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Journal of Heredity Advance Access originally published online on June 30, 2005
Journal of Heredity 2005 96(5):529-535; doi:10.1093/jhered/esi069
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© The American Genetic Association. 2005. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org.

Discovery of SNPs in Soybean Genotypes Frequently Used as the Parents of Mapping Populations in the United States and Korea

K. Van, E.-Y. Hwang, M. Y. Kim, H. J. Park, S.-H. Lee, and P. B. Cregan

From the Department of Plant Science, Seoul National University, Seoul 151-921, Republic of Korea (Van, Hwang, Kim, and Lee); Biosafety Division, National Institute of Agricultural Biotechnology, Suwon 441-707, Republic of Korea (Park); and Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705 (Hwang and Cregan)

Address correspondence to S.-H. Lee at the address above, or e-mail: sukhalee{at}snu.ac.kr.

Single nucleotide polymorphisms (SNPs) including insertion/deletions (indels) serve as useful and informative genetic markers. The availability of high-throughput and inexpensive SNP typing systems has increased interest in the development of SNP markers. After fragments of genes were amplified with primers derived from 110 soybean GenBank ESTs, sequencing data of PCR products from 15 soybean genotypes from Korea and the United States were analyzed by SeqScape software to find SNPs. Among 35 gene fragments with at least one SNP among the 15 genotypes, SNPs occurred at a frequency of 1 per 2,038 bp in 16,302 bp of coding sequence and 1 per 191 bp in 16,960 bp of noncoding regions. This corresponds to a nucleotide diversity ({theta}) of 0.00017 and 0.00186, respectively. Of the 97 SNPs discovered, 78 or 80.4% were present in the six North American soybean mapping parents. The addition of "Hwaeomputkong," which originated from Japan, increased the number to 92, or 94.8% of the total number of SNPs present among the 15 genotypes. Thus, Hwaeomputkong and the six North American mapping parents provide a diverse set of soybean genotypes that can be successfully used for SNP discovery in coding DNA and closely associated introns and untranslated regions.


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