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Frequency and Distribution of Crossovers in Caenorhabditis elegans Meiosis by SNP Genotyping using Real-time PCR

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

Randy Lambreghts¹, Mi Shi, William J Belden

¹Department of Environmental and Biomolecular Systems, Oregon Health & Science University, Beaverton, Oregon 97006, USA.

|November 19, 2008

Summary

Researchers developed 250 cleaved amplified polymorphic sequence (CAPS) markers for Neurospora crassa, enabling precise gene mapping and isolation of novel genes from mutants.

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Area of Science:

Genetics
Molecular Biology
Mycology

Background:

Genetic mapping in Neurospora crassa is crucial for understanding gene function.
High-density genetic markers are needed for efficient fine mapping of mutations.

Purpose of the Study:

To discover and validate single nucleotide polymorphisms (SNPs) for high-resolution genetic mapping in Neurospora crassa.
To develop a robust set of genetic markers for gene discovery and fine mapping.

Main Methods:

Sequencing of Mauriceville strain cDNAs and alignment to the Oak Ridge strain genome to identify putative SNPs.
Validation of SNPs using cleaved amplified polymorphic sequence (CAPS) assays.
Bulked segregant analysis and interval mapping to locate mutations.

Main Results:

19,087 putative SNPs were identified between the Oak Ridge and Mauriceville strains.
250 CAPS markers were experimentally validated and evenly distributed across the genome.
The csp-1 mutation was mapped to a 74 kbp region on LGI, and the causative gene NCU02713.3 was identified.

Conclusions:

A high-density set of CAPS markers facilitates fine mapping and gene isolation in Neurospora crassa.
The developed methods provide a straightforward approach for identifying genes responsible for mutations.
The SNP and CAPS marker data are publicly available for community use.