Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations

Authors

D. L. Hyten, Soybean Genomics and Improvement Laboratory, USDA Agricultural Research Service, Beltsville, MarylandFollow
Ik-Young Choi, Soybean Genomics and Improvement Laboratory, USDA Agricultural Research Service, Beltsville, MarylandFollow
Qijian Song, University of Maryland - College ParkFollow
Randy C. Shoemaker, Iowa State University
Randall L. Nelson, University of IllinoisFollow
Jose M. Costa, University of Maryland - College Park
James E. Specht, University of Nebraska-LincolnFollow
P. B. Cregan, Soybean Genomics and Improvement Laboratory, USDA Agricultural Research Service, Beltsville, MarylandFollow

ORCID IDs

D. L. Hyten

Document Type

Article

Date of this Version

2007

Citation

Genetics 175: 1937–1944 (April 2007)

Comments

Copyright 2007 by the Genetics Society of America

Abstract

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.