Abstract
Naturally occurring DNA sequence variation within a species underlies evolutionary adaptation and can give rise to phenotypic changes that provide novel insight into biological questions. This variation exists in laboratory populations just as in wild populations and, in addition to being a source of useful alleles for genetic studies, can impact efforts to identify induced mutations in sequence-based genetic screens. The Western clawed frog Xenopus tropicalis (X. tropicalis) has been adopted as a model system for studying the genetic control of embryonic development and a variety of other areas of research. Its diploid genome has been extensively sequenced and efforts are underway to isolate mutants by phenotype- and genotype-based approaches. Here, we describe a study of genetic polymorphism in laboratory strains of X. tropicalis. Polymorphism was detected in the coding and non-coding regions of developmental genes distributed widely across the genome. Laboratory strains exhibit unexpectedly high frequencies of genetic polymorphism, with alleles carrying a variety of synonymous and non-synonymous codon substitutions and nucleotide insertions/deletions. Inter-strain comparisons of polymorphism uncover a high proportion of shared alleles between Nigerian and Ivory Coast strains, in spite of their distinct geographical origins. These observations will likely influence the design of future sequence-based mutation screens, particularly those using DNA mismatch-based detection methods which can be disrupted by the presence of naturally occurring sequence variants. The existence of a significant reservoir of alleles also suggests that existing laboratory stocks may be a useful source of novel alleles for mapping and functional studies.
Highlights
The Western clawed frog Xenopus tropicalis (X. tropicalis) has enormous potential to enhance our understanding of the molecular control of embryonic development and the evolution of biological pathways [1]
In embryos of both X. laevis and X. tropicalis, gene function can be inhibited by microinjection of morpholino oligonucleotides that block translation or splicing of specific messenger RNAs but, being a diploid species with a shorter generation time, X. tropicalis presents the opportunity to combine what we know of its embryonic development with genetic analysis
We looked for sequence variation between the two independent F1 sibling groups, as these may carry distinct alleles
Summary
The Western clawed frog Xenopus tropicalis (X. tropicalis) has enormous potential to enhance our understanding of the molecular control of embryonic development and the evolution of biological pathways [1]. The X. tropicalis genome contains orthologs of at least 1,700 human genes known to be involved in disease and the frog will be a valuable biomedical model in the future, for studies of congenital diseases. In embryos of both X. laevis and X. tropicalis, gene function can be inhibited by microinjection of morpholino oligonucleotides that block translation or splicing of specific messenger RNAs but, being a diploid species with a shorter generation time, X. tropicalis presents the opportunity to combine what we know of its embryonic development with genetic analysis. The isolation of alleles that harbor functionally significant sequence variation is an essential step in this approach and this can be achieved by screening either for sequence variation (or polymorphism) that exists naturally within populations or for novel mutations, the frequency of which can be dramatically increased by chemical or radiological mutagenesis [3]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
