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United States Department of Agriculture

Agricultural Research Service


item Specht, James
item Lark, K
item Chase, Kevin
item Choi, Ik-young
item Song, Qijian
item Hyten, David
item Shoemaker, Randy
item Cregan, Perry

Submitted to: American Society of Agronomy Meetings
Publication Type: Abstract Only
Publication Acceptance Date: 12/30/2005
Publication Date: 12/30/2005
Citation: Specht, J.E., Lark, K.G., Chase, K., Choi, I., Song, Q., Hyten, D.L., Shoemaker, R.C., Cregan, P.B. 2005. Soybean single nucleotide polymorphisms - from genotypic assay to genetic map position [abstract]. American Society of Agronomy Meetings. November 9, 2005. (

Interpretive Summary:

Technical Abstract: In our most recently published genetic map of soybean markers (cf, Song et al. 2004 TAG 109:122-128), 1849 marker loci, including 1015 SSRs, 709 RFLPs, 73 RAPDs, 24 classical traits, 10 isozymes, six AFLPs, and 12 others were positioned on 20 linkage groups that span 2,524 cM of Kosambi map distance in five mapping populations. Single nucleotide polymorphism (i.e., SNP) markers constitute a new kind of marker that is of great value in genetic research, especially when positioned on the existing soybean map. Our goal is to determine the map positions of about 10,000 SNP markers by 2007, using four mapping populations. About 2370 soybean genes with at least one SNP have been identified to date, of which 94% are mappable in our four mapping populations. We expect to have 1500 of these SNPs mapped by the end of 2005. For SNP genotyping assays, our lab uses a microbead-based single base extension (SBE) method involving a labeled terminator (i.e., biotin-streptavidin) for a presence/absence (of florescence) detection of the base (A,C,T, or G) constituting a given SNP allele. Up to 100 differentially colored microbeads can be multiplex-assayed using a flow cytometer to identify a given color-coded microbead (=SNP) and its biotin-streptavidin emission (=Y/N). However, heterozygotes (if present in the mapping population) requre two SBE assays. Another method used for SNP detection involves SBE to create a mass difference in the SNP alleles and then MALTI-TOF mass spectrometry is used to detect the mass differences in the SBE products to make the genotypic calls (a homozygote for allele 1 or 2, or a heterozygote). Our presentation will provide insights about our map population assay data and the use of these data to incorporate SNPs into the current soybean genetic map.

Last Modified: 07/26/2017
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