High-resolution, high-throughput SNP mapping in Drosophila melanogaster

Chen, Doris; Ahlford, Annika; Schnorrer, Frank; Kalchhauser, Irene; Fellner, Michaela; Virágh, Erika; Kiss, István; Syvänen, Ann Christine; Dickson, Barry J.

doi:10.1038/nmeth.1191

Cited by 50 publications

(44 citation statements)

References 27 publications

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“…One approach is to rely on recombination in females and perform meiotic mapping against visible markers (Lindsley and Zimm 1992), P-element insertions (Zhai et al 2003), or SNPs (Berger et al 2001;Hoskins et al 2001;Martin et al 2001;Nairz et al 2002;Chen et al 2008), all of which are labor-intensive strategies or require specialized infrastructure. An alternative is complementation mapping using deficiencies, which requires only a single cross.…”

Section: T He X Chromosome Of Drosophila Melanogastermentioning

confidence: 99%

A Molecularly Defined Duplication Set for the X Chromosome of Drosophila melanogaster

et al. 2010

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We describe a molecularly defined duplication kit for the X chromosome of Drosophila melanogaster. A set of 408 overlapping P[acman] BAC clones was used to create small duplications (average length 88 kb) covering the 22-Mb sequenced portion of the chromosome. The BAC clones were inserted into an attP docking site on chromosome 3L using FC31 integrase, allowing direct comparison of different transgenes. The insertions complement 92% of the essential and viable mutations and deletions tested, demonstrating that almost all Drosophila genes are compact and that the current annotations of the genome are reasonably accurate. Moreover, almost all genes are tolerated at twice the normal dosage. Finally, we more precisely mapped two regions at which duplications cause diplo-lethality in males. This collection comprises the first molecularly defined duplication set to cover a whole chromosome in a multicellular organism. The work presented removes a long-standing barrier to genetic analysis of the Drosophila X chromosome, will greatly facilitate functional assays of X-linked genes in vivo, and provides a model for functional analyses of entire chromosomes in other species.

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Section: T He X Chromosome Of Drosophila Melanogastermentioning

confidence: 99%

A Molecularly Defined Duplication Set for the X Chromosome of Drosophila melanogaster

et al. 2010

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“…Mapping of the mutation can greatly reduce the number of candidate changes that need to be analyzed. Although fine genetic mapping is quite labor intensive, intermediate levels of genetic mapping where a mutation is mapped to within a few megabases (Mb) can be achieved efficiently using methods such as P element or SNP mapping in Drosophila (Zhai et al 2003;Chen et al 2008). Once a mutation is mapped to an interval of several megabases or less, it is then necessary to sequence only the candidate region (often <1% of the genome) instead of the entire genome, resulting in significant cost reduction.…”

Section: Sra012301]mentioning

confidence: 99%

Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing

Wang

Chattopadhyay²,

Li³

et al. 2010

Genome Res.

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One of the key advantages of using Drosophila melanogaster as a genetic model organism is the ability to conduct saturation mutagenesis screens to identify genes and pathways underlying a given phenotype. Despite the large number of genetic tools developed to facilitate downstream cloning of mutations obtained from such screens, the current procedure remains labor intensive, time consuming, and costly. To address this issue, we designed an efficient strategy for rapid identification of heterozygous mutations in the fly genome by combining rough genetic mapping, targeted DNA capture, and second generation sequencing technology. We first tested this method on heterozygous flies carrying either a previously characterized dac 5 or sens E2 mutation. Targeted amplification of genomic regions near these two loci was used to enrich DNA for sequencing, and both point mutations were successfully identified. When this method was applied to uncharacterized twr mutant flies, the underlying mutation was identified as a single-base mutation in the gene Spase18-21. This targeted-genomesequencing method reduces time and effort required for mutation cloning by up to 80% compared with the current approach and lowers the cost to <$1000 for each mutant. Introduction of this and other sequencing-based methods for mutation cloning will enable broader usage of forward genetics screens and have significant impacts in the field of model organisms such as Drosophila.

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“…In fact, in humans, SNPs are now at the heart of whole genome association mapping of common variants (Carlson et al 2004). SNPs have also been used in Caenorhabditis elegans (Wicks et al 2001;Swan et al 2002;Davis et al 2005) and other model organisms, (Van Eijk et al 2004;Chen et al 2008) but to date these usually require multiple handling steps and are relatively complicated. Because the mapping of new mutants, particularly suppressors and enhancers, remains central to the study of these organisms, we sought to develop a more efficient method that would exploit advances in SNP detection on a large scale.…”

mentioning

confidence: 99%

Rapid High Resolution Single Nucleotide Polymorphism–Comparative Genome Hybridization Mapping in Caenorhabditis elegans

et al. 2009

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We have developed a significantly improved and simplified method for high-resolution mapping of phenotypic traits in Caenorhabditis elegans using a combination of single nucleotide polymorphisms (SNPs) and oligo array comparative genome hybridization (array CGH). We designed a custom oligonucleotide array using a subset of confirmed SNPs between the canonical wild-type Bristol strain N2 and the Hawaiian isolate CB4856, populated with densely overlapping 50-mer probes corresponding to both N2 and CB4856 SNP sequences. Using this method a mutation can be mapped to a resolution of $200 kb in a single genetic cross. Six mutations representing each of the C. elegans chromosomes were detected unambiguously and at high resolution using genomic DNA from populations derived from as few as 100 homozygous mutant segregants of mutant N2/CB4856 heterozygotes. Our method completely dispenses with the PCR, restriction digest, and gel analysis of standard SNP mapping and should be easy to extend to any organism with interbreeding strains. This method will be particularly powerful when applied to difficult or hard-tomap low-penetrance phenotypes. It should also be possible to map polygenic traits using this method.

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High-resolution, high-throughput SNP mapping in Drosophila melanogaster

Cited by 50 publications

References 27 publications

A Molecularly Defined Duplication Set for the X Chromosome of Drosophila melanogaster

A Molecularly Defined Duplication Set for the X Chromosome of Drosophila melanogaster

Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing

Rapid High Resolution Single Nucleotide Polymorphism–Comparative Genome Hybridization Mapping in Caenorhabditis elegans

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