DEFINING THE GENETIC DIVERSITY AND STRUCTURE OF THE SOYBEAN GENOME AND APPLICATIONS TO GENE DISCOVERY IN SOYBEAN AND WHEAT GERMPLASM
Location: Soybean Genomics and Improvement
Title: Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean
Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 15, 2010
Publication Date: July 1, 2010
Citation: Song, Q., Jia, G., Zhu, Y., Hwang, E., Hyten, D.L., Cregan, P.B., Grant, D.M., Nelson, R. 2010. Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Science. 50:1950-1960.
Interpretive Summary: DNA markers serve as genetic landmarks and are interspersed among the genes throughout the genome of higher organisms including the soybean. If a marker is located near a gene of interest, the marker can be used to select for the desired form of the gene. For example, a soybean breeder can use a DNA marker to identify plants that carry the form of the gene that gives resistance to a disease rather than the form that leads to susceptibility. With the recent release of the whole DNA sequence of the soybean genome it became possible to identify thousands of DNA markers called Simple Sequence Repeat or SSR markers across the 20 soybean chromosomes. We report here the screening of the DNA sequence of the 20 soybean chromosomes and the identification of more than 30,000 SSR markers with a high probability of functioning well for use in DNA marker assisted soybean breeding and for the discovery of the positions of genes on the soybean chromosomes. A database called BARCSOYSSR_1.0 was created which contains the information required for the use of each of the more than 30,000 SSR DNA markers as well as the specific position of each marker on one of the 20 soybean chromosomes. The information in this database will be useful to soybean breeders and soybean geneticists as a source of DNA markers for gene cloning and for DNA marker assisted soybean breeding.
Simple sequence repeat (SSR) genetic markers also referred to as microsatellites function in fine mapping for purposes of map-based cloning and for marker assisted selection in plant breeding. The availability of the whole genome sequence of soybean [(Glycine max L. (Merr.)] facilitates the identification of SSRs. Thus, the objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri- and tetra-nucleotide repeats of five or more were identified in the soybean genome which included 61,458 SSRs with repeat units equal to or greater than 10, 8, and 7 for di-, tri- and tetra-nucleotide SSRs, respectively. When the SSRs with a high likelihood of length polymorphism in soybean germplasm, those with repeat units of di-(=10), tri-(=8), and tetra-nucleotide(=7) were considered, (AT)n, (ATT)n and (AAAT)n are the most abundant motifs among di-, tri- and tetra-nucleotide SSRs, respectively. After screening for a number of factors including locus-specificity using e-PCR, a soybean SSR database (BARCSOYSSR_1.0) with the genome position and primer sequences for 33,065 SSRs was created. The average density of these SSR loci in the whole genome was 35/Mbp. To examine the likelihood that primers in the database would function to amplify locus-specific polymorphic products, 1034 primer sets were evaluated by amplifying DNAs of seven diverse G. max and one wild soybean [G. soja (Sieb. and Zucc.)] genotypes. A total of 1005 (97.2%) of the primer sets amplified a single discrete PCR product and 842 (81.4%) amplified polymorphic amplicons as determined by agarose gel electrophoresis. The polymorphism rate of loci among seven G. max genotypes was 69.3%.