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United States Department of Agriculture

Agricultural Research Service

Title: Single Nucleotide Polymorphism Discovery in 3-Est Sequence of Soybean

Authors
item Cregan, Perry
item Hyten, David
item Matukumalli, Lakshmi - GEORGE MASON UNIV.
item Cho, Ik-Young - REP. OF KOREA

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: December 20, 2002
Publication Date: N/A

Technical Abstract: More than 22,000 soybean unigenes have been defined and 3'-end EST sequence is available for each. The TIGR soybean gene index contains more that 24,000 tentative consensus sequences (TCs) for soybean and provides an assessment of gene structure. It is the goal of the work reported here to determine how best to use these data for purposes of single nucleotide polymorphism (SNP) discovery. Using 3'EST data, PCR primers were designed to 230 sequences with mean predicted product length of 466 bp. Many of these primers sets amplified multiple fragments as would be anticipated from the soybean genome that is an ancient tetraploid. High quality sequences of the PCR product were obtained from each of six diverse soybean genotypes for 114 (50%) of the 230 primer pairs. A total of 57 of the 114 fragments contained at least one intron. Intron lengths varied from 28 to more than1000 bp with an average length of 209 bp. There was an average of 1.8 introns per 3' sequence. SNP frequency was 1.4/kbp in exon sequence and 2.0 in intron sequence. The position of stop codons was not always certain but a large proportion of the SNPs discovered in exons appear to be in the 3' UTR sequence as would be anticipated. These data are currently undergoing further analysis to optimize SNP discovery in the soybean unigenes.

Last Modified: 10/22/2014
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