An Initial Assessment of Genome-wide Linkage Disequilibrium in Soybean.
David Hyten1, Ik-Young Choi1, Moon-Sup Yoon2, Qijian Song1, James Specht3, Randall L. Nelson4, Kevin Chase5, Nevin Young6, K. Gordon Lark5, Randy Shoemaker1, and Perry Cregan1. (1) USDA-ARS, 10300 Baltimore Ave., Bldg-006 BARC-West, Beltsville, MD 20705, (2) National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon, South Korea, (3) Department of Agronomy and Horticulture, University of Nebraska-Lincoln, P. O. Box 830915, Lincoln, NE 68503, (4) USDA-ARS/Univ. of Illinois, 1101 West Peabody, Urbana, IL 61801, (5) University of Utah, Dep. of Biology, Salt Lake City, UT 84112, (6) University of Minnesota, St. Paul, MN 55108
Linkage disequilibrium (LD) is the "non-random association of alleles" and can be utilized through association analysis to discover quantitative trait loci (QTL). The largest resource of soybean germplasm is the Asian landraces that are the most immediate result of domestication. Previously it has been found that the extent and structure of LD is highly variable between three genomic regions in this germplasm. Due to the high variability in LD, a genome-wide map of LD is needed in the landraces to determine optimum marker coverage to have sufficient power to detect most QTL present in a whole-genome genetic association analysis. To assess genome-wide LD we have selected 96 G. max Asian landraces to represent maximum diversity based on origin and maturity. A total of 384 SNPs were selected for an Illumina GoldenGate assay to provide an initial assessment of LD in the Asian landraces. The 384 SNPs were initially tested and mapped in three soybean mapping populations, Minsoy x Noir 1, Minsoy x Archer, and Evans x Peking. A total of 345 SNPs were successfully mapped and used for the initial assessment of LD and population structure in the Asian landraces. This initial assessment of LD will help determine the average extent of LD in soybean. The ability of the GoldenGate assay to be multiplexed to test 1,536 SNPs simultaneously makes this a good platform to assess genome-wide LD in a plant species such as soybean that has high levels of LD. Such an analysis will assist in determining which regions require only low marker density and which regions need high marker density for a thorough genome scan.