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Abstract:
The availability of polymorphic strains of P. pacificus and a genomic BAC library of Pristionchus pacificus with large insert sizes encouraged us to use a BAC end based strategy to achieve our goal of constructing genetic and physical maps of the satellite model system Pristionchus pacificus. We looked for polymorphisms in the sequenced BAC ends using the SSCP ( single stranded conformation polymorphism) technique. The BAC end sequences were obtained from our Genome Centre at the institute and primers were designed to amplify 180-250 bp amplicons within these BAC end sequences. We used an inhouse program Prime Array 3.0 to design the primers. These primers were used to amplify both California and Washington DNA's and the resulting PCR products were run on an agarose gel to check for the presence or absence of bands. Later they were run on an SSCP gel to check for mobility differences. We found a total 131 SNP's . BAC ends that showed mobility differerences were then rechecked by sequencing the Washington PCR product and compared to the already available California sequence. Sequence comparison was done on a commercially available program Sequencher3.0. We found that the percentage of insertions and deletions in Pristionchus pacificus was more than in C.elegans (data from Wicks et al) However the single base pair substitutions were lesser than in C.elegans. This result indicates that insertion and deletion events are more common in Pristionchus pacificus than single base pair substitution events.
