a toolkit for rapid gene mapping in the nematode caenorhabditis briggsae一个工具包快速线虫秀丽briggsae基因图谱.pdfVIP

Koboldt et al. BMC Genomics 2010, 11:236 /1471-2164/11/236 R E S E A R C H A R T I C L E Open Access Research article A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae 1 1 2 2 3 4 Daniel C Koboldt , Julia Staisch , Bavithra Thillainathan , Karen Haines , Scott E Baird , Helen M Chamberlin , 5 1 2 Eric S Haag , Raymond D Miller and Bhagwati P Gupta* 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 i