SpringerProtocols: Abstract: 6. Single-Nucleotide Polymorphism Mapping

6. Single-Nucleotide Polymorphism Mapping

By: M. Wayne Davis⁴, Marc Hammarlund⁴

Abstract

Full Text

Download PDF (313K)

Single-nucleotide polymorphism (SNP) mapping is the easiest and most reliable way to map genes in Caenorhabditis elegans. SNPs are extremely dense and usually have no associated phenotype, making them ideal markers for mapping. SNP mapping has three steps. First, recombinant mutant animals are generated over a polymorphic strain (usually CB4856) using standard genetic techniques. Second, the genotype of these animals at SNP loci is determined using one of a variety of SNP detection technologies. Third, linkage between the mutant and one or more SNPs is used to position the mutant on the chromosome relative to the SNPs. This chapter presents a detailed procedure for generating recombinant animals, for assaying SNPs using restriction enzymes, and for analyzing mapping data.

Affiliation(s): (4) Department of Biology, University of Utah, Salt Lake City, UT

Book Title: C. elegans: Methods and Applications

Series: Methods in Molecular Biology | Volume: 351 | Pub. Date: Aug-15-2006 | Page Range: 75-92 | DOI: 10.1385/1-59745-151-7:75

Subject: Genetics/Genomics

Key Words: C. elegans - single-nucleotide polymorphism - mapping - restriction fragment polymorphism - genetics

References

Download References

1.	Jakubowski, J. and Kornfeld, K. (1999) A local, high-density, single-nucleotide polymorphism map used to clone Caenorhabditis elegans cdf-1. Genetics 153,743–752.

2.	Hodgkin, J. and Doniach, T. (1997) Natural variation and copulatory plug formation in Caenorhabditis elegans. Genetics 146, 149–164.

3.	Wicks, S. R., Yeh, R. T., Gish, W. R., et al. (2001) Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat. Genet. 28, 160–164.

4.	Swan, K. A., Curtis, D. E., McKusick, K. B., et al. (2002) High-throughput gene mapping in Caenorhabditis elegans. Genome Res. 12, 1100–1105.

5.	Zipperlen, P., Nairz, K., Rimann, I., et al. (2005) A universal method for automated gene mapping. Genome Biol. 6, R19.

6.	Davis, M. W., Hammarlund, M., Harrach, T., et al. (2005) Rapid single nucleotide polymorphism mapping in C. elegans. BMC Genomics 12, 118.

7.	Bessereau, J. L., Wright, A., Williams, D. C., et al. (2001) Mobilization of a Drosophila transposon in the Caenorhabditis elegans germ line. Nature 413, 70–74.

8.	Fraser, A. G., Kamath, R. S., Zipperlen, P., et al. (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408, 325–330.

9.	Zwaal, R. R., Broeks, A., van Meurs, J., et al. (1993) Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank. Proc. Natl. Acad. Sci. USA 90, 7431–7435.

10.	Jorgensen, E. M. and Mango, S. E. (2002) The art and design of genetic screens: Caenorhabditis elegans. Nat. Rev. Genet. 3, 356–369.

11.	Sapolsky, R. J., Hsie, L., Berno, A., et al. (1999) High-throughput polymorphism screening and genotyping with high-density oligonucleotide arrays. Genet. Anal. 14, 187–192.

12.	Johnson, M. P., Haupt, L. M., and Griffiths, L. R. (2004) Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res. 32, E55.

13.	Latorra, D., Campbell, K., Wolter, A., et al. (2003) Enhanced allele-specific PCR discrimination in SNP genotyping using 3′ locked nucleic acid (LNA) primers. Hum. Mutat. 22, 79–85.

14.	Qi, X., Bakht, S., Devos, K. M., et al. (2001) L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs). Nucleic Acids Res. 29, E116.

15.	Livak, K. J. (1999) Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genet. Anal. 14, 143–149.

16.	Ross, P., Hall, L., Smirnov, I., et al. (1998) High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat. Biotechnol. 16, 1347–1351.

17.	van Eijk, M. J., Broekhof, J. L., van der Poel, H. J., et al. (2004) SNPWave: a flexible multiplexed SNP genotyping technology. Nucleic Acids Res. 32, E47.

18.	de Bono, M. and Bargmann, C. I. (1998) Natural variation in a neuropeptide Y receptor homolog modifies social behavior and food response in C. elegans. Cell 94, 679–689.

19.	Hodgkin, J. and Doniach, T. (1997) Natural variation and copulatory plug formation in Caenorhabditis elegans. Genetics 146, 149–164.

20.	Tijsterman, M., Okihara, K. L., Thijssen, K., et al. (2002) PPW-1, a PAZ/PIWI protein required for efficient germline RNAi, is defective in a natural isolate of C.elegans. Curr. Biol. 12, 1535–1540.

21.	Davies, A. G., Bettinger, J. C., Thiele, T. R., et al. (2004) Natural variation in the npr-1 gene modifies ethanol responses of wild strains of C. elegans. Neuron 42, 731–743.

Comments (Loading...)

Post comment/View all comments