High-Density Detection of Restriction-Site-Associated DNA Markers for Rapid Mapping of Mutated Loci in Neurospora

Lewis, Zachary A.; Shiver, Anthony L.; Stiffler, Nicholas; Miller, Michael R.; Johnson, Eric A.; Selker, Eric U.

doi:10.1534/genetics.107.078147

Cited by 42 publications

(35 citation statements)

References 28 publications

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“…These sets were developed either by trial and error or from a limited amount of sequencing data and thus cannot be easily expanded to include a higher density of confirmed markers in a region of interest. Recently, a microarray-based method for mapping in Neurospora (restriction site associated DNA or RAD) has been described (Lewis et al 2007). This technique allows the mapping of an unknown gene to a relatively small region with unprecedented ease and is independent of the presence of OR-type markers in the mutant strain.…”

Section: Discussionmentioning

confidence: 99%

A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa

Lambreghts¹,

Shi²,

Belden³

et al. 2009

Genetics

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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.

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Section: Discussionmentioning

confidence: 99%

A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa

Lambreghts¹,

Shi²,

Belden³

et al. 2009

Genetics

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show abstract

“…These markers have clear advantage over the existing marker systems (for example, restriction fragment length polymorphisms, AFLPs and DArT markers) that could assay only a subset of SNPs that disrupt restriction sites. RAD markers were successfully developed in a number of organisms including fruit fly, zebrafish, threespine stickleback, Neurospora (Lewis et al, 2007;Miller et al, 2007a, b) and will certainly find their way in most of the laboratories working on higher plants.…”

Section: Rad Markersmentioning

confidence: 99%

Array-based high-throughput DNA markers for crop improvement

2008

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The last two decades have witnessed a remarkable activity in the development and use of molecular markers both in animal and plant systems. This activity started with lowthroughput restriction fragment length polymorphisms and culminated in recent years with single nucleotide polymorphisms (SNPs), which are abundant and uniformly distributed. Although the latter became the markers of choice for many, their discovery needed previous sequence information. However, with the availability of microarrays, SNP platforms have been developed, which allow genotyping of thousands of markers in parallel. Besides SNPs, some other novel marker systems, including single feature polymorphisms, diversity array technology and restriction site-associated DNA markers, have also been developed, where arraybased assays have been utilized to provide for the desired ultra-high throughput and low cost. These microarray-based markers are the markers of choice for the future and are already being used for construction of high-density maps, quantitative trait loci (QTL) mapping (including expression QTLs) and genetic diversity analysis with a limited expense in terms of time and money. In this study, we briefly describe the characteristics of these array-based marker systems and review the work that has already been done involving development and use of these markers, not only in simple eukaryotes like yeast, but also in a variety of seed plants with simple or complex genomes.

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“…The CloudMap pipelines can be modified to perform RNA-seq-based mapping-by-sequencing (R.J.P., unpublished observations). Restriction site-associated DNA mapping (RAD mapping) is another NGS-based approach that has been successfully used for genetic mapping (Lewis et al 2007;Miller et al 2007;Baird et al 2008). It requires the availability of divergent strains and a mapping cross.…”

Section: Non-wgs-based Approachesmentioning

confidence: 99%

Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification inCaenorhabditis elegans

2016

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The use of next-generation sequencing (NGS) has revolutionized the way phenotypic traits are assigned to genes. In this review, we describe NGS-based methods for mapping a mutation and identifying its molecular identity, with an emphasis on applications in Caenorhabditis elegans. In addition to an overview of the general principles and concepts, we discuss the main methods, provide practical and conceptual pointers, and guide the reader in the types of bioinformatics analyses that are required. Owing to the speed and the plummeting costs of NGS-based methods, mapping and cloning a mutation of interest has become straightforward, quick, and relatively easy. Removing this bottleneck previously associated with forward genetic screens has significantly advanced the use of genetics to probe fundamental biological processes in an unbiased manner.

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High-Density Detection of Restriction-Site-Associated DNA Markers for Rapid Mapping of Mutated Loci in Neurospora

Cited by 42 publications

References 28 publications

A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa

A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa

Array-based high-throughput DNA markers for crop improvement

Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification inCaenorhabditis elegans

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