Snog1a bulk segregant analysis
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ABSTRACT:
PROVIDER: PRJEB88224 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Phenotype-driven forward genetic experiments are among the most powerful approaches for linking biology and disease to genomic elements. Although widely used in a range of model organisms, positional cloning of causal variants is still a very laborious process. Here, we describe a novel universal approach, named fast forward genetics that combines traditional bulk segregant techniques with next-generation sequencing technology and targeted genomic enrichment, to dramatically improve the process of mapping and cloning multiple mutants in a single experiment. In a two-step procedure the mutation is first roughly mapped by ‘light’ sequencing of the bulk segregant pool, followed by genomic enrichment and deep-sequencing of the mutant pool for the linked genomic region. The latter step allows for simultaneous fine-mapping and mutation discovery. We successfully applied this approach to three Arabidopsis mutants, but the method can in principle be applied to any model organism of interest and is largely independent of the genome size. Moreover, we show that both steps can be performed in multiplex using barcoded samples, thereby increasing efficiency enormously.
2010-12-31 | GSE24511 | GEO
Project description:Phenotype-driven forward genetic experiments are among the most powerful approaches for linking biology and disease to genomic elements. Although widely used in a range of model organisms, positional cloning of causal variants is still a very laborious process. Here, we describe a novel universal approach, named fast forward genetics that combines traditional bulk segregant techniques with next-generation sequencing technology and targeted genomic enrichment, to dramatically improve the process of mapping and cloning multiple mutants in a single experiment. In a two-step procedure the mutation is first roughly mapped by ‘light’ sequencing of the bulk segregant pool, followed by genomic enrichment and deep-sequencing of the mutant pool for the linked genomic region. The latter step allows for simultaneous fine-mapping and mutation discovery. We successfully applied this approach to three Arabidopsis mutants, but the method can in principle be applied to any model organism of interest and is largely independent of the genome size. Moreover, we show that both steps can be performed in multiplex using barcoded samples, thereby increasing efficiency enormously. Inducible overexpression of the RETINOBLASTOMA-RELATED (RBR-OE) gene in Arabidopsis roots causes the complete differentiation of stem cells and premature differentiation of daughter cells, leading to a full exhaustion of the primary root meristem. In order to identify regulators of RBR function in cell differentiation, RBR-OE plants in the Columbia background (Col0) were treated with EMS mutagenesis and a set of genetic suppressors of RBR-OE, which restores root growth capacity, were isolated. In this study, we used one the identified suppressor lines, which segregated as a recessive mutation. Mapping populations were generated by outcrossing to Ler ecotype. Seedlings from the F2 population were grown for 15 days post germination (dpg). A pool of 60 seedlings each with a clear suppressor phenotype (homozygous for suppressor mutation) and of 60 seedlings showing RBOE phenotype (Heterozygous for the suppressor mutation) were prepared and genomic DNA was isolated with the RNeasy Plant Mini Kit from QIAGEN according to manufacturer's protocol. The other two, mutants 136 and 193 were obtained in fluorescence based mutant screen and a QCmarker based mutagenesis, respectively. Mutants were generated by chemical mutagenesis (EMS) in Colombia (Col) genetic background. Mutants were subsequently crossed to the Landsberg (Ler) ecotype to create the mapping populations. Bulk-segregant pools of about 200 mutant as well as wild-type plants were generated for every mutant line.
2010-12-31 | E-GEOD-24511 | biostudies-arrayexpress
Project description:This project aimed to discover genes that regulate the transition from 2D to 3D growth in the moss Physcomitrella patens. Mutants were generated that do not pattern 3D growth. Bulk segregant analysis was conducted to identify the causative genes. This experiment contains two samples - WT-pool, Mt-pool.
2020-12-11 | E-MTAB-7502 | biostudies-arrayexpress
Project description:This project aimed to discover genes that regulate the transition from 2D to 3D growth in the moss Physcomitrella patens. Mutants were generated that failed to initiate 3D growth. Bulk segregant analysis was conducted to identify the causative genes. This experiment contains four samples - GdGFP, VxmCherry, WT-pool, Mt-pool.
2018-09-19 | E-MTAB-5096 | biostudies-arrayexpress
Project description:Genome sequence data results are reported from experimental and bioinfomatic work using the technique 'Bulk Segregant Analysis' to determine the genetic basis of observed resistance to the azole antifungal compound itraconazole in the opportunistic fungal pathogen Aspergillus fumigatus.
2022-05-11 | GSE193956 | GEO
Project description:Bulk segregant analysis of 3D growth defective mutant in Physcomitrella patens (Vx501).
| PRJEB15436 | ENA
Project description:Bulk segregant analysis of 3D growth defective mutant in Physcomitrella patens (nog2)
| PRJEB30303 | ENA
Project description:Bulk segregant sequencing (Bulk-Seq) analysis to identify paternal suppressors of medea in Arabidopsis thaliana
| PRJEB17703 | ENA
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
2016-11-18 | E-MTAB-5196 | biostudies-arrayexpress
Project description:Cryptococcus neoformans is a ubiquitous free-living soil yeast and opportunistic pathogen that causes ~223,100 cases of cryptococcal meningitis per year, killing over 180,000 people. The pathogenicity of C. neoformans relies on its adaptation to the host conditions. An important difference between its natural environment and the mammalian host is the concentration of CO2. CO2 levels in the host fluctuate around 5%, which is ~125-fold higher than in ambient air. We recently found that while clinical isolates are tolerant to host levels ofCO2, many environmental isolates are CO2-sensitive and virulence-attenuated in animal models. The genetic basis responsible for cryptococcal adaptation to high levels of CO2 is unknown. Here, we utilized quantitative trait loci (QTL) mapping with 374 progeny from a cross between a CO2-tolerant clinical isolate and a CO2-sensitive environmental isolate to identify genetic regions regulating CO2 tolerance. To identify specific quantitative trait genes (QTGs), we applied fine mapping through backcrossing and bulk segregant analysis coupled with pooled genome sequencing of near-isogenic progeny but with distinct tolerance levels to CO2. The roles of the identified QTGs in CO2 tolerance were verified by targeted gene deletion. We further demonstrated that virulence levels among near-isogenic strains in a murine model of cryptococcosis correlate with their levels of CO2 tolerance. Moreover, we discovered that sensitive strains may adapt in vivo to become more tolerant to increased CO2 levels and more virulent. These findings highlight the underappreciated role of the host CO2 tolerance and its importance in the ability of an opportunistic environmental pathogen to cause disease.
2024-08-09 | GSE260932 | GEO