A high-density single nucleotide polymorphism map for Neurospora crassa

Randy Lambreghts, Mi Shi, William J. Belden, David DeCaprio, Danny Park, Matthew R. Henn, James E. Galagan, Meray Baştürkmen, Bruce W. Birren, Matthew S. Sachs, Jay C. Dunlap, Jennifer J. Loros

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora crassa strain Oak Ridge and the Mauriceville strain (FGSC 2555), of sufficient density to allow fine mapping of most loci. Sequencing of Mauriceville cDNAs and alignment to the completed genomic sequence of the Oak Ridge strain identified 19,087 putative SNPs. Of these, a subset was validated by cleaved amplified polymorphic sequence (CAPS), a simple and robust PCR-based assay that reliably distinguishes between SNP alleles. Experimental confirmation resulted in the development of 250 CAPS markers distributed evenly over the genome. To demonstrate the applicability of this map, we used bulked segregant analysis followed by interval mapping to locate the csp-1 mutation to a narrow region on LGI. Subsequently, we refined mapping resolution to 74 kbp by developing additional markers, resequenced the candidate gene, NCU02713.3, in the mutant background, and phenocopied the mutation by gene replacement in the WT strain. Together, these techniques demonstrate a generally applicable and straightforward approach for the isolation of novel genes from existing mutants. Data on both putative and validated SNPs are deposited in a customized public database at the Broad Institute, which encourages augmentation by community users.

Original languageEnglish (US)
Pages (from-to)767-781
Number of pages15
JournalGenetics
Volume181
Issue number2
DOIs
StatePublished - Feb 1 2009

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Neurospora crassa
Single Nucleotide Polymorphism
Genes
Mutation
Complementary DNA
Alleles
Genome
Databases
Polymerase Chain Reaction

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Lambreghts, R., Shi, M., Belden, W. J., DeCaprio, D., Park, D., Henn, M. R., ... Loros, J. J. (2009). A high-density single nucleotide polymorphism map for Neurospora crassa. Genetics, 181(2), 767-781. https://doi.org/10.1534/genetics.108.089292
Lambreghts, Randy ; Shi, Mi ; Belden, William J. ; DeCaprio, David ; Park, Danny ; Henn, Matthew R. ; Galagan, James E. ; Baştürkmen, Meray ; Birren, Bruce W. ; Sachs, Matthew S. ; Dunlap, Jay C. ; Loros, Jennifer J. / A high-density single nucleotide polymorphism map for Neurospora crassa. In: Genetics. 2009 ; Vol. 181, No. 2. pp. 767-781.
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Lambreghts, R, Shi, M, Belden, WJ, DeCaprio, D, Park, D, Henn, MR, Galagan, JE, Baştürkmen, M, Birren, BW, Sachs, MS, Dunlap, JC & Loros, JJ 2009, 'A high-density single nucleotide polymorphism map for Neurospora crassa', Genetics, vol. 181, no. 2, pp. 767-781. https://doi.org/10.1534/genetics.108.089292

A high-density single nucleotide polymorphism map for Neurospora crassa. / Lambreghts, Randy; Shi, Mi; Belden, William J.; DeCaprio, David; Park, Danny; Henn, Matthew R.; Galagan, James E.; Baştürkmen, Meray; Birren, Bruce W.; Sachs, Matthew S.; Dunlap, Jay C.; Loros, Jennifer J.

In: Genetics, Vol. 181, No. 2, 01.02.2009, p. 767-781.

Research output: Contribution to journalArticle

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T1 - A high-density single nucleotide polymorphism map for Neurospora crassa

AU - Lambreghts, Randy

AU - Shi, Mi

AU - Belden, William J.

AU - DeCaprio, David

AU - Park, Danny

AU - Henn, Matthew R.

AU - Galagan, James E.

AU - Baştürkmen, Meray

AU - Birren, Bruce W.

AU - Sachs, Matthew S.

AU - Dunlap, Jay C.

AU - Loros, Jennifer J.

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