Ontology highlight
ABSTRACT:
PROVIDER: PRJNA890449 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21902436_1.fastq.gz | Fastqsanger.gz | |||
| SRR21902436_2.fastq.gz | Fastqsanger.gz | |||
| SRR21902437_1.fastq.gz | Fastqsanger.gz | |||
| SRR21902437_2.fastq.gz | Fastqsanger.gz | |||
| SRR21902438_1.fastq.gz | Fastqsanger.gz |
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Project description:Breeding day-neutral strawberry (Fragaria x ananassa Duchesne) is pivotal to extend fruit-bearing season and increase the efficiency of production. However, genetic improvement of day-neutrality by the means of molecular marker technologies remains slow due to genome complexity of octoploid strawberry. This study employs an innovative approach by integrating the Subtracted Diversity Array (SDA) technology and Bulked Segregant Analysis (BSA) to facilitate the identification of molecular markers associated with day-neutrality in octoploid strawberry. A Fragaria Discovery Panel (FDP) containing 287 features specific to strawberry genome was constructed as a platform for rapid screening of DNA polymorphism between one short day (SD) strawberry DNA bulk and three day-neutral (DN) bulks varrying in flowering strength. Differential array hybridisation patterns between the DN and SD bulks revealed a novel molecular marker, FaP2E11, closely linked to CYTOKININ OXIDASE 1 (CKX1) gene possibly involved in promoting flowering under non-inductive condition. Interestingly, a 12 bp deletion was observed within the FaP2E11 sequence cloned from SD genotypes but not DN genotypes. As cytokinin is required to induce flowering, this result indicates that full sequence of FaP2E11 and the sequence with deletion are allelic variants linked to the low enzyme activity CKX1 and the wild type alleles, respectively.
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Project description:In order to understand effects of defective circadian clock on the global barley transcriptome, we analyzed the diel and circadian leaf transcriptomes in the barley cultivar Bowman and derived introgression lines carrying mutations in EARLY FLOWERING 3 (ELF3), LUX1, and EARLY MATURITY 7 (EAM7).
2020-05-25 | E-MTAB-8372 | biostudies-arrayexpress
Project description:Bulk segregant analysis using microarrays, and extreme array mapping have recently been used to rapidly identify genomic regions associated with phenotypes in multiple species. These experiments, however require the identification of single feature polymorphisms between the cross parents for each new combination of genotypes, which raises the cost of experiments. The availability of the genomic polymorphism data in Arabidopsis thaliana, coupled with the efficient designs of Single Nucleotide Polymorphism (SNP) genotyping arrays removes the requirement for SFP detection and lowers the per array cost, thereby lowering the overall cost per experiment. To demonstrate that these approaches would be functional on SNP arrays and determine confidence intervals, we analyzed hybridizations of natural accessions to the Arabidopsis ATSNPTILE array and simulated BSA or XAM given a variety of gene models, populations, and bulk selection parameters. Our results show a striking degree of correlation between the genotyping output of both methods, which suggests that the benefit of SFP genotyping in context of BSA can be had with the cheaper, more efficient SNP arrays. As a final proof of concept, we hybridized the DNA from bulks of an F2 mapping population of a Sulfur and Selenium ionomics mutant to both the Arabidopsis ATTILE1R and ATSNPTILE arrays, which produced almost identical results. We have produced R scripts that prompt the user for the required parameters and perform the BSA analysis using the ATSNPTILE1 array and have provided them as supplemental data files. Keywords: genomic hybridization of inbred lines and bulked segregant analysis
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Project description:Wood stiffness is the most important wood quality trait of forest trees for structural timber production. We investigated genes differentially transcribed in radiate pine trees with distinct wood stiffness using bulked segregant analysis (BSA) and cDNA microarrays. Transcript accumulation in earlywood (EW) and latewood (LW) of high (HS) and low stiffness (LS) trees in two progeny trials was compared.
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Project description:Abstract: Multiple nodes and dwarf mutants in barley are a valuable resource for identifying genes that control shoot branching, vegetative growth, and development. In this study, physiological, microscopic and genetic analylsis were conducted to characterize and fine-map the underling gene of A a barley mutant with Multiple Stem Nodes and Spikes and Dwarf (msnsd) , which was selected from EMS- and 60Co-treated barley cv. Edamai 934 (E934) to characterize the mutant and fine-map its underlying gene. The msnsd mutant had more stem nodes and , lower plant height and a shorter plastochron than Edamai 934the wild type. Moreover, the mutant had two or more spikes on each tiller., emerging from the lower nodes or the base of the top spike, and a shorter plastochron. Microscopic analysis showed that the dwarf phenotype of msnsd resulted from reduced cell lengths and cell numbers in the stem. Further physiological analysis showed that msnsd was GA3-deficient, with its plant height increasing after external GA3 application. Genetic analysis revealed that a single recessive nuclear gene, namely, HvMSNSD, controlled the msnsd phenotype. Using a segregating population derived from Harrington and the msnsd mutant, HvMSNSD was fine-mapped on chromosome 5H in a 200 kb interval using bulked segregant analysis (BSA) coupled with RNA-sequencing (BSR-seq), with a C-T substitution in the exon of HvTCP25 co-segregating with the msnsd phenotype. RNA-seq analysis showed that a gene encoding gibberellin 2-oxidase 8, a negative regulator of GA biosynthesis, was upregulated in the msnsd mutant. Transcriptomic analysis identified several Several known genes related to inflorescence development that were also upregulated and enriched in the msnsd mutant. Collectively, we propose that HvMSNSD regulates the plastochron and morphology of reproductive organs, likely by coordinating GA homeostasis and changed expression of floral development related genes in barley. this This study offers valuable insights into the molecular regulation of barley plant architecture and inflorescence development
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Project description:Neurospora crassa bulked segregant analysis
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Project description:Positional gene isolation requires either a local or global reference genome sequence or an inference of gene content based on conservation of synteny with a genomic model. In the large unsequenced genomes of the Triticeae cereals the latter, i.e. conservation of synteny with the rice and Brachypodium genomes, provides a powerful proxy for establishing local gene content and order. However, exploiting conservation of synteny requires 'homology bridges' between the model genome and the target region that contains a gene of interest. As effective homology bridges are generally the sequences of genetically mapped genes, increasing the density of mapped these genes around a target locus is an important step in the process. We used Bbulked Ssegregantte Aanalysis (BSA) of transcript abundance data to identify genes located in a specific region of the barley genome. The approach is valuable because only a relatively small proportion of barley genes are currently placed on a genetic map. We analyzed eQTL datasets from the reference Steptoe x Morex doubled haploid population and showed a strong association between differential gene expression and cis-regulation, with 83% of differentially expressed genes co-locating with their eQTL. We then performed bulked segregant analysis (BSA) by assembling allele-specific bulks pools based on the genotypes of individuals at the partial resistance QTL Rphq11. BSA identified a total of 411 genes as differentially expressed, including HvPHGPx, that was previously identified as being a promising candidate for Rphq11. The genetic location of 276 of these genes could be determined from both eQTL datasets and conservation of synteny, and 254 (92%) of these were located on the target chromosome. We conclude that identification of differential expression by BSA constitutes a novel method to identify genes located in specific regions of interest. The datasets obtained from such studies provide a high-profile repertoirerobust set of candidate genes for analysis and serve as valuable resources for targeted marker development and comparative mapping with other grass species.
2011-02-01 | E-TABM-1069 | biostudies-arrayexpress
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Project description:Powdery mildew resistance gene Pm4b, originating from Triticum perscicum, is effective against the prevalent Blumeria graminis f. sp. tritici (Bgt) isolates from certain regions of wheat production in China. The lack of tightly linked molecular markers with the target gene prevents the precise identification of Pm4b during the application of molecular marker-assisted selection (MAS). The strategy that combines the RNA-seq technique and the bulked segregant analysis (BSR-seq) was applied in an F2:3 mapping population (237 families) derived from a pair of isogenic lines VPM1/7*Bainong 3217 F4 (carrying Pm4b) and Bainong 3217 to develop more closely linked molecular markers. RNA-seq analysis of the two phenotypically contrasting RNA bulks prepared from the representative F2:3 families generated 20,745,939 and 25,867,480 high-quality read pairs, and 82.8% and 80.2% of them were uniquely mapped to the wheat whole genome draft assembly for the resistant and susceptible RNA bulks, respectively. Variant calling identified 283,866 raw single nucleotide polymorphisms (SNPs) and InDels between the two bulks. The SNPs that were closely associated with the powdery mildew resistance were concentrated on chromosome 2AL. Among the 84 variants that were potentially associated with the disease resistance trait, forty-six variants were enriched in an about 25 Mb region at the distal end of chromosome arm 2AL. Four Pm4b-linked SNP markers were developed from these variants. Based on the sequences of Chinese Spring where these polymorphic SNPs were located, 98 SSR primer pairs were designed to develop distal markers flanking the Pm4b gene. Three markers, Xics13, Xics43 and Xics76, were incorporated in the new genetic linkage map, which located Pm4b in a 3.0 cM genetic interval spanning a 6.7 Mb physical genomic region. This region had a co-linear relationship with Brachypodium distachyum chromosome 5, rice chromosome 4, and sorghum chromosome 6. Seven genes associated with disease resistance were predicted in this collinear genomic region, which included protein kinases of PKc_like super family, C2 domain protein, peroxidase activity protein, Mlo family protein, and catalytic domain of the serine/threonine kinases (PKc_like super family). The markers developed in the present study facilitate identification of Pm4b during its MAS practice.
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