Distinguishing C. elegans chromosomes with amplicon size polymorphisms 1
Distinguishing C. elegans chromosomes with amplicon size polymorphisms
, Hannah Lyman2
, Elizabeth Vargas2
, Frank McNally2
, Ian Korf1,2
UC Davis Genome Center, University of California, Davis, California 95616, USA; 2
Molecular and Cellular Biology, University of California, Davis, California 95616, USA
Researchers investigating chromosomal loss in aneuploid C. elegans currently have no
cost-effective method of distinguishing homologous chromosomes from different strains. Even though
genome sequencing and fluorescence in situ hybridization (FISH) are possible solutions in distinguishing
homologous chromosomes, they are both costly and inefficient. In this paper, we propose a viable,
cost-effective method involving indel polymorphisms on primer-isolated sequences of different strains.
To distinguish homologous chromosomes by strain, size differences of these sequences will be amplified
through PCR and the resulting amplicons will be run through gel electrophoresis. A dataset of mutations
referenced with the N2 strain was processed to identify strain pairs with significant relative size
polymorphisms. We were able to find six strain pairs with at least two regions of these polymorphisms on
each chromosome. In addition, laboratory work validated our method on one region in one strain pair. We
currently await further results. Nevertheless, our current results indicate that amplicon size
polymorphisms are a viable, cost-effective method of distinguishing homologous chromosomes in C.
elegans and possibly other organisms.