A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

Simple item page
dc.contributor.authorKoboldt, Daniel C
dc.contributor.authorStaisch, Julia
dc.contributor.authorThillainathan, Bavithra
dc.contributor.authorHaines, Karen
dc.contributor.authorBaird, Scott E
dc.contributor.authorChamberlin, Helen M
dc.contributor.authorHaag, Eric S
dc.contributor.authorMiller, Raymond D
dc.contributor.authorGupta, Bhagwati P
dc.date.accessioned2021-11-15T19:57:44Z
dc.date.available2021-11-15T19:57:44Z
dc.date.issued2010-04-13
dc.description.abstractThe 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. 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. 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.en_US
dc.description.urihttps://doi.org/10.1186/1471-2164-11-236
dc.identifierhttps://doi.org/10.13016/lzuf-pcas
dc.identifier.citationKoboldt, D.C., Staisch, J., Thillainathan, B. et al. A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae. BMC Genomics 11, 236 (2010).en_US
dc.identifier.urihttp://hdl.handle.net/1903/28118
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Physical Sciencesen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtBiologyen_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectRestriction Fragment Length Polymorphismen_US
dc.subjectSequence Assemblyen_US
dc.subjectBulk Segregant Analysisen_US
dc.subjectSmall Indelsen_US
dc.subjectGenome Sequence Assemblyen_US
dc.titleA toolkit for rapid gene mapping in the nematode Caenorhabditis briggsaeen_US
dc.typeArticleen_US

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
1471-2164-11-236.pdf
Size:
3.46 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.57 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

Biology Research Works