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ABSTRACT:
PROVIDER: PRJEB45961 | ENA |
REPOSITORIES: ENA
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Project description:Understanding how polygenic traits evolve and respond to selection is a major unsolved problem, because challenges exist for identifying genes underlying a complex trait and understanding how multi-locus selection operates in the genome. Here we used artificial selection experiments to study polygenic response to selection. Inbred strains from seven independent long-term selection experiments in mice for extreme bodyweight (“High” lines weigh 77-42g vs. 40-16g in “Controls” lines), were genotyped at 527,572 SNPs to identify genetic variants controlling bodyweight. We identified 67 high-resolution parallel selected regions (PSRs) where multiple High lines share variants rarely found among the Controls. By comparing allele frequencies in one selection experiment against its unselected control, we found classical selective sweep signatures centered on the PSRs. Multiple lines of evidence support two G protein-coupled receptors GPR133 and Prlhr, as positional candidate genes controlling bodyweight. Artificial selection may mimic natural selection in the wild: compared to control loci, we detected reduced heterozygosity in PSRs in wild populations of unusually large mice on islands. Many PSRs overlap loci associated with human height variation, possibly through evolutionary conservation of functional pathways. Our data suggest that parallel selection on complex traits may evoke parallel responses at many genes involved in diverse but relevant pathways. These samples were used to test the enrichment of certain gene functional categories. Genomic DNA SNP comparison between artificially selected high lines (BEH, DAHi, DUH, MUH, EDH, RAHi, Du6/G154 and Du6i/G80) and unselected control lines.
2012-06-29 | E-GEOD-36409 | biostudies-arrayexpress
Project description:Understanding how polygenic traits evolve and respond to selection is a major unsolved problem, because challenges exist for identifying genes underlying a complex trait and understanding how multi-locus selection operates in the genome. Here we used artificial selection experiments to study polygenic response to selection. Inbred strains from seven independent long-term selection experiments in mice for extreme bodyweight (“High” lines weigh 77-42g vs. 40-16g in “Controls” lines), were genotyped at 527,572 SNPs to identify genetic variants controlling bodyweight. We identified 67 high-resolution parallel selected regions (PSRs) where multiple High lines share variants rarely found among the Controls. By comparing allele frequencies in one selection experiment against its unselected control, we found classical selective sweep signatures centered on the PSRs. Multiple lines of evidence support two G protein-coupled receptors GPR133 and Prlhr, as positional candidate genes controlling bodyweight. Artificial selection may mimic natural selection in the wild: compared to control loci, we detected reduced heterozygosity in PSRs in wild populations of unusually large mice on islands. Many PSRs overlap loci associated with human height variation, possibly through evolutionary conservation of functional pathways. Our data suggest that parallel selection on complex traits may evoke parallel responses at many genes involved in diverse but relevant pathways. These samples were used to test the enrichment of certain gene functional categories.
2012-06-30 | GSE36409 | GEO
Project description:Understanding how polygenic traits evolve and respond to selection is a major unsolved problem, because challenges exist for identifying genes underlying a complex trait and understanding how multi-locus selection operates in the genome. Here we used artificial selection experiments to study polygenic response to selection. Inbred strains from seven independent long-term selection experiments in mice for extreme bodyweight (“High” lines weigh 77-42g vs. 40-16g in “Controls” lines), were genotyped at 527,572 SNPs to identify genetic variants controlling bodyweight. We identified 67 high-resolution parallel selected regions (PSRs) where multiple High lines share variants rarely found among the Controls. By comparing allele frequencies in one selection experiment against its unselected control, we found classical selective sweep signatures centered on the PSRs. Multiple lines of evidence support two G protein-coupled receptors GPR133 and Prlhr, as positional candidate genes controlling bodyweight. Artificial selection may mimic natural selection in the wild: compared to control loci, we detected reduced heterozygosity in PSRs in wild populations of unusually large mice on islands. Many PSRs overlap loci associated with human height variation, possibly through evolutionary conservation of functional pathways. Our data suggest that parallel selection on complex traits may evoke parallel responses at many genes involved in diverse but relevant pathways. These samples were used to test the enrichment of certain gene functional categories.
2012-06-30 | GSE36443 | GEO
Project description:Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci likely to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.
2019-07-09 | GSE121565 | GEO
Project description:Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci likely to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.
2019-07-09 | GSE121564 | GEO
Project description:High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Each single wood trait was found to be highly polygenic in its nature. However, gene hierarchies need to be assessed with the most important gene variants controlling a specific trait within the complex network of interacting secondary cell wall characteristics that defines the overall wood phenotype. We tested the available genetic and genomic information in an integrative approach to effectively predict wood properties in Populus trichocarpa.Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49K Nimblegen array elements and for 28,831 polymorphic SNPs. Pre-selected transcripts and SNPs with high statistical dependency on the phenotypic trait were used in a Bayesian network learning procedure with stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at much lower logBF threshold than SNPs and were not accommodated in the networks. Complexity of phenotype-centric networks with 100% predictive accuracy ranged from 7 (glucose) to 39 SNPs (alpha-cellulose). Pleiotropic gene actions were accommodated in genetic networks of correlated traits; such gene variants help to understand independent evolution of trait values, and they represent new tools to support the maximization of correlated response to selection. Developing xylem harvested at breast height from the north side of each tree stem from 17 genotypes with two biological replicates and from two additional genotypes without a second replicate previously identified as most extreme phenotypes in six wood traits was individually profiled for transcriptome analysis totaling 36 hybridizations to three NimbleGen 12-plex poplar arrays.
2013-02-26 | E-GEOD-44606 | biostudies-arrayexpress
Project description:Understanding how polygenic traits evolve and respond to selection is a major unsolved problem, because challenges exist for identifying genes underlying a complex trait and understanding how multi-locus selection operates in the genome. Here we used artificial selection experiments to study polygenic response to selection. Inbred strains from seven independent long-term selection experiments in mice for extreme bodyweight (M-bM-^@M-^\HighM-bM-^@M-^] lines weigh 77-42g vs. 40-16g in M-bM-^@M-^\ControlsM-bM-^@M-^] lines), were genotyped at 527,572 SNPs to identify genetic variants controlling bodyweight. We identified 67 high-resolution parallel selected regions (PSRs) where multiple High lines share variants rarely found among the Controls. By comparing allele frequencies in one selection experiment against its unselected control, we found classical selective sweep signatures centered on the PSRs. Multiple lines of evidence support two G protein-coupled receptors GPR133 and Prlhr, as positional candidate genes controlling bodyweight. Artificial selection may mimic natural selection in the wild: compared to control loci, we detected reduced heterozygosity in PSRs in wild populations of unusually large mice on islands. Many PSRs overlap loci associated with human height variation, possibly through evolutionary conservation of functional pathways. Our data suggest that parallel selection on complex traits may evoke parallel responses at many genes involved in diverse but relevant pathways. These samples were used to test the enrichment of certain gene functional categories. Mouse tissue samples (muscle and liver) were collected from 44 and 45 days old males from each of the nine out of thirteen lines (5 High lines: BEHi, DUHi, EDHi, MUHi, ROHi and 4 Control lines: BELi, EDLi, MULi and ROLi; n=23 total) at the University of Edinburgh. Frozen tissue samples were stored at -80M-BM-:C until use. Tissues were dissociated using TissueLyser II with steel beads (both Qiagen) following manufacturersM-bM-^@M-^Y instructions. mRNA was extracted and purified using TRIzol Reagent and the PureLink RNA Mini Kit (Life Technologies GmbH, Darmstadt, Germany). cDNA was synthesized using Maxima First Strand cDNA synthesis kit (Thermo Fisher Scientific, St. Leon-Rot, Germany). Muscle and liver cDNA samples were hybridized on a Mouse GE 4x44k Microarray (Agilent Technologies, Inc., Waldbronn, Germany) according to manufacturerM-bM-^@M-^Ys recommendations. Three technical replicate each was done on pooled cDNA samples from each mouse line.
2012-06-29 | E-GEOD-36443 | biostudies-arrayexpress
Project description:High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Each single wood trait was found to be highly polygenic in its nature. However, gene hierarchies need to be assessed with the most important gene variants controlling a specific trait within the complex network of interacting secondary cell wall characteristics that defines the overall wood phenotype. We tested the available genetic and genomic information in an integrative approach to effectively predict wood properties in Populus trichocarpa.Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49K Nimblegen array elements and for 28,831 polymorphic SNPs. Pre-selected transcripts and SNPs with high statistical dependency on the phenotypic trait were used in a Bayesian network learning procedure with stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at much lower logBF threshold than SNPs and were not accommodated in the networks. Complexity of phenotype-centric networks with 100% predictive accuracy ranged from 7 (glucose) to 39 SNPs (alpha-cellulose). Pleiotropic gene actions were accommodated in genetic networks of correlated traits; such gene variants help to understand independent evolution of trait values, and they represent new tools to support the maximization of correlated response to selection.
2013-02-26 | GSE44606 | GEO
Project description:The existence of overlapping genes (OLGs) with significant coding overlaps revolutionises our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the medically important Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing data. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically highly restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here, designated olg1 and olg2, are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes.
2022-03-21 | PXD023992 | Pride