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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.
Fig 2. X. tropicalis strain phylogeny.
A consensus, unrooted, neighbor-joining tree representing the phylogenetic relationships between 55 sequenced individuals is shown. The UNC Nigerian F5 strain is represented by four individuals, the genotyped parents of the group 1 and group 2 animals previously analyzed. The Ivory Coast F8 and commercial Nigerian F5 individuals are labeled IC1-22 and N1-29 respectively. The bootstrap values are shown alongside the branches, indicating the number of times the partition of the individuals into the two sets separated by the branch occurred amongst the 100 trees on which the consensus tree is based.
Figure 1. Overview of shared and unique polymorphism amongst sequenced strains.This Venn diagram summarizes the pattern of shared and unique polymorphism between the UNC Nigerian F5, commercial Nigerian F5 and Ivory Coast F8 inbred frogs genotyped for 28 polymorphisms in 12 polymorphic genes.
Figure 2. X. tropicalis strain phylogeny.A consensus, unrooted, neighbor-joining tree representing the phylogenetic relationships between 55 sequenced individuals is shown. The UNC Nigerian F5 strain is represented by four individuals, the genotyped parents of the group 1 and group 2 animals previously analyzed. The Ivory Coast F8 and commercial Nigerian F5 individuals are labeled IC1-22 and N1-29 respectively. The bootstrap values are shown alongside the branches, indicating the number of times the partition of the individuals into the two sets separated by the branch occurred amongst the 100 trees on which the consensus tree is based.
Barkley,
Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals.
2008, Pubmed
Barkley,
Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals.
2008,
Pubmed
Ben-Ari,
Application of SNPs for assessing biodiversity and phylogeny among yeast strains.
2005,
Pubmed
Bowcock,
High resolution of human evolutionary trees with polymorphic microsatellites.
1994,
Pubmed
Buetow,
Influence of aberrant observations on high-resolution linkage analysis outcomes.
1991,
Pubmed
Cargill,
Characterization of single-nucleotide polymorphisms in coding regions of human genes.
1999,
Pubmed
Comai,
Efficient discovery of DNA polymorphisms in natural populations by Ecotilling.
2004,
Pubmed
Gilchrist,
Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.
2006,
Pubmed
Goda,
Genetic screens for mutations affecting development of Xenopus tropicalis.
2006,
Pubmed
,
Xenbase
Goldstein,
The effects of genotyping errors and interference on estimation of genetic distance.
1997,
Pubmed
Grammer,
Identification of mutants in inbred Xenopus tropicalis.
2005,
Pubmed
,
Xenbase
Hackett,
Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps.
2003,
Pubmed
Hellsten,
The genome of the Western clawed frog Xenopus tropicalis.
2010,
Pubmed
,
Xenbase
Ideraabdullah,
Genetic and haplotype diversity among wild-derived mouse inbred strains.
2004,
Pubmed
Johnson,
Identification of RAPD primers that reveal extensive polymorphisms between laboratory strains of zebrafish.
1994,
Pubmed
Pompanon,
Genotyping errors: causes, consequences and solutions.
2005,
Pubmed
Postlethwait,
Zebrafish genomics: from mutants to genes.
1997,
Pubmed
Postlethwait,
A genetic linkage map for the zebrafish.
1994,
Pubmed
Sachidanandam,
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.
2001,
Pubmed
Showell,
Decoding development in Xenopus tropicalis.
2007,
Pubmed
,
Xenbase
Showell,
Tissue sampling and genomic DNA purification from the western clawed frog Xenopus tropicalis.
2009,
Pubmed
,
Xenbase
Showell,
Natural mating and tadpole husbandry in the western clawed frog Xenopus tropicalis.
2009,
Pubmed
,
Xenbase
Taberlet,
Reliable genotyping of samples with very low DNA quantities using PCR.
1996,
Pubmed
Till,
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.
2006,
Pubmed
Wells,
A genetic map of Xenopus tropicalis.
2011,
Pubmed
,
Xenbase
Wienholds,
Efficient target-selected mutagenesis in zebrafish.
2003,
Pubmed
Williams,
DNA polymorphisms amplified by arbitrary primers are useful as genetic markers.
1990,
Pubmed
Wright,
Systems of Mating. II. the Effects of Inbreeding on the Genetic Composition of a Population.
1921,
Pubmed
Xu,
Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis.
2008,
Pubmed
,
Xenbase
