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Discovery of single nucleotide polymorphisms in soybean using primers designed from ESTs

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Abstract

Discovery of single nucleotide polymorphisms (SNPs), including small insertions and deletions (indels), is one of the hot topics in genetic research. SNPs were surveyed using nine soybean genotypes from Korea. Sequence variations in a total of 110 genes from GenBank among the nine genotypes were studied using genomic DNA as a template. Direct fluorescent dideoxynucleotide sequencing data of PCR products from primers designed from soybean ESTs were analyzed by SeqScape software to ensure high accuracy. Approximately 70% of the primer sets produced a single PCR product from which reliable sequence data were obtained, and 23.6% of these had at least one SNP. Overall, a total of 110 ESTs for SNPs were screened in 33,262 bp, consisting of 16,302 bp from coding regions and 16,960 bp from adjacent non-coding regions (5′ UTR, 3′ UTR and introns). SNPs in coding and non-coding regions occurred at a frequency of 1 per 3,260 bp, corresponding to a nucleotide diversity (θ) of 0.00011, and 1 per 278 bp (θ = 0.00128), respectively. This suggested that the higher level of sequence variation in non-coding regions would make them good regions in which to search for SNPs. The SNPs in partial cDNA sequences could be valuable for gene-targeted map construction in soybean.

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Authors and Affiliations

  1. School of Plant Science, Seoul National University, San 56-1, Shillim-dong, Kwanak-gu, Seoul, 151-921, The Republic of Korea

    Kyujung Van, Eun-Young Hwang, Moon Young Kim, Young-Il Cho & Suk-Ha Lee

  2. Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, U.S.A.

    Eun-Young Hwang & Perry B. Cregan

  3. National Institute of Agricultural Biotechnology, Suwon, 441-707, The Republic of Korea

    Yong-Hwan Kim

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  1. Kyujung Van
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  4. Yong-Hwan Kim
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Correspondence to Suk-Ha Lee.

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Van, K., Hwang, EY., Kim, M. et al. Discovery of single nucleotide polymorphisms in soybean using primers designed from ESTs. Euphytica 139, 147–157 (2004). https://doi.org/10.1007/s10681-004-2561-0

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