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Title: SINGLE NUCLEOTIDE POLYMORPHISM DISCOVERY IN SOYBEAN USING PRIMERS DESIGNED TO METHYL-FILTRATED CLONES

Author
item HWANG, EUN-Y0UNG - UNIVERSITY OF MARYLAND
item VAN, KYUJUNG - SEOUL NATIONAL UNIVERSITY
item KIM, MOON YOUNG - SEOUL NATIONAL UNIVERSITY
item KUMAR, LAKSHMI - GEORGE MASON UNIVERSITY
item LEE, SUK-HA - SEOUL NATIONAL UNIVERSITY
item STACEY, GARY - UNIVERSITY OF MISSOURI
item Cregan, Perry

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/31/2005
Publication Date: 1/31/2005
Citation: Hwang, E., Van, K., Kim, M., Kumar, L., Lee, S., Stacey, G., Cregan, P.B. 2005. Single nucleotide polymorphism discovery in soybean using primers designed to methyl-filtrated clones. Meeting Abstract. Plant & Animal Genome XIII Abstract. P192.

Interpretive Summary:

Technical Abstract: Single nucleotide polymorphisms (SNPs) are a useful and abundant source of polymorphic markers. However, the detection of SNPs in genes is difficult because sequence variation is extremely low in coding sequence of soybean. In addition, because soybean is an ancient polyploid, gene duplications make the development of sequence tagged sites (STS) difficult. It was our objective to overcome the difficulties associated with STS development and low sequence variation in coding sequence. The general approach is to identify genomic clones in which coding sequence is present in one end and non-coding sequence in the opposite end. Because non-coding DNA is less well conserved than coding sequence, the likelihood of developing a STS from non-coding DNA is greater than from coding sequence. Likewise, the greater sequence variation in non-coding sequence would enhance the likelihood of SNP discovery. End sequences of genomic clones 2-3 kbp in length from a methyl-filtered library were determined and analyzed for the presence of coding sequence. PCR primers were designed to the end sequences of 61 methyl-filtered clones. A somewhat higher proportion of the primers designed to the non-genic ends (77% vs. 69%) yielded STS as verified by sequence analysis of the PCR product. The prevalence of SNPs in the non-genic ends was only slightly higher than that of the genic ends, nucleotide diversity (theta) = 0.0021 vs. 0.0017, respectively. A second set of clones is presently being analyzed to further examine this approach for the development of SNPs in proximity to coding sequence.