ARS | Publication request: Development of Asymmetric Single-Strand Sequence Polymorphism (SSCP) to Separate COSII Alleles in Potato, Tomato, Sweet Potato and Carrot

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 10, 2009
Publication Date: N/A

Technical Abstract: Conserved Orthologous Sequences (COSII sequences), are a class of DNA sequences that are potentially orthologous (single-copy), and hence of great utility for applications as diverse as genetic linkage mapping, phylogeny, and diversity. We are applying them for phylogeny in potato and tomato, and for genetic linkage mapping in potato, and characterization for possible future mapping and phylogeny in sweet potato and carrot. Such sequences are potentially very powerful for these applications, but the technique can be very time consuming and expensive when the target genotypes are highly heterozygous. This is especially a problem with polyploids, common in wild potato that has many tetraploids and hexaploids. Asymmetric single-strand sequence polymorphisms (SSCP) represent a gel-based technique that can greatly alleviate these problems. The technique relies on the separation of the alleles by isolating just a single strand (asymmetric PCR) of DNA, separated in non-denaturing gels, followed by direct sequencing of excised bands. This technique is saving us 30% of a sequencing budget constructed before use of this technique, allowing us work more efficiently with polyploids and examining more accessions.