The DrosDel Collection

Abstract

We describe a collection of P-element insertions that have considerable utility for generating custom chromosomal aberrations in Drosophila melanogaster. We have mobilized a pair of engineered P elements, p{RS3} and p{RS5}, to collect 3243 lines unambiguously mapped to the Drosophila genome sequence. The collection contains, on average, an element every 35 kb. We demonstrate the utility of the collection for generating custom chromosomal deletions that have their end points mapped, with base-pair resolution, to the genome sequence. The collection was generated in an isogenic strain, thus affording a uniform background for screens where sensitivity to genetic background is high. The entire collection, along with a computational and genetic toolbox for designing and generating custom deletions, is publicly available. Using the collection it is theoretically possible to generate Ͼ12,000 deletions between 1 bp and 1 Mb in size by simple eye color selection. In addition, a further 37,000 deletions, selectable by molecular screening, may be generated. We are now using the collection to generate a second-generation deficiency kit that is precisely mapped to the genome sequence. G ENETICALLY tractable model organisms are valufor components that function in particular pathways and characterize how individual genes participate in able research tools for uncovering basic biological such pathways. principles that are conserved through evolution. ManyThe fruit fly, Drosophila melanogaster, is one such tractamolecular pathways, such as signaling cascades, gene ble model that has been used extensively to elucidate regulatory pathways, and cell cycle control circuits, were many conserved genetic hierarchies. One particularly first characterized genetically in model systems. The powerful approach with Drosophila is the ability to rapsubsequent molecular cloning of the genes involved in idly carry out focused genome-wide screens for pathsuch pathways has shown how evolution has utilized way components by identifying loci that modify specific basic molecular building blocks to control a wide variety phenotypes (see St. Johnston 2002 for review). In this of biological processes. Key to the success of such apapproach, a sensitized genetic background, most comproaches has been the ability to carry out genetic screens monly exhibiting an easily scored adult phenotype such as rough eyes or a wing defect, is used to search for mutations in genes that make the phenotype more se- sensitized background and the phenotype is assessed. specific recombinase (FRT site) placed within intron one. In the case of RS3, a second FRT site is placed Importantly, the mutagenized chromosome is heterozygous, allowing genetic interactions between the sensiupstream of the first of the mini-white exons; in the case of RS5 the second FRT site is located downstream of tized background and mutations that are homozygous lethal to be detected. Particularly useful tools for such the mini-white exons. Golic and Golic demonstrated how a pair of RS3 and RS5 e...

Effect of genomic deficiencies on sexual size dimorphism through modification of developmental time in Drosophila melanogaster

“…To assess the effect of artificially introduced genetic variation on the SSD and SDtD, and in search for genomic regions with effects on SSD, we reanalyzed the deficiency screening data published in Takahashi et al (2011a, b). These authors measured multiple phenotypic traits for a collection of DrosDel isogenic deficiency strains of D. melanogaster (Ryder et al, 2004) and the corresponding control strain. Because the breakpoints of the deletions in the deficiency strains were determined at a single base-pair resolution, they are a suitable tool for high resolution mapping of the candidate genomic regions (Ryder et al, 2004;Ryder et al, 2007).…”

“…These authors measured multiple phenotypic traits for a collection of DrosDel isogenic deficiency strains of D. melanogaster (Ryder et al, 2004) and the corresponding control strain. Because the breakpoints of the deletions in the deficiency strains were determined at a single base-pair resolution, they are a suitable tool for high resolution mapping of the candidate genomic regions (Ryder et al, 2004;Ryder et al, 2007). The control strain (DSK001: w 1118 iso ; 2 iso ; 3 iso ), whose X, second and third chromosomes are isogenized, share the same genetic background with the deficiency strains (Ryder et al, 2004;Ryder et al, 2007).…”

“…Because the breakpoints of the deletions in the deficiency strains were determined at a single base-pair resolution, they are a suitable tool for high resolution mapping of the candidate genomic regions (Ryder et al, 2004;Ryder et al, 2007). The control strain (DSK001: w 1118 iso ; 2 iso ; 3 iso ), whose X, second and third chromosomes are isogenized, share the same genetic background with the deficiency strains (Ryder et al, 2004;Ryder et al, 2007). Here, we focus on 376 deficiency strains whose trait scores were measured in both studies (Takahashi et al, 2011a, b; Figure 1).…”

Pickpocket1 Is an Ionotropic Molecular Sensory Transducer

“…Generation of ppk1 Deletion and Transgenic Flies-FRT/flippase recombinase targeted recombination was used to generate flies harboring the ppk1 gene deletion (ppk1 ESB ) (21,22). Specifically, the ppk1 gene was deleted using Flippase-mediated recombination between the PBac insertion lines f07052 and d02171.…”

The Drosophila genesdisconnectedanddisco-relatedtogether specify development of adult legs

“…The following fly lines were obtained form the Bloomington Stock Center: Df (1) ED7355 (FBst0008899, Ryder et al, 2004); tubP-GAL80 ts (FBst0007108, McGuire et al, 2003); the disco-r RNAi line y [1] sc [*] v[1]; P[y[+t7.7] v[+t1.8] The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/052811 doi: bioRxiv preprint first posted online May.…”