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.

Figure 1.—

Population structure based upon haplotype data of 102 genes of the four soybean populations taken from Hyten et al. (2006). K is the assumption of the number of clusters present (K = 2–5). Each colored vertical line represents an individual that is assigned proportionally to one of the K clusters with the proportions represented by the relative lengths of the K different colors. The individuals within each population are ordered by maturity group (MG) where the earliest-maturing individuals are to the left of each individual population and the latest-maturing individuals are to the right of each individual population.

Figure 2.—

D′ plots of the three chromosomal regions CR-A2, CR-G, and CR-J in G. soja, Landraces, N. Am. Ancestors, and Elite Cultivars: bright red, D′ = 1 and LOD ≥ 2; shades of pink/red, D′ < 1 and LOD ≥ 2; blue, D′ = 1 and LOD < 2; white, D′ < 1 and LOD < 2.

Figure 3.—

Linkage disequilibrium plots of r² vs. distance for the three chromosomal regions CR-A2, CR-G, and CR-J in G. soja, Landraces, N. Am. Ancestors, and Elite Cultivars.

Figure 4.—

r² plots of the three chromosomal regions CR-A2, CR-G, and CR-J in the Landraces and Elite Cultivars, which are likely candidate populations for whole-genome association analysis in soybean: solid, r² = 1; shadings, 0 < r² < 1; open, r² = 0.