Genetica

Divergent evolution of molecular markers during laboratory adaptation in Drosophila subobscura.

Publication Date: 2010 Aug 31 PMID: 20803349
Authors: Simoes, P. - Pascual, M. - Coelho, M. M. - Matos, M.
Journal: Genetica

The impact of genetic drift in population divergence can be elucidated using replicated laboratory experiments. In the present study we used microsatellite loci to study the genetic variability and differentiation of laboratory populations of Drosophila subobscura derived from a common ancestral natural population after 49 generations in the laboratory. We found substantial genetic variability in all our populations. The high levels of genetic variability, similar across replicated populations, suggest that careful maintenance procedures can efficiently reduce the loss of genetic variability in captive populations undergoing adaptation, even without applying active management procedures with conservation purposes, in organisms that generate a high number of offspring such as Drosophila. Nevertheless, there was a significant genetic differentiation between replicated populations. This shows the importance of genetic drift, acting through changes in allele frequencies among populations, even when major changes in the degree of genetic diversity in each population are not involved.

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Evidence based on studies of the mus309 mutant, deficient in DNA double-strand break repair, that meiotic crossing over in Drosophila melanogaster is a two-phase process.

Publication Date: 2010 Aug 31 PMID: 20803348
Authors: Portin, P.
Journal: Genetica

The mus309 gene in Drosophila melanogaster encodes a RecQ helicase which is involved in DNA double-strand break (DSB) repair and specifically in the choice between the different pathways of the repair. In a brood pattern analysis of mus309 and wild type females which either had or had not experienced a temperature shock, different parameters of meiotic crossing over including map distances and crossover interference in the X chromosome were measured. The results suggest that, like in other eukaryotes studied, the control of meiotic crossover formation also in D. melanogaster is a two-phase process. The first phase seems to be temperature shock sensitive, independent of the mus309 gene and coincidental with the premeiotic DNA synthesis, thus most likely representing the formation of DSBs. The second phase seems to be temperature shock tolerant, dependent on the mus309 gene, occurring during the meiotic prophase and most likely representing the choice made by the oocyte between the different pathways of the DSB repair. A hypothesis of the localization of chiasmata is also presented, combining the mechanisms of interference and the so-called centromere effect, and based on the balance between the SDSA and DSBR pathways of DSB repair.

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A non-parametric mixture model for genome-enabled prediction of genetic value for a quantitative trait.

Publication Date: 2010 Aug 25 PMID: 20737196
Authors: Gianola, D. - Wu, X. L. - Manfredi, E. - Simianer, H.
Journal: Genetica

A Bayesian nonparametric form of regression based on Dirichlet process priors is adapted to the analysis of quantitative traits possibly affected by cryptic forms of gene action, and to the context of SNP-assisted genomic selection, where the main objective is to predict a genomic signal on phenotype. The procedure clusters unknown genotypes into groups with distinct genetic values, but in a setting in which the number of clusters is unknown a priori, so that standard methods for finite mixture analysis do not work. The central assumption is that genetic effects follow an unknown distribution with some "baseline" family, which is a normal process in the cases considered here. A Bayesian analysis based on the Gibbs sampler produces estimates of the number of clusters, posterior means of genetic effects, a measure of credibility in the baseline distribution, as well as estimates of parameters of the latter. The procedure is illustrated with a simulation representing two populations. In the first one, there are 3 unknown QTL, with additive, dominance and epistatic effects; in the second, there are 10 QTL with additive, dominance and additive x additive epistatic effects. In the two populations, baseline parameters are inferred correctly. The Dirichlet process model infers the number of unique genetic values correctly in the first population, but it produces an understatement in the second one; here, the true number of clusters is over 900, and the model gives a posterior mean estimate of about 140, probably because more replication of genotypes is needed for correct inference. The impact on inferences of the prior distribution of a key parameter (M), and of the extent of replication, was examined via an analysis of mean body weight in 192 paternal half-sib families of broiler chickens, where each sire was genotyped for nearly 7,000 SNPs. In this small sample, it was found that inference about the number of clusters was affected by the prior distribution of M. For a set of combinations of parameters of a given prior distribution, the effects of the prior dissipated when the number of replicate samples per genotype was increased. Thus, the Dirichlet process model seems to be useful for gauging the number of QTLs affecting the trait: if the number of clusters inferred is small, probably just a few QTLs code for the trait. If the number of clusters inferred is large, this may imply that standard parametric models based on the baseline distribution may suffice. However, priors may be influential, especially if sample size is not large and if only a few genotypic configurations have replicate phenotypes in the sample.

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Development of transgenic strains for the biological control of the Mexican fruit fly, Anastrepha ludens.

Publication Date: 2010 Aug 25 PMID: 20737195
Authors: Meza, J. S. - Nirmala, X. - Zimowska, G. J. - Zepeda-Cisneros, C. S. - Handler, A. M.
Journal: Genetica

The Mexican fruit fly, Anastrepha ludens, is a highly significant agricultural pest species that has been genetically transformed with a piggyBac-based transposon vector system using independent vector and transposase helper plasmids. Minimum estimated germ-line transformation frequencies were approximately 13-21% per fertile G(0) individual, similar to previously reported frequencies using single vector-helper plasmids. Two vector constructs were tested with potential importance to transgenic strain development for mexfly biological control. The first allows post-integration stabilization of a transposon-vector by deletion of a terminal sequence necessary for mobilization. The complete pB[L1-EGFP-L2-DsRed-R1] vector was integrated into the Chiapas wild type strain with subsequent deletion of the L2-DsRed-R1 sub-vector carrying the piggyBac 3' terminal sequence. Quality control tests for three of the stabilization vector lines (previous to stabilization) assessed viability at all life stages, fertility, adult flight ability, and adult male sexual competitiveness. All three transgenic lines were less fit compared to the wild strain by approximately 5-10% in most tests, however, there was no significant difference in sexual competitiveness which is the major prerequisite for optimal strain release. The second vector, pB[XL-EGFP, Asss2-tub-DsRed.T3], has the DsRed.T3 fluorescent protein reporter gene regulated by the A. suspensa Asss2-tubulin promoter, that resulted in testis and sperm-specific DsRed fluorescence in transgenic male mexflies. Fluorescent sperm bundles were unambiguously observed in the spermathecae of non-transgenic females mated to transgenic males. One transgenic line apparently had a male-specific Y-chromosome insertion, having potential use for sexing by fluorescent-embryo sorting. All transgenic lines expressed easily detectable and stable fluorescence in adults allowing their identification after trapping in the field.

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Genetic diversity of the killifish Aphanius fasciatus paralleling the environmental changes of Tarquinia salterns habitat.

Publication Date: 2010 Aug 26 PMID: 20737194
Authors: Angeletti, D. - Cimmaruta, R. - Nascetti, G.
Journal: Genetica

The habitat in the Natural Reserve of the Tarquinia salterns, located on the Tyrrhenian coast of central Italy, has undergone dramatic alterations over the last 10 years. After salt production was terminated in 1997 the site was abandoned until 2002, with consequent degradation of habitat quality and stiffening of the environmental conditions. From 2003 to 2006 ecological rehabilitation of the site was carried out, restoring water circulation to its previous equilibrium. The genetic variation in the killifish Aphanius fasciatus inhabiting the salterns was monitored using allozymes from 1998. The results showed that the genetic variability of the killifish strongly reduced through time: a high number of rare alleles were lost and both heterozygosity and allele richness were significantly decreased. The most recent samples, taken after the ecological restoration, showed that to date the genetic erosion of A. fasciatus gene pool has slowed down, since no significant differences have been detected for any genetic variability parameter. Concerning the mechanisms leading to the impoverishment of the genetic variability, the strong loss of rare alleles suggests a role of genetic drift, which accords with the fluctuation of the effective population size recorded over the period of study and with the low gene flow typical of this species. The low levels of gene flow reported for this species imply that once lost, the genetic variability can rarely be restored through immigration from highly variable populations.

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Safe and fit genetically modified insects for pest control: from lab to field applications.

Publication Date: 2010 Aug 20 PMID: 20725766
Authors: Scolari, F. - Siciliano, P. - Gabrieli, P. - Gomulski, L. M. - Bonomi, A. - Gasperi, G. - Malacrida, A. R.
Journal: Genetica

Insect transgenesis is continuously being improved to increase the efficacy of population suppression and replacement strategies directed to the control of insect species of economic and sanitary interest. An essential prerequisite for the success of both pest control applications is that the fitness of the transformant individuals is not impaired, so that, once released in the field, they can efficiently compete with or even out-compete their wild-type counterparts for matings in order to reduce the population size, or to spread desirable genes into the target population. Recent research has shown that the production of fit and competitive transformants can now be achieved and that transgenes may not necessarily confer a fitness cost. In this article we review the most recent published results of the fitness assessment of different transgenic insect lines and underline the necessity to fulfill key requirements of ecological safety. Fitness evaluation studies performed in field cages and medium/large-scale rearing will validate the present encouraging laboratory results, giving an indication of the performance of the transgenic insect genotype after release in pest control programmes.

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Novel female-specific splice form of dsx in the silkworm, Bombyx mori.

Publication Date: 2010 Aug 18 PMID: 20714790
Authors: Shukla, J. N. - Jadhav, S. - Nagaraju, J.
Journal: Genetica

The Bombyx mori doublesex (Bmdsx), a homologue of doublesex of Drosophila, is the bottom most gene of the sex determination cascade. Bmdsx plays a very crucial role in somatic sexual development. Its pre-mRNA sex-specifically splices to generate two splice variants; one encodes female-specific and the other encodes male-specific polypeptides which differ only at their C-termini. The open reading frame of Bmdsx consists of 5 exons, of which exons 3 and 4 are female-specific and are skipped in males. In the present study, we have identified a third splice form of the Bmdsx which is specific only to females and differs from the previously reported Bmdsxf isoform by the presence of 15 bp sequence. This new female splice form is generated as a result of alternative 5' splice site selection in the third exon adding additional 15 bp sequence in exon 3 which results in alteration of the reading frame leading to incorporation of an early stop codon. Thus the protein encoded by this splice form is 20 aa shorter than the known BmDsxF. Initial results obtained from the study of dsx homologues in Saturniid silkmoths suggest that both the female-specific Dsx proteins are essential for female sexual differentiation. It remains to be seen whether female-specific multiple splice forms of dsx are characteristic feature of only silkmoths or widespread among lepidopterans. The findings that sex determination mechanism is unique in lepidopterans offer an opportunity to develop genetic sexing methods in beneficial as well as economically destructive lepidopteran pests.

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Nuclear copies of mitochondrial genes: another problem for ancient DNA.

Publication Date: 2010 Aug 11 PMID: 20700629
Authors: den Tex, R. J. - Maldonado, J. E. - Thorington, R. - Leonard, J. A.
Journal: Genetica

The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.

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Drcd-1 related: a positively selected spermatogenesis retrogene in Drosophila.

Publication Date: 2010 Aug 8 PMID: 20694743
Authors: Quezada-Diaz, J. E. - Muliyil, T. - Rio, J. - Betran, E.
Journal: Genetica

Gene duplication is a major force driving genome evolution, and examples of this mode of evolution and of the functions of duplicated genes are needed to reveal general patterns. Here, our study focuses on a particular retrogene (i.e., CG9573) that originated about 5-13 million years ago that we have named Drcd-1 related. It originated in Drosophila through retroposition of the parental gene Required for cell differentiation 1 of Drosophila (Drcd-1; CG14213), which is a known transcription cofactor. Drcd-1r is only present in D. melanogaster, D. simulans, D. sechellia, and D. mauritiana. Drcd-1r is an X to autosome retroposition event. Many retrogenes are X to autosome copies and it has been shown that positive selection underlies this bias. We sought to understand Drcd-1r mode of evolution and function to contribute to the understanding of the selective pressures acting on X to autosome retrogenes. Drcd-1r overlaps with another gene, it is within the 3' UTR of the gene CG13102 and is encoded in the opposite orientation. We have studied the characteristics of the transcripts and quantified expression of CG13102 and Drcd-1r in wild-type flies. We found that Drcd-1r is transcribed specifically in testes. We also studied the molecular evolution of Drcd-1r and Drcd-1 and found that the parental gene has evolved under very strong purifying selection but the retrogene has evolved very rapidly (Ka/Ks ~1) under both positive and purifying selection, as revealed using divergence and polymorphism data. These results indicate that Drcd-1r has a novel function in the Drosophila testes. To further explore Drcd-1r function we used a strain containing a P element inserted in the region where CG13102 and Drcd-1r are located that shows recessive male sterility. Analysis of this strain reveals the difficulties that can be encountered in studying the functions of genes with overlapping transcripts. Avenues for studying of the function of this gene are proposed.

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