Originally published as Genetics Published Articles Ahead of Print on February 7, 2007.

Genetics, Vol. 175, 1937-1944, April 2007, Copyright © 2007
doi:10.1534/genetics.106.069740

Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations

David L. Hyten*,{dagger}, Ik-Young Choi*,1, Qijian Song*,{dagger}, Randy C. Shoemaker{ddagger}, Randall L. Nelson§, Jose M. Costa{dagger}, James E. Specht** and Perry B. Cregan*,2

* Soybean Genomics and Improvement Laboratory, U. S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705, {dagger} Natural Resource Sciences and Landscape Architecture, University of Maryland, College Park, Maryland 20742, {ddagger} Department of Agronomy, U. S. Department of Agriculture, Agricultural Research Service, Iowa State University, Ames, Iowa 50011, § Soybean/Maize Germplasm, Pathology, and Genetics Research Unit and Department of Crop Sciences, U. S. Department of Agriculture, Agricultural Research Service, University of Illinois, Urbana, Illinois 61801 and ** Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583

2 Corresponding author: Beltsville Agricultural Research Center, 10300 Baltimore Ave., Bldg. 006, Room 100, Beltsville, MD 20705.
E-mail: creganp{at}ba.ars.usda.gov

Prospects for utilizing whole-genome association analysis in autogamous plant populations appear promising due to the reported high levels of linkage disequilibrium (LD). To determine the optimal strategies for implementing association analysis in soybean (Glycine max L. Merr.), we analyzed the structure of LD in three regions of the genome varying in length from 336 to 574 kb. This analysis was conducted in four distinct groups of soybean germplasm: 26 accessions of the wild ancestor of soybean (Glycine soja Seib. et Zucc.); 52 Asian G. max Landraces, the immediate results of domestication from G. soja; 17 Asian Landrace introductions that became the ancestors of North American (N. Am.) cultivars, and 25 Elite Cultivars from N. Am. In G. soja, LD did not extend past 100 kb; however, in the three cultivated G. max groups, LD extended from 90 to 574 kb, likely due to the impacts of domestication and increased self-fertilization. The three genomic regions were highly variable relative to the extent of LD within the three cultivated soybean populations. G. soja appears to be ideal for fine mapping of genes, but due to the highly variable levels of LD in the Landraces and the Elite Cultivars, whole-genome association analysis in soybean may be more difficult than first anticipated.




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