title: Highly variable patterns of linkage disequilibrium in multiple soybean populations.
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.
authors.affiliation: Soybean Genomics and Improvement Laboratory, U. S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Hyten
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
authors.forename: Qijian
authors.initials: Q
authors.lastname: Song
authors.forename: Randy C
authors.initials: RC
authors.lastname: Shoemaker
authors.forename: Randall L
authors.initials: RL
authors.lastname: Nelson
authors.forename: Jose M
authors.initials: JM
authors.lastname: Costa
authors.forename: James E
authors.initials: JE
authors.lastname: Specht
authors.forename: Perry B
authors.initials: PB
authors.lastname: Cregan
mesh_terms: D000483:Alleles; D005828:Genetics, Population; D018745:Genome, Plant; D006239:Haplotypes; D015810:Linkage Disequilibrium; D009656:North America; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D013025:Glycine max / Q000235:genetics*