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

Single nucleotide polymorphisms (SNPs) are useful markers for genetic mapping experiments in model organisms. Here we report the establishment of a high-density SNP map and high-throughput genotyping assays for Drosophila melanogaster. Our map comprises 27,367 SNPs in common laboratory Drosophila stocks. These SNPs were clustered within 2,238 amplifiable markers at an average density of 1 marker every 50.3 kb, or 6.3 genes. We have also constructed a set of 62 Drosophila stocks, each of which facilitates the generation of recombinants within a defined genetic interval of 1-2 Mb. For flexible, high-throughput SNP genotyping, we used fluorescent tag-array mini-sequencing (TAMS) assays. We designed and validated TAMS assays for 293 SNPs at an average resolution of 391.3 kb, and demonstrated the utility of these tools by rapidly mapping 14 mutations that disrupt embryonic muscle patterning. These resources enable high-resolution high-throughput genetic mapping in Drosophila.     

Cytotype regulation by telomeric P elements in Drosophila melanogaster: evidence for involvement of an RNA interference gene

P elements inserted at the left telomere of the X chromosome evoke the P cytotype, a maternally inherited condition that regulates the P-element family in the Drosophila germline. This regulation is completely disrupted in stocks heterozygous for mutations in aubergine, a gene whose protein product is involved in RNA interference. However, cytotype is not disrupted in stocks heterozygous for mutations in two other RNAi genes, piwi and homeless (spindle-E), or in a stock heterozygous for a mutation in the chromatin protein gene Enhancer of zeste. aubergine mutations exert their effects in the female germline, where the P cytotype is normally established and through which it is maintained. These effects are transmitted maternally to offspring of both sexes independently of the mutations themselves. Lines derived from mutant aubergine stocks reestablish the P cytotype quickly, unlike lines derived from stocks heterozygous for a mutation in Suppressor of variegation 205, the gene that encodes the telomere-capping protein HP1. Cytotype regulation by telomeric P elements may be tied to a system that uses RNAi to regulate the activities of telomeric retrotransposons in Drosophila.     

Analysis of the visible mutations induced by x-rays and ethyl methanesulfonate in the mature spermatozoa of Drosophila melanogaster

The recessive visible mutations spectrum of chromosome II induced by X-rays and ethylmethanesulfonata (EMS) in mature Drosophila melanogaster spermatozoa has been studied. Treatment of both mutagens resulted in mutations in all 5 genes in stock mei-9LI and only 4--in D-32. The comparison of mutation frequencies of the same genes in two stocks under EMS-treatment demonstrated the statistical difference of mutation frequencies j, pr, cn of two stocks, genes b and vg did not differ. Under the influence of X-rays the differencies have been observed only for gene b. In stock D-32 the mutation frequency differes from the control for b and vg (EMS treatment) and j, pr, vg (under the action of X-rays), in mei-9LI--the mutation frequency of all 5 genes (under the X-rays) and 4 of 5 genes (EMS treatment).     

Ribosomal DNA content and bobbed phenotype in Drosophila hydei.

The number of ribosomal RNA genes in different Drosophila hydei stocks has been determined by filter saturation hybridisation experiments. It has been shown that there is no marked correlation between the average rRNA gene number per cell in the whole animal and the bobbed phenotype when Y chromosomal nucleolar organisers are present.     

Quantitative analysis of the amount of larval serum protein-1 (LSP-1) synthesized by flies with different doses of the LSP-1 coding sequences

Larval serum protein-1 (LSP-1) and LSP-2 are the major proteins of Drosophila larval serum. The amount of LSP-1 synthesized is strictly proportional to the number of LSP-1 genes present within the range 1-10. The normal number in female flies is 6. Flies with extreme amounts of LSP-1 were, by our criteria, as fit as the wild type. The ratio of LSP-2:LSP-1 was analyzed in 169 different stocks and was constant in 164 of these. The significantly different ratios in five stocks were all due to the lack of one of the LSP-1 gene products.     

Proper control of genetic background with precise allele substitution: a comment on Coyne and Elwyn

Coyne and Elwyn report that, using Drosophila stocks provided by us, they were unable to replicate our experiments measuring the effects of desaturase-2 on stress tolerance. In this note, we provide evidence that these authors did not properly control for the differences in genetic background between the lines. Their experiments are thus not meaningful replications of our previous ones. We discuss ways of circumventing this problem in studies involving induced mutations in single genes.     

A reexamination of spreading of position-effect variegation in the white-roughest region of Drosophila melanogaster

In Drosophila, heterochromatin causes mosaic silencing of euchromatic genes brought next to it by chromosomal rearrangements. Silencing has been observed to "spread": genes closer to the heterochromatic rearrangement breakpoint are silenced more frequently than genes farther away. We have examined silencing of the white and roughest genes in the variegating rearrangements In(1)w(m4), In(1)w(mMc), and In(1)w(m51b). Eleven stocks bearing these chromosomes differ widely in the strength of silencing of white and roughest. Stock-specific differences in the relative frequencies of inactivation of white and roughest were found that map to the white-roughest region or the adjacent heterochromatin. Most stock-specific differences did not correlate with gross differences in the heterochromatic content of the rearranged chromosomes; however, two stocks, In(1)w(m51b) and In(1)w(mMc), were found to have anomalous additional heterochromatin that may act in trans to suppress variegating alleles. In comparing different stocks, the frequency of silencing of the roughest gene, which is more distant from heterochromatin, does not correlate with the frequency of silencing of the more proximal white gene on the same chromosome, in contradiction to the expectation of models of continuous linear propagation of silencing. We frequently observed rough eye tissue that is pigmented, as though an active white gene is skipped.     

The allelic forms of three larval salivary proteins from Drosophila melanogaster

Summary Sodium dodecyl sulphate (SDS) gel electrophoresis shows distinct differences in the number and mobility of the major salivary proteins produced by various stocks of Drosophila melanogaster. Genetic analysis showed that the variation was due to the presence of allelic forms of these proteins and demonstrated the absence of certain types of modifying genes. The variation in the mobility of two non-allelic proteins is so large that it is not possible to group variants of these proteins into specific mobility classes. Some results from the genetic analysis of these variants are of relevance to similar analyses of groups of genes determining related proteins in Drosophila.     

Flamenco, a Gene Controlling the Gypsy Retrovirus of Drosophila Melanogaster

Gypsy is an endogenous retrovirus of Drosophila melanogaster. It is stable and does not transpose with detectable frequencies in most Drosophila strains. However, we have characterized unstable strains, known as MG, in which it transposes at high frequency. These stocks contain more copies of gypsy than usual stocks. Transposition results in mutations in several genes such as ovo and cut. They are stable and are due to gypsy insertions. Integrations into the ovo(D1) female sterile-dominant mutation result in a null allele of the gene and occurrence of fertile females. This phenomenon, known as the ovo(D1) reversion assay, can be used to quantitate gypsy activity. We have shown that the properties of MG strains result from mutation of a host gene that we called flamenco (flam). It has a strict maternal effect on gypsy mobilization: transposition occurs at high frequency only in the germ line of the progeny of females homozygous for mutations of the gene. It is located at position 65.9 (20A1-3) on the X chromosome. The mutant allele present in MG strains is essentially recessive. Flamenco seems to control the infective properties of gypsy.     

Identification of an amber nonsense mutation in the rosy516 gene by germline transformation of an amber suppressor tRNA gene.

Seven xanthine dehydrogenase and cross-reacting material negative Drosophila melanogaster rosy stocks were screened for amber and ochre nonsense mutations. Amber and ochre nonsense suppressors were created by site-directed mutagenesis starting from a wild-type tRNA(Tyr) gene. The suppressor tRNA genes were subcloned into a pUChsneo transformation vector providing heat-shock controlled neomycin resistance. The seven rosy stocks were germline transformed with amber and ochre tDNA(Tyr), and the G1 generation was screened for Geneticin resistance. Surviving rosy516 flies transformed with the amber suppressor showed an eye colour intermediate between the original ry516 stock and the wild-type, suggesting that ry516 is an amber nonsense mutant. This was confirmed by sequencing the relevant part of the ry516 gene; the analysis revealed a C-to-T transition in a CAG glutamine codon at nucleotide 1522 of the wild-type rosy gene.     

The effect of multi-locus deletions in heterozygotes; a model study using Drosophila

In a model study using Drosophila, we examined the heterozygous effects of a number of well-defined X-chromosomal deletions (i.e., those differing in location, but of about the same length, and those differing in length but located in the same general region), using relative viability and/or fertility as indicators. Most of the deletions were originally isolated in radiation or chemical mutagenesis experiments and maintained since then in stocks using appropriate balancer chromosomes. The results show that (i) most of the deletions have pronounced deleterious effects in heterozygotes; (ii) the size of the deletion per se is not a critical factor in determining relative heterozygous viability, but its location is and (iii) it is possible to tentatively identify, with respect to the deletions, putative genes that affect viability in Drosophila.     

New research resources at the Bloomington Drosophila Stock Center

The Bloomington Drosophila Stock Center (BDSC) is a primary source of Drosophila stocks for researchers all over the world. It houses over 27,000 unique fly lines and distributed over 160,000 samples of these stocks this past year. This report provides a brief overview of significant recent events at the BDSC with a focus on new stock sets acquired in the past year, including stocks for φC31 transformation, RNAi knockdown of gene expression, and SNP and quantitative trait loci discovery. We also describe additions to sets of insertions and molecularly defined chromosomal deficiencies, the creation of a new Deficiency Kit, and planned additions of X chromosome duplication sets.     

Fly culture collapse disorder: detection,prophylaxis and eradication of the microsporidian parasite Tubulinosema ratisbonensis infecting Drosophila melanogaster

Drosophila melanogaster is a robust model to investigate many biological problems. It is however prone to some infections, which may endanger fly stocks if left unchecked for. One such infection is caused by an obligate fungal intracellular parasite, Tubulinosema ratisbonensis, which can be found in laboratory stocks. Here, we identify and briefly characterize a T. ratisbonensis strain that was infesting our Drosophila cultures and that required intensive measures to contain and eradicate the infection. We describe the phenotypes of infested stocks. We also report PCR-based techniques that allow the detection of infested stocks with a high sensitivity. We have developed a high-throughput qPCR assay that allows the efficient parallel screening of a large number of potentially-infested stocks. We also have investigated several prophylactic measures to prevent the further contamination of stocks, namely UV-exposure, ethanol treatment, bleaching, and desiccation. Bleaching was found to kill all spores. Other treatments were less effective but were found to be sufficient to prevent further contamination of noninfested stocks. Two treatments were efficacious in curing infested stocks (1) bleaching of eggs and subsequent raising of the larvae in clean vials; (2) fumagillin treatment. These cures only work on stocks that have not become too weak to withstand the procedures.     

Non-Mendelian Inheritance of "Heat-Sensitivity" in DROSOPHILA MELANOGASTER

Non-Mendelian inheritance was revealed for the "heat-sensitivity" character of the poikilothermic insect Drosophila melanogaster. Genetic analyses were performed on heat-sensitive (S, S(1)) strains, derived through indirect selection, and on stocks constructed through extensive chromosomal and cytoplasmic substitutions between strains obtained from two replicate cage populations. The populations were kept for about 7 years under different temperatures (14 degrees -25 degrees ) and exhibited different survival. We conclude that the character studied is quantitative, responds to selection pressure and is transmitted through the maternal cytoplasm, while nuclear genes modify its expression.     

Isolation of Drosophila melanogaster strain y+ snw sc wa transformed by a series of P-element mediated vectors using microinjections into early embryos

P-element-mediated transformation of Drosophila melanogaster was performed and the effectivity of transformation determined using the y+snwsc wa stock. Some new D. melanogaster stocks with sne and sn+ phenotypes were obtained as well as the stocks containing bacterial "neo" gene integrated into the genome.     

Isolation of memory-deficient Drosophila mutants in conditioned courtship suppression paradigm]

Among 33 mutant stocks of Drosophila melanogaster generated by means of P-insertional mutagenesis in the system with single P element, 4 stocks have been isolated as demonstrating deficient memory in the conditioned courtship suppression paradigm. Localization of the P insertions never coincided with that of previously known mutations affecting memory.     

Factors on the third chromosome affect the level of cyp6a2 and cyp6a8 expression in Drosophila melanogaster

The expression of two second chromosome-linked cytochrome P450 genes, Cyp6a2 and Cyp6a8, of Drosophila melanogaster was measured in various strains. Six different strains, including ry(506) and 91-C, showed low or undetectable levels of CYP6A2 and CYP6A8 mRNAs, suggesting that low expression is the wild-type phenotype of Cyp6a2 and Cyp6a8 genes. In the 91-R and MHIII-D23 strains, however, both these genes are overexpressed. In order to examine the genetic basis of Cyp6a2 and Cyp6a8 expression, CYP6A2 and CYP6A8 RNA levels were measured in the F1 hybrids of overproducer (91-R and MHIII-D23) and underproducer (ry(506) and 91-C) strains. Results showed that the total amounts of CYP6A2 and CYP6A8 mRNAs in the F1 hybrids were lower than half the amounts of these RNAs found in the overproducer parental strains. This suggested that the underproducer strains carry loci which downregulate Cyp6a2 and Cyp6a8 gene expression. To determine the chromosome linkage of these loci, several stocks homozygous for the second chromosome of overproducer 91-R strain and, therefore, homozygous for the Cyp6a2-91R and Cyp6a8-91R alleles were synthesized. The third chromosomes in all these stocks were from the underproducer ry(506) strain. The levels of expression of both Cyp6a2-91R and Cyp6a8-91R genes in these three stocks were significantly lower than that observed in the 91-R strain. One of these stocks, named iso-2, showing reduced expression, was used to synthesize two new isogenic stocks by resubstituting the third chromosome of ry(506) origin with third chromosomes of the 91-R strain. Expression of both Cyp6a2-91R and Cyp6a8-91R alleles was found to be much higher in these two resubstituted isogenic stocks than in the progenitor iso-2 stock. Taken together, these results suggest that the second chromosome-linked Cyp6a2 and Cypa8 genes are regulated by loci present on the third chromosome, and the wild-type function of these loci is to repress these two Cyp genes. The data also suggest that Cyp6a2 and Cyp6a8 overexpression in the 91-R and MHIII-D23 strains is more likely due to mutation in the repressor locus (or loci) rather than in the cis-regulatory sequences of the Cyp6a2 and Cyp6a8 genes.     

The number and location of genes for 5S ribonucleic acid within the genome of Drosophila melanogaster

DNA was prepared from wild-type and two mutant stocks of Drosophila melanogaster that differed in their dosage of the nucleolar organizer region. The relative amounts of DNA from the nucleolar organizer region in these preparations of DNA were determined by hybridization with (3)H-labelled 28S rRNA. As expected, the amount of (3)H-labelled 28S rRNA that hybridized was directly related to the dosage of nucleolar organizer region. No positive correlation was observed between the amount of (3)H-labelled 5S RNA that hybridized and the dosage of nucleolar organizer region. Thus genes for 5S RNA are located primarily, if not exclusively, outside the nucleolar organizer region. The haploid genome of the wild-type D. melanogaster used in this work has 106 genes for 28S rRNA and 96-105 genes for 5S RNA.     

A meristic trait in Drosophila melanogaster x simulans hybrids

A quantitative trait, abdominal bristle number, is described in a number of stocks of the two sibling species Drosophila melanogaster and Drosophila simulans and in interspecific hybrids obtained from these stocks. Coefficients of variation for the trait in the parental species and the hybrids are compared, and in the case of the latter are found to fall in the same range as those of the pure species. The results are discussed in the light of previous findings on other bristle systems.