SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) IN SOBYEAN

Authors: Cregan, Perry; Fickus, Edward; HYATT, S - PRIVATE INDUSTRY; ZHU, Y - VISITING SCIENTIST; SONG, Q - VISITING SCIENTIST; YOUNG, N - UNIV OF MINNESOTA; GRIMM, D - TAMPA, FLORIDA; Hyten, David; Van Tassell, Curtis - Curt; MATUKUMALLI, L - GEORGE MASON UNIVERSITY

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2003
Publication Date: 3/1/2003
Citation: Cregan, P.B., Fickus, E.W., Hyatt, S.M., Zhu, Y.L., Song, Q.J., Young, N.P., Grimm, D.R., Hyten, D.L., Van Tassell, C.P., Matukumalli, L.K. Single nucleotide polymorphisms (snps) in sobyean. Genetics.

Interpretive Summary: Nearly 2000 DNA markers have been developed in soybean for use in genome analysis but very few of these are located in the genes that control the growth and productivity of the plant. A new type of DNA marker called a single nucleotide polymorphism (SNP) can be targeted to genes. A SNP represents a single letter difference in DNA alphabet between two individuals. DNA markers serve as genetic landmarks interspersed in or near the 30,000 or more genes in the soybean genome. If a marker is located in or near a gene of interest it can be used to select for the desired form of the gene. Thus, 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. 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 soybean genes in sufficient quantity to develop a genetic map based upon SNPs as has been done in humans. We analyzed the DNA sequence of portions of 98 genes in 25 different soybeans and found 156 SNPs. At least one SNP was present in 63 of the 98 genes. These results indicate that the construction of genetic maps using this new and powerful DNA marker system is feasible in soybean and it will allow the mapping of genes by virtue of their containing a SNP. This information is of use to soybean geneticists who are interested in developing genome maps using SNP DNA markers.

Technical Abstract: Our objectives were to determine 1) single nucleotide polymorphism (SNP) frequency in coding and non-coding DNA sequence derived from complete genes, cDNAs, and random genomic sequence of soybean and the 2) the proportion of genes and cDNAs in which SNPs could be discovered. These data were needed to evaluate the feasibility 1) of mapping expressed sequence tags (ESTs) via the presence of an associated SNP and 2) of developing a large set of SNPs from random genome sequence. Primers were successfully designed to amplify a locus specific product from 62 of 90 complete genes and 36 of 90 cDNAs. About 25 kbp of coding- and 30 kbp of non-coding DNA was sequenced in each of 25 diverse soybean genotypes and a mean of 1.72 and 3.77 SNPs per kbp was discovered in coding and non- coding regions, respectively. Clustering of SNPs was observed. At least one SNP was found in 63 of the 97 genes suggesting some difficulty in mapping ESTs using SNPs. In random genomic sequence derived from BAC subclones and SSR flanking regions, the frequency of SNPs was 5.53/kbp indicating that large numbers of SNPs could be discovered in random genomic sequence. Haplotype analysis of SNP-containing DNA fragments revealed a paucity of haplotypes. In only two of 50 fragments that contained more than one SNP were more than four haplotypes detected among the 25 genotypes. The paucity of haplotypes suggests a genetic bottleneck or that the small number of haplotypes are derived from a small number of soybean domestication events either of which have implications on the efficient discovery of SNPs.