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Genomic consequences of background effects on scalloped mutant expressivity in the wing of Drosophila

ABSTRACT: Genetic background effects contribute to the phenotypic consequences of mutations, and are pervasive across all domains of life that have been examined, yet little is known about how they modify genetic systems. In part this is due to the lack of tractable model systems that have been explicitly developed to study the genetic and evolutionary consequences of background effects. In this study we demonstrate that phenotypic expressivity of the scalloped[E3] mutation of Drosophila melanogaster is background dependent, and is the result of at least one major modifier segregating between two standard lab wild-type strains. Microarrays were used to examine the consequences of genetic background effects on the global transcriptome. Expression differences between wild-type strains were found to be as large or larger than the effects of mutations with substantial phenotypic effects, and expression differences between wild-type and mutant varied significantly between genetic backgrounds. Significantly, we demonstrate that the epistatic interaction between sd[E3] and an optomotor blind mutation is background dependent. The results are discussed within the context of developing a complex but more realistic view of the consequences of genetic background effects with respect to mutational analysis, and studies of epistasis and cryptic genetic variation segregating in natural populations Keywords: Mutant vs wild-type comparison

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE13779 | GEO | 2008/12/03

SECONDARY ACCESSION(S): PRJNA110605

REPOSITORIES: GEO

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Genomic consequences of background effects on scalloped mutant expressivity in the wing of Drosophila

Project description:Genetic background effects contribute to the phenotypic consequences of mutations, and are pervasive across all domains of life that have been examined, yet little is known about how they modify genetic systems. In part this is due to the lack of tractable model systems that have been explicitly developed to study the genetic and evolutionary consequences of background effects. In this study we demonstrate that phenotypic expressivity of the scalloped[E3] mutation of Drosophila melanogaster is background dependent, and is the result of at least one major modifier segregating between two standard lab wild-type strains. Microarrays were used to examine the consequences of genetic background effects on the global transcriptome. Expression differences between wild-type strains were found to be as large or larger than the effects of mutations with substantial phenotypic effects, and expression differences between wild-type and mutant varied significantly between genetic backgrounds. Significantly, we demonstrate that the epistatic interaction between sd[E3] and an optomotor blind mutation is background dependent. The results are discussed within the context of developing a complex but more realistic view of the consequences of genetic background effects with respect to mutational analysis, and studies of epistasis and cryptic genetic variation segregating in natural populations Keywords: Mutant vs wild-type comparison 2 wild-type strains of D. melanogaster (Oregon-R and Samarkand, both marked with white) each with and without the scalloped[E3] mutation. Thus a 2x2 factorial design with a balanced incomplete block (block=slide) design in a full loop configuration with dye swapping.

2010-05-15 | E-GEOD-13779 | biostudies-arrayexpress

Profiling expression changes caused by a segmental aneuploid in maize meristem tissues

Project description:Segmental aneuploidy refers to the relative excess or deficiency of specific chromosome regions. This condition results in gene dosage imbalance and often causes severe phenotypic alterations in plants and animals. The mechanisms by which gene dosage imbalance effects gene expression and phenotype are not completely clear. The effects of aneuploidy on the transcriptome may depend on the types of cells analyzed and on the developmental stage. We performed global gene expression profiling to determine the effects of segmental aneuploidy on gene expression levels in two different maize tissues and a detailed analysis of expression of 30 genes affected by aneuploidy in multiple maize tissues. Multiple genes demonstrated qualitative changes in gene expression due to aneuploidy, when the gene became ectopically expressed or erroneously transcriptionally silenced in aneuploids relative to wild type plants. Our data strongly suggested that quantitative changes in gene expression at developmental transition points caused by variation in gene copy number progressed through tissue development and resulted in stable qualitative changes in gene expression patterns. Thus, aneuploidy in maize results in alterations of gene expression patterns that differ between tissues and developmental stages of maize seedlings. RNA was extracted from meristem tissues of 14 day-old maize seedlings segregating for segmental trisome of a short arm of chromosome 5. There are three biological replicates of pooled wild-type siblings and three biological replicates of pooled DpDf plants. The DpDf plants are segmental aneuploids that contain three copies of the short arm of chromosome 5. These plants are all in the B73 inbred genetic background.

2010-01-01 | E-GEOD-19212 | biostudies-arrayexpress

Drosophila melanogaster

Project description:An integrative genomic approach illuminates the causes and consequences of genetic background effects

| PRJNA233426 | ENA

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Project description:Genetic variation that underlies phenotypic differences provides the material on which evolutionary selection acts. Gene duplication/amplification is one type of genetic variation that can allow an organism to rapidly respond to environmental changes by increasing gene dosage. While the potential benefits afforded by gene amplification during evolution are well known, there is also a significant fitness cost to increasing gene dosage including resource shortages and burdening cellular systems. Although the evolutionary importance of gene duplication has long been appreciated, little is known about natural variation in the tolerance of duplication of specific genes. To investigate this question, we expressed the same high-copy gene overexpression (OE) library in a laboratory strain and 14 different wild S. cerevisiae isolates, together representing 4 lineages and several admixed strains, to explore the natural variation in tolerance to gene OE. Our results distinguish universal effects common to many studied strains versus strain-specific effects including broad-scale and gene-specific differences in the consequences of OE. These results raise important implications for the accessibility of evolutionary trajectories afforded by gene OE, depending on genetic background.

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Comparison of Transcript Profiles in Wild-type and o2 Maize Endosperm in Different Genetic Backgrounds

Project description:Mutations in the Opaque2 (O2) gene of maize (Zea Mays L.) improve the nutritional value of maize by reducing the level of zeins in the kernel. The phenotype of o2 grain is controlled by many modifier genes and is therefore strongly dependent on the genetic background. We sought to distinguish between two hypotheses to explain differences in phenotypic severity: 1. Differences in phenotypic severity are due to genotype specific differentially expressed genes and 2. Differences in phenotypic severity are due to differences in the degree of differential expression of a set of differentially expressed genes. Eight pairs of inbred lines and their o2 counterparts were characterized for phenotypes controlled by o2 (lysine content, kernel density, seed weight and shoot to root ratio of seedlings). The inbred line B46 was identified as having severe o2 effects while the line M14 was identified as having minimal o2 effects. Transcripts that were differentially expressed between the wild-type and o2 versions of these two lines were identified by microarray hybridization. While genotype specific differentially expressed transcripts were identified, many transcripts were identified with reduced degree of differential expression in M14 relative to B46. Thus, a combination of genotype specific transcripts and degree of differential expression of transcripts can explain differences in phenotypic severity in these two genetic backgrounds. To identify the transcripts most likely to be differentially expressed in a given genetic background, we used RNA from eight genotype pools in microarray hybridization. By averaging across genotypes in this way, genotype-specific changes are minimized. Keywords: Genetic modification

2005-10-22 | GSE3490 | GEO

48 apple trees from a segregating F1 population from a cross of 'Ottawa 3' x 'Robusta 5'

Project description:48 apple trees from a segregating F1 population from a cross of 'Ottawa 3' x 'Robusta 5' were analyzed by microarray to identify gene expression differences between the individuals to correlate gene expression patterns with phenotypic traits segregating in the population

2013-11-04 | GSE43268 | GEO

Systems genetics of single nucleotide substitutions at the Drosophila Obp56h locus

Project description:Individual variation in complex traits results from allelic variants of multiple segregating genes, which are expressed as coregulated ensembles that are modulated by the environment. Coregulated transcriptional networks around focal genes, defined as their ‘transcriptional niches’, are sensitive to genetic and environmental perturbations. Understanding how single base pair substitutions affect this complex genotype-phenotype relationship by perturbing transcriptional niches is possible in Drosophila, which allows precise control of both the genetic background and the environment. We used a two-step CRISPR-Cas9 mediated gene deletion and reinsertion strategy to generate in a common genetic background five single nucleotide substitutions in the D. melanogaster Obp56h gene that correspond to naturally occurring allelic variants. Changes in single base pairs give rise to differential, sexually dimorphic effects on a plethora of fitness traits, including viability, sex ratio, feeding behavior, starvation resistance, recovery from a chill-induced coma, response to heat shock, activity, and sleep traits. These pleiotropic effects are accompanied by sexually dimorphic shifts in the transcriptional niche of Obp56h. Pairwise comparisons between the lines show common coregulated genes along with varying numbers of transcripts unique to one or few Obp56h alleles. Gene ontology enrichment analyses indicate that fundamental cellular processes for each sex underlie the phenotypic pleiotropy revealed by the Obp56h allelic series. Furthermore, different Obp56h alleles in a common genetic background give rise to allele-specific, sexually dimorphic microenvironmental variation. The reverse genetic engineering strategy, illustrated here, can be generally applied to other genes to dissect variation in the genotype-phenotype relationship at single base pair resolution.

2022-03-10 | GSE178635 | GEO

Metabolic Biomarkers of Ageing in C57BL/6J Wild-Type and Flavin-Containing Monooxygenase 5 (FMO5)-Knockout Mice

Project description:It was recently demonstrated in mice that knockout of the flavin-containing monooxygenase 5 gene, Fmo5, slows metabolic ageing via pleiotropic effects. We have now used an NMR-based metabonomics approach to study the effects of ageing directly on the metabolic profiles of urine and plasma from male, wild-type C57BL/6J and Fmo5−/− (FMO5 KO) mice back-crossed onto the C57BL/6J background. The aim of this study was to identify metabolic signatures that are associated with ageing in both these mouse lines and to characterize the age-related differences in the metabolite profiles between the FMO5 KO mice and their wild-type counterparts at equivalent time points. We identified a range of age-related biomarkers in both urine and plasma. Some metabolites, including urinary 6-hydroxy-6-methylheptan-3-one (6H6MH3O), a mouse sex pheromone, showed similar patterns of changes with age, regardless of genetic background. Others, however, were altered only in the FMO5 KO, or only in the wild-type mice, indicating the impact of genetic modifications on mouse ageing. Elevated concentrations of urinary taurine represent a distinctive, ageing-related change observed only in wild-type mice.

2018-06-20 | MTBLS667 | MetaboLights

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Project description:Interplay between genetic background and genome evolution

| PRJNA101919 | ENA

Bulk segregant sequencing (Bulk-Seq) analysis to identify paternal suppressors of medea in Arabidopsis thaliana

Project description:Arabidopsis thaliana seeds that maternally inherit a medea (mea) mutant allele abort before completing embryogenesis. However, mea seeds can be rescued by pollen from several natural ecotypes of A. thaliana, including the Cape Verdian accession Cvi-0. We developed a method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks. The strategy is to create an F2 population that contains one set of chromosomes from the maternal parent (mea, in a Ler background) but inherits two segregating sets (Ler and Cvi-0) from the other parent. The two paternally segregating sets have opposite effects in mea penetrance: Ler fathers allow full mea seed abortion, while Cvi fathers rescue 90% of medea seeds. Therefore, the two segregating paternal sets are not equally transmitted to the next generation. DNA extracted from pools of viable F2 seedlings was sequenced on an Illumina HiSeq 2000 platform, mapped to the reference TAIR10 A. thaliana genome and the ratio between Ler and Cvi-0 SNPs used to identify chromosomal regions enriched in Cvi-0 sequences. As a control, DNA pools extracted from crosses between a wild-type Ler mother and a hybrid Cvi-0:Ler father were also sequenced. Three biological replicates were made for each pool. Ler-1 x Ler-1:Cvi-0 hybrid viable seedlings pools (each is a biological replicate): WT_pool_1, WT_pool_2, WT_pool_3 mea-1/mea-1; MEA-GR x Ler-1:Cvi-0 hybrid viable seedlings pool (each is a biological replicate): mea_pool_1, mea_pool_2, mea_pool_3

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