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United States Department of Agriculture

Agricultural Research Service

Title: An Initial Assessment of Genome-wide Linkage Disequilibrium in Soybean

Authors
item Hyten, David
item Choi, Ik-Young - KOREA
item Yoon, Moon Sup - KOREA
item Song, Qijian - UNIVERSITY OF MARYLAND
item Specht, James - UNIVERSITY OF NEBRASKA
item Nelson, Randall - UNIVERSITY OF ILLINOIS
item Chase, Kevin - UNIVERSITY OF UTAH
item Young, Nevin - UNIVERSITY OF MINNESOTA
item Lark, Gordon - UNIVERSITY OF UTAH
item Shoemaker, Randy
item Cregan, Perry

Submitted to: Agronomy Society of America, Crop Science Society of America, Soil Science Society of America Meeting
Publication Type: Abstract Only
Publication Acceptance Date: September 15, 2006
Publication Date: September 15, 2006
Citation: Hyten, D.L., Choi, I., Yoon, M., Song, Q., Specht, J.E., Nelson, R., Chase, K., Young, N., Lark, G., Shoemaker, R.C., Cregan, P.B. 2006. An Initial Assessment of Genome-wide Linkage Disequilibrium in Soybean [abstract]. Agronomy Society of America, Crop Science Society of America, Soil Science Society of America Meeting. Paper No. 23311. http://a-c-s.confex.com/crops/2006am/techprogram/P23311.htm.

Technical Abstract: Linkage disequilibrium (LD) is the "non-random association of alleles" and can be utilized through association analysis to discover quantitative trait loci (QTLs). 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 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.

Last Modified: 8/21/2014
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