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United States Department of Agriculture

Agricultural Research Service


item Van, Kyujung - KOREA
item Hwang, Eun-Young - KOREA
item Kim, Moon Young - KOREA
item Lee, Suk-Ha - KOREA
item Cregan, Perry

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 25, 2005
Publication Date: December 25, 2005
Citation: Van, K., Hwang, E., Kim, M., Lee, S., Cregan, P.B. 2005. Discovery of snps in soybean genotypes frequently used as the parents of mapping populations in the united states and korea. Journal of Heredity. 96:529-535.

Interpretive Summary: DNA markers serve as genetic landmarks along the chromosomes of higher organisms and are interspersed among or are actually present in the 50,000 or more genes in the genome of 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, the 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. DNA landmarks that are based upon single changes in the DNA alphabet are called single nucleotide polymorphisms, abbreviated SNPs. Huge investments are being made in human genome research to find SNPS in humans and to develop technologies for rapid and cost effective SNP detection. These technologies can be just as easily used by plant geneticists to expedite the plant improvement process. It was our objective to define a small set if soybean varieties that we could examine in order to find SNP DNA markers in the most efficient manner. We analyzed the DNA sequence of portions of 110 genes in 15 different soybeans and found 97 SNPs. We identified a subset of seven soybeans that we could analyze and still find 95% of the SNPs that were found via the analysis of all 15 soybean varieties. Analyzing this subset of varieties increases the efficiency and reduces the cost of developing SNP DNA markers in soybean. This information is of particular use to soybean geneticists who are interested in developing genome maps using SNP DNA markers.

Technical Abstract: Single nucleotide polymorphisms (SNPs) including insertion/deletions (Indels) serve as useful and informative genetic markers. High throughput and inexpensive SNP typing systems have increased interest in the development of SNP markers. After fragments were amplified with primers derived from 110 soybean GenBank ESTs, direct fluorescent dideoxynucleotide sequencing data of PCR products from fifteen soybean genotypes from Korea and the USA were analyzed by SeqScape software to find SNPs. Among 35 ESTs with at least one SNP in the 15 soybean genotypes, SNPs occurred at a frequency of 1 per 2,038 bp in 16,302 bp of coding sequence and 1 per 191 bp in 16,960 bp from non-coding regions. This corresponds to a nucleotide diversity (theta) of 0.00017 and 0.00186, respectively. Of the 97 SNPs discovered, 80.4% were present in the six North American soybean mapping parents. The addition of 'Hwaeomputkong', which originated from Japan, increased the number to 92, or 94.8% of the total number of SNPs present among the 15 genotypes. Thus, Hwaeomputkong and the six North American mapping parents provide a diverse set of soybean genotypes that can be successfully used for SNP discovery in coding DNA and closely associated introns and untranslated regions.

Last Modified: 11/26/2015
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