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United States Department of Agriculture

Agricultural Research Service

Title: Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations

item Hyten, David
item Choi, Ik-young
item Song, Qijian
item Shoemaker, Randy
item Nelson, Randall
item Costa, Jose
item Specht, James
item Cregan, Perry

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2007
Publication Date: 5/25/2007
Citation: Hyten, D.L., Choi, I., Song, Q., Shoemaker, R.C., Nelson, R.L., Costa, J.M., Specht, J.E., Cregan, P.B. 2007. Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations. Genetics. 175:1937-1944.

Interpretive Summary: Human geneticists are increasingly using an approach called "genetic association analysis" to discover the genes in human populations that are responsible for human disease. The success of genetic association analysis is dependent upon the extent of a genetic phenomenon referred to as "Linkage Disequilibrium" (LD) in the population under observation. The extensiveness of LD depends upon the length of chromosome segments that are passed intact from generation to generation without genetic recombination. Extensive LD would greatly increase the likelihood of successful genetic association analysis for the discovery of genes that control traits of interest in soybean germplasm. Therefore, it was the objective of the work reported here to assess the extent of LD in soybean germplasm via the DNA sequence analysis of portions of three different chromosome regions in each of 120 diverse soybean germplasm accessions. It was determined that the extent of LD varied greatly between the three regions and thus no clear conclusion could be drawn about the extent of LD in the soybean genome as a whole. This finding suggests that the successful application of genetic association analysis in soybean may be more difficult than was first anticipated. This information will be of particular interest to geneticists interested in new approaches for gene discovery in crop germplasm collections.

Technical 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 330-600 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 introduction that became the ancestors of N. Am. cultivars, and 25 N. Am. Elite cultivars. In G. soja, LD did not extend past 100 kb; however, in the three cultivated G. max groups, LD extended from 90 kb to 600 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 N. Am. Elite cultivars, whole genome association analysis in soybean may be more difficult than first anticipated.

Last Modified: 06/24/2017
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