Worm Breeder's Gazette 15(5): 17 (February 1, 1999)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

World-wide worm SNPs

Romke Koch, Henri G.A.M. van Luenen, Ronald H.A. Plasterk

The Netherlands Cancer Institute, Division of Molecular Biology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

The previous WBG described that Single Nucleotide Polymorphisms (SNP) between the RC301 strain and the canonical genome sequence of Bristol N2 were detected after directed PCR amplification of intergenic regions and subsequent sequencing (Jakubowski and Kornfeld, WBG 15#4, p 16) or restriction digestions (Schaefer et al., WBG 15#4, p 17). Jakubowski and Kornfeld found on average one SNP per 1.4 kbp.

We sampled the genome of C. elegans for SNPs, taking a different approach. We shotgun cloned fragments of around 1.5 kbp of genomic DNA, sequenced these, then compared them to the Bristol N2 genome sequence, to ask: does the clone map to a unique sequence, and -if so- do we recognise polymorphisms? We performed this analysis for 4 natural isolates, 2 from the USA, one from Germany, and one from Australia. We found the following:

strainisolated inbp sequencedSNPsSNP/bp
AB1Adelaide, Australia760031/2500
CB4857Claremont, California1900081/2400
RC301Freiburg, Germany1600041/4000
TR403Madison, Wisconsin1900051/3700

The SNPs found thus far seem to be spread over the genome (4 SNPs on chromosome I, 4 on II, 5 on III, 1 on IV, 2 on V and 4 on X). Our current numbers are too low to investigate whether indeed SNPs are more common in non-coding regions.

For the first few SNPs, we asked whether the sequences in the other natural isolates resembled that of Bristol N2, or that of the SNP. As expected, we found that several SNPs initially detected in one strain were also found in some but not in all other isolates. One example: a T in the Australian AB1, is a G in Bristol N2, and we found it to be like AB1 in the Californian CB4857 strain and the German RC301 strain, while the TR403 strain from Wisconsin resembled the Bristol N2 strain. Thus different patches of the genome have different common ancestors.

We are now scaling up this approach, with the goal to find in the order of 500 SNPs spread over the genome. We will then probe these positions in the other 3 strains (and possibly some more natural isolates), to try and generate a world-wide SNP map of the species. This should allow one to make statements such as: the strain from California has the centre of chromosome III in common with the Australian strain, but the left arm in common with the German strain.

The SNPs will be added to ACeDB, and can be used as markers on the genetic map. They can be recognised by PCR followed by sequencing, but we also found that the SNPs we looked at could be visualised by SSCP analysis.