Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 30, 2004
Publication Date: December 30, 2004
Citation: Van, K., Hwang, E., Kim, M., Kim, Y., Cho, Y., Cregan, P.B. 2004. Discovery of single nucleotide polymorphisms in soybean using primers designed from ests. Euphytica 139: 147-157.
Interpretive Summary: DNA markers serve as genetic landmarks along the chromosomes 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 in or 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 determine if SNPs were present in or around soybean genes in sufficient quantity to develop a genome map using gene-based SNPs. Via the analysis of fragments of 110 soybean genes and DNA in close proximity to those genes it was determined that relatively few SNPs were present in the protein coding portions of genes. In contrast, SNPs were 11 times more frequent in the DNA closely associated with the protein coding regions. This suggested that the regions near genes are good places to search for SNPs. This information is of particular use to soybean geneticists who are interested in the development of SNP DNA markers.
Discovery of single nucleotide polymorphisms (SNPs), including small insertions and deletions (indels), is a topic of great current interest. SNPs were surveyed using nine soybean genotypes from Korea. Sequence variations in a total of 110 genes from GenBank were assessed among the nine genotypes using genomic DNA as a template. Direct fluorescent dideoxynucleotide sequencing data of PCR products from primers designed from soybean ESTs were analyzed by SeqScape software to ensure high accuracy of SNP discovery. Approximately 70% of the primer sets produced a single PCR product from which reliable sequence data were obtained, and 23.6% of these had at least one SNP. Overall, a total of 110 ESTs were screened for SNPs in 33,262 bp, consisting of 16,302 bp from coding regions and 16,960 bp from adjacent non-coding regions (5' UTR, 3' UTR and introns). SNPs in coding and non-coding regions occurred at a frequency of 1 per 3260 bp, corresponding to a nucleotide diversity (theta) of 0.00011, and 1 per 278 bp (theta = 0.00128), respectively. This suggested that the higher level of sequence variation in non-coding regions would make them good regions in which to search for SNPs.