Skip to main content
PMC home page
Genetics logoLink to Genetics
. 2002 Sep;162(1):129–134. doi: 10.1093/genetics/162.1.129

A bacterial artificial chromosome-based genetic linkage map of the nematode Pristionchus pacificus.

Jagan Srinivasan 1, Waltraud Sinz 1, Christa Lanz 1, Alexandra Brand 1, Ramkumar Nandakumar 1, Günter Raddatz 1, Hanh Witte 1, Heike Keller 1, Isabel Kipping 1, André Pires-daSilva 1, Taco Jesse 1, Jun Millare 1, Michiel de Both 1, Stephan C Schuster 1, Ralf J Sommer 1
PMCID: PMC1462235  PMID: 12242228

Abstract

To understand the evolution of developmental processes, nonmodel organisms in the nematodes, insects, and vertebrates are compared with established model systems. Often, these comparisons suffer from the inability to apply sophisticated technologies to these nonmodel species. In the nematode Pristionchus pacificus, cellular and genetic analyses are used to compare vulva development to that of Caenorhabditis elegans. However, substantial changes in gene function between P. pacificus and C. elegans limit the use of candidate gene approaches in studying P. pacificus mutations. To facilitate map-based cloning of mutations in P. pacificus, we constructed a BAC-based genetic linkage map. A BAC library of 13,440 clones was generated and completely end sequenced. By comparing BAC end and EST sequences between the "wild-type" strain P. pacificus var. California and the polymorphic strain P. pacificus var. Washington, 133 single-stranded conformational polymorphisms were identified. These markers were tested on a meiotic mapping panel of 46 randomly picked F(2) animals after a cross of the two strains, providing the first genetic linkage map of P. pacificus. A mapping strategy using two selected markers per chromosome was devised and the efficiency of this approach was illustrated by the mapping of the Ppa-unc-1/Twitchin gene.

Full Text

The Full Text of this article is available as a PDF (226.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. C. elegans Sequencing Consortium Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 1998 Dec 11;282(5396):2012–2018. doi: 10.1126/science.282.5396.2012. [DOI] [PubMed] [Google Scholar]
  2. Eizinger A., Jungblut B., Sommer R. J. Evolutionary change in the functional specificity of genes. Trends Genet. 1999 May;15(5):197–202. doi: 10.1016/s0168-9525(99)01728-x. [DOI] [PubMed] [Google Scholar]
  3. Eizinger A., Sommer R. J. The homeotic gene lin-39 and the evolution of nematode epidermal cell fates. Science. 1997 Oct 17;278(5337):452–455. doi: 10.1126/science.278.5337.452. [DOI] [PubMed] [Google Scholar]
  4. Jungblut B., Sommer R. J. The Pristionchus pacificus mab-5 gene is involved in the regulation of ventral epidermal cell fates. Curr Biol. 1998 Jun 18;8(13):775–778. doi: 10.1016/s0960-9822(98)70301-x. [DOI] [PubMed] [Google Scholar]
  5. Jungblut B., Sommer R. J. The nematode even-skipped homolog vab-7 regulates gonad and vulva position in Pristionchus pacificus. Development. 2001 Jan;128(2):253–261. doi: 10.1242/dev.128.2.253. [DOI] [PubMed] [Google Scholar]
  6. Kent W. J., Zahler A. M. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 2000 Aug;10(8):1115–1125. doi: 10.1101/gr.10.8.1115. [DOI] [PubMed] [Google Scholar]
  7. Koch R., van Luenen H. G., van der Horst M., Thijssen K. L., Plasterk R. H. Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans. Genome Res. 2000 Nov;10(11):1690–1696. doi: 10.1101/gr.gr-1471r. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Lander E. S., Green P., Abrahamson J., Barlow A., Daly M. J., Lincoln S. E., Newberg L. A., Newburg L. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1987 Oct;1(2):174–181. doi: 10.1016/0888-7543(87)90010-3. [DOI] [PubMed] [Google Scholar]
  9. Orita M., Suzuki Y., Sekiya T., Hayashi K. Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics. 1989 Nov;5(4):874–879. doi: 10.1016/0888-7543(89)90129-8. [DOI] [PubMed] [Google Scholar]
  10. Osoegawa K., Tateno M., Woon P. Y., Frengen E., Mammoser A. G., Catanese J. J., Hayashizaki Y., de Jong P. J. Bacterial artificial chromosome libraries for mouse sequencing and functional analysis. Genome Res. 2000 Jan;10(1):116–128. [PMC free article] [PubMed] [Google Scholar]
  11. Raddatz G., Dehio M., Meyer T. F., Dehio C. PrimeArray: genome-scale primer design for DNA-microarray construction. Bioinformatics. 2001 Jan;17(1):98–99. doi: 10.1093/bioinformatics/17.1.98. [DOI] [PubMed] [Google Scholar]
  12. Shizuya H., Birren B., Kim U. J., Mancino V., Slepak T., Tachiiri Y., Simon M. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8794–8797. doi: 10.1073/pnas.89.18.8794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Sommer R. J. As good as they get: cells in nematode vulva development and evolution. Curr Opin Cell Biol. 2001 Dec;13(6):715–720. doi: 10.1016/s0955-0674(00)00275-1. [DOI] [PubMed] [Google Scholar]
  14. Sommer R. J., Eizinger A., Lee K. Z., Jungblut B., Bubeck A., Schlak I. The Pristionchus HOX gene Ppa-lin-39 inhibits programmed cell death to specify the vulva equivalence group and is not required during vulval induction. Development. 1998 Oct;125(19):3865–3873. doi: 10.1242/dev.125.19.3865. [DOI] [PubMed] [Google Scholar]
  15. Srinivasan J., Pires-daSilva A., Gutierrez A., Zheng M., Jungblut B., Witte H., Schlak I., Sommer R. J. Microevolutionary analysis of the nematode genus Pristionchus suggests a recent evolution of redundant developmental mechanisms during vulva formation. Evol Dev. 2001 Jul-Aug;3(4):229–240. doi: 10.1046/j.1525-142x.2001.003004229.x. [DOI] [PubMed] [Google Scholar]
  16. Wicks S. R., Yeh R. T., Gish W. R., Waterston R. H., Plasterk R. H. Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat Genet. 2001 Jun;28(2):160–164. doi: 10.1038/88878. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES