLINA STATE UNIV
item Doebley, John - UNIVERSITY OF WISCONSIN

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 27, 2001
Publication Date: N/A

Interpretive Summary: Currently, the genetic basis of most agronomic traits is only resolved to within 20 million base pairs. To gain higher resolution, researchers can use high the level of recombination (mixing of genes) that has occurred during the evolution and domestication of maize. Recombination within genes reduces the correlation between neighboring polymorphisms that are the basis of agronomic traits. By sequencing a large set of genes from diverse maize, we were able to show the correlation between neighboring polymorphisms dropped very rapidly. This suggests that future research, which exploits the correlation between neighboring polymorphisms, will be able to identify the genetic basis of agronomic traits to within 1000 base pairs.

Technical Abstract: Association studies based on linkage disequilibrium (LD) can provide powerful resolution for identifying genes that may contribute to phenotypic variation. However, genetic drift and selection can generate LD between genes and unlinked markers in structured populations such as that of cultivated maize. We report on patterns of local and genome-wide LD in 102 2maize inbred lines representing much of the genetic diversity used in maiz breeding, and address its implications for association studies in maize. In a survey of six genes, we found that LD generally declined rapidly with distance (r2 < 0.1 within 1000 bp), but the rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize and its wild relatives and high levels of recombination within genes. SSR loci showed stronger evidence of genome- wide LD than did 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 for flowering time may have played a role in generating population structure in maize. We conclude that association studies should have high resolution for identifying genes responsible for desirable traits in maize, but the effects of population structure cannot be ignored.

Last Modified: 11/28/2014
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