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A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae.

Koboldt DC, Staisch J, Thillainathan B, Haines K, Baird SE, Chamberlin HM, Haag ES, Miller RD, Gupta BP - BMC Genomics (2010)

Bottom Line: The utility of polymorphisms in genetic studies was demonstrated by successful mapping of 12 mutations, including 5 that were localized to sub-chromosomal regions.We also show that molecular markers can be useful tools to improve the C. briggsae genome sequence assembly.Our polymorphism resource promises to accelerate genetic and functional studies of C. briggsae genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.

ABSTRACT

Background: The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers.

Results: We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 bp and 2 kb. We established bulk segregant and single animal-based PCR assay conditions and used these to test 107 polymorphisms. A total of 75 polymorphisms, consisting of 14 snip-SNPs and 61 indels, were experimentally confirmed with an overall success rate of 83%. The utility of polymorphisms in genetic studies was demonstrated by successful mapping of 12 mutations, including 5 that were localized to sub-chromosomal regions. Our mapping experiments have also revealed one case of a misassembled contig on chromosome 3.

Conclusions: We report a comprehensive set of polymorphisms in C. briggsae wild-type strains and demonstrate their use in mapping mutations. We also show that molecular markers can be useful tools to improve the C. briggsae genome sequence assembly. Our polymorphism resource promises to accelerate genetic and functional studies of C. briggsae genes.

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A polymorphism-based genetic linkage map of C. briggsae. The map consists of 13 snip-SNPs (italics), 22 medium indels, and 32 small (bold) indels.
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Figure 3: A polymorphism-based genetic linkage map of C. briggsae. The map consists of 13 snip-SNPs (italics), 22 medium indels, and 32 small (bold) indels.

Mentions: Altogether we experimentally confirmed 75 polymorphisms (14 snip-SNPs, 29 medium indels, and 32 small indels) on all six chromosomes (Figure 3, Table 5). The utility of these 'working' markers in genetic studies is demonstrated by successful mapping of several mutations that cause visible phenotypes. In two cases these mapping experiments also helped improve the genome sequence assembly. Specifically, the bhP42 contig fpc4184 was placed near the center of chromosome 1 and bhP18 contig fpc4010 was reassigned to the left arm of chromosome 3 (see below).


A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae.

Koboldt DC, Staisch J, Thillainathan B, Haines K, Baird SE, Chamberlin HM, Haag ES, Miller RD, Gupta BP - BMC Genomics (2010)

A polymorphism-based genetic linkage map of C. briggsae. The map consists of 13 snip-SNPs (italics), 22 medium indels, and 32 small (bold) indels.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864247&req=5

Figure 3: A polymorphism-based genetic linkage map of C. briggsae. The map consists of 13 snip-SNPs (italics), 22 medium indels, and 32 small (bold) indels.
Mentions: Altogether we experimentally confirmed 75 polymorphisms (14 snip-SNPs, 29 medium indels, and 32 small indels) on all six chromosomes (Figure 3, Table 5). The utility of these 'working' markers in genetic studies is demonstrated by successful mapping of several mutations that cause visible phenotypes. In two cases these mapping experiments also helped improve the genome sequence assembly. Specifically, the bhP42 contig fpc4184 was placed near the center of chromosome 1 and bhP18 contig fpc4010 was reassigned to the left arm of chromosome 3 (see below).

Bottom Line: The utility of polymorphisms in genetic studies was demonstrated by successful mapping of 12 mutations, including 5 that were localized to sub-chromosomal regions.We also show that molecular markers can be useful tools to improve the C. briggsae genome sequence assembly.Our polymorphism resource promises to accelerate genetic and functional studies of C. briggsae genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.

ABSTRACT

Background: The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers.

Results: We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 bp and 2 kb. We established bulk segregant and single animal-based PCR assay conditions and used these to test 107 polymorphisms. A total of 75 polymorphisms, consisting of 14 snip-SNPs and 61 indels, were experimentally confirmed with an overall success rate of 83%. The utility of polymorphisms in genetic studies was demonstrated by successful mapping of 12 mutations, including 5 that were localized to sub-chromosomal regions. Our mapping experiments have also revealed one case of a misassembled contig on chromosome 3.

Conclusions: We report a comprehensive set of polymorphisms in C. briggsae wild-type strains and demonstrate their use in mapping mutations. We also show that molecular markers can be useful tools to improve the C. briggsae genome sequence assembly. Our polymorphism resource promises to accelerate genetic and functional studies of C. briggsae genes.

Show MeSH