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

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 stu...

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Bibliographic Details
Published in:Euphytica 2004, Vol.139 (2), p.147-157
Main Authors: VAN, Kyujung, HWANG, Eun-Young, MOON YOUNG KIM, KIM, Yong-Hwan, CHO, Young-Il, CREGAN, Perry B, LEE, Suk-Ha
Format: Article
Language:English
Subjects:
Agronomy. Soil science and plant productions
Biological and medical sciences
Deoxyribonucleic acid
DNA
Fundamental and applied biological sciences. Psychology
Generalities. Genetics. Plant material
Genetic resources, diversity
Genetics and breeding of economic plants
Genomics
Genotypes
Glycine max
Plant material
Soybeans
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Summary: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 ([theta]) of 0.00011, and 1 per 278 bp ([theta] = 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.[PUBLICATION ABSTRACT]
ISSN:0014-2336
1573-5060
DOI:10.1007/s10681-004-2561-0