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Title: SNP DISCOVERY IN 3'-EST SEQUENCE OF SOYBEAN

Author
item CHOI, IK-YOUNG - REPUBLIC OF KOREA
item Hyten, David
item MATUKUMALLI, L - GEORGE MASON UNIVERSITY
item YOON, M - REPUBLIC OF KOREA
item Cregan, Perry

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 2/5/2005
Publication Date: 2/5/2005
Citation: Choi, I., Hyten, D.L., Matukumalli, L.K., Yoon, M.S., Cregan, P.B. 2005. Snp discovery in 3'-est sequence of soybean. Meeting Abstract. Plant & Animal Genome XIII Abstract. P193.

Interpretive Summary:

Technical Abstract: Expressed sequence tag (EST) data are a useful source of sequence for the discovery of single nucleotide polymorphisms (SNP) that are the most common type of genetic variation among individuals within species. More than 25,000 soybean unigenes have been defined with 3'-end EST sequence available for each. The unigenes provide a source of sequence data for primer design and SNP discovery via resequencing. Discovering SNPs within unigenes will not only provide genetic markers but can permit the positioning of the corresponding gene on the genetic map. The resulting transcript map can be used in a number of applications including comparative genomics, the assessment of genome structure and organization, and for QTL discovery. A total of 3397 (66.9%) of the 5074 primer sets designed to 3'-end EST sequence produced a single discrete band on an agarose gel. High quality sequence data for each of six diverse soybean genotypes were successfully obtained from 2603 genes (1,417,510bp). A total of 1103 genes contained at least one SNP. A total of 3014 SNPs were discovered with 1677 distributed in exon sequence and 1337 in introns. At least 1 SNP was identified on average every 470bp in the soybean genotypes. In the 1.4 Mbp of sequence analyzed, the mean nucleotide diversity (theta) was 0.00093. This value is very similar to that reported by Zhu et al (2003) and supports the contention that nucleotide diversity is 4 to 8 fold lower than reported in the autogamous species A. thaliana and approximately one-tenth of that reported in maize.