SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) IN SOYBEAN: DISCOVERY AND DETECTION.

Authors: Cregan, Perry; ZHU, YOULIN - CHINA; SONG, QIJIAN - CHINA; Quigley, Charles - Chuck; Fickus, Edward; Fernalld, Raymond; Smith, Carolyn

Submitted to: Mid Atlantic Plant and Molecular Biology Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 10/5/2001
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: SNPs are rapidly becoming the marker of choice for many applications in genome analysis. Information on the frequency and distribution of SNPs in plants is limited. Our laboratory is defining approaches for both the discovery and the high throughput detection of SNPs in soybean. Our objectives were to determine 1) SNP frequency in coding and non-coding soybean DNA sequence derived from complete genes, cDNAs, and random genomic sequence and 2) the proportion of genes and cDNAs in which SNPs could be discovered. These data address the feasibility 1) of mapping expressed sequence tags (ESTs) via the presence of an associated SNP in order to create a transcript map and 2) of developing a large set of SNPs from random genome sequence. Primers were successfully designed to amplify a locus-specific product from 65 of 90 complete genes and 52 of 90 cDNAs. In total, about 29 kbp of coding- and 38 kbp of non-coding (introns, 5' and 3' untranslated, and associated genomic region) DNA was sequenced in each of 25 diverse soybean genotypes and a mean of 1.69 and 3.94 SNPs per kbp was discovered in coding and non-coding regions, respectively. At least one SNP was found in 74 of the 180 genes to which primers were designed.