Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 10/13/2004
Publication Date: 11/15/2005
Citation: Nelson, R., Grant, D.M., Shoemaker, R.C. 2005. Preliminary analysis of single nucleotide polymorphisms in soybean detected b estminer analysis. Plant and Animal Genome Abstracts. p. 433.
Technical Abstract: Analysis of sequence variation between homologs in the various soybean genotypes hold the promise of identifying alleles which confer traits of vital agronomic importance such as resistance to pathogens or susceptibility to abiotic stresses. These data could be used by breeders to assemble beneficial alleles in a single commercially viable genetic background. To this end, we have developed a suite of PERL programs to identify unique gene transcripts from EST libraries (ESTminer, Bioinformatics, accepted). This algorithm was used to identify approximately 39,000 potential gene transcripts (pHaps) from the isogenic soybean cultivars Williams and Williams 82 based on locus (gene) defining polymorphisms (LDPs). These LDPs allow us to identify homologous gene transcripts of each pHap in EST libraries derived from other Non-Williams (NW) genotypes on the basis of shared LDPs. This analysis revealed that approximately 23,000 pHaps matched one or more NW ESTs on the basis of shared LDPs. Sequence variation between pHaps and NW ESTs reveals allelic differences between different genetic backgrounds. These polymorphisms (SNPs and indels) could be used as molecular markers in marker assisted breeding systems as well as contribute to genetic and physical mapping efforts. Thus they will form an important resource for the advancement of knowledge of soybean genetics and breeding.