Ontology highlight
ABSTRACT:
PROVIDER: PRJNA663409 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12640200_1.fastq.gz | Fastqsanger.gz | |||
| SRR12640200_2.fastq.gz | Fastqsanger.gz | |||
| SRR12640300_1.fastq.gz | Fastqsanger.gz | |||
| SRR12640300_2.fastq.gz | Fastqsanger.gz | |||
| SRR12640400_1.fastq.gz | Fastqsanger.gz |
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Project description:Many crop species have complex genomes, making the conventional pathway to associating molecular markers with trait variation, which includes genome sequencing, both expensive and time-consuming. We used a streamlined approach to rapidly develop a genomics platform for hexaploid wheat based on the inferred order of expressed sequences. This involved assembly of the transcriptomes for the progenitor genomes of bread wheat, the development of a genetic linkage map comprising 9495 mapped transcriptome-based SNP markers, use of this map to rearrange the genome sequence of Brachypodium distachyon into pseudomolecules representative of the genome organization of wheat and sequence similarity-based mapping onto this resource of the transcriptome assemblies. To demonstrate that this approximation of gene order in wheat is appropriate to underpin association genetics analysis, we undertook Associative Transcriptomics for straw biomass traits, identifying associations and even candidate genes for height, weight and width.
2014-01-31 | E-MTAB-4414 | biostudies-arrayexpress
Project description:We have collected RNA-seq data from the total RNA isolated from the 2-week seedlings of 198 diverse wheat accessions. These accessions were selected among nearly 3,000 lines to represent the broad geographic and genetic diversity of wheat populations. On average, 65.7 million paired-end Illumina reads (2 x 100 bp) were collected for each sample, and after quality trimming were mapped to the wheat reference genome RefSeq v.1.0. The proportion of reads unambiguously mapped to the individual wheat genomes was 81%, with the accuracy of correct read mapping estimated by simulation achieving 98%. The expression levels measured as Transcripts Per Million (TPM) were estimated for high confidence (HC) gene models in the wheat reference genome, with 82,092 gene models (66,333 genes) showing TPM > 0.5 in at least two wheat lines (PRJNA670223)
2022-01-17 | GSE167479 | GEO
Project description:The huge size, the redundancy and the great repeated portion of the bread wheat genome [Triticum aestivum (L.)], placed it among the most difficult species to be sequenced and dissected at the genetic, structural and evolutionary levels. To overcome the limitations, a strategy based on the genome compartmentalization in individual chromosomes and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium. A total of 95,812 BAC clones of short (5AS) and long (5AL) arm-specific BAC libraries, were fingerprinted and assembled into contigs by complementary analytical approaches based on FingerPrinted Contigs and Linear Topological Contig. Combined anchoring approaches based on PCR marker screening, microarray and BlastN searches, applied to interlinked genomic tools, that is genetic maps, deletion bin map, high-density neighbor map, BAC end sequences, genome zipper and chromosome survey sequences, allowed the development of a high quality physical map, with an anchored physical coverage of 75% for 5AS and 53% for 5AL, with high portions (64 and 48%, respectively) ordered along the chromosome. The gene distribution along the wheat chromosome 5A compared with the closest related genomes showed a pattern of syntenic blocks belonging to different chromosomes of Brachypodium, rice and sorghum and regions involving translocations and inversions. The physical map presented here is currently the most comprehensive map for 5A chromosome and represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits, and a reference for the 5A sequencing projects.
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Project description:constraction of high density genetic map of common wheat
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Project description:Bread wheat is allohexaploid with 16 Gb genome, which has large intergenic region with abundant TEs and regulatory sequences . Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide the first systematic epigenomic map for functional annotation of the allohexaploid wheat genome.
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Project description:Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. However, we recently constructed the first physical map of a wheat chromosome (3B). But gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridized to a barley Agilent 15K expression microarray. This led to the identification of 738 barley genes with a homolog on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.
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Project description:The huge size, the redundancy and the great repeated portion of the bread wheat genome [Triticum aestivum (L.)], placed it among the most difficult species to be sequenced and dissected at the genetic, structural and evolutionary levels. To overcome the limitations, a strategy based on the genome compartmentalization in individual chromosomes and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium. A total of 95,812 BAC clones of short (5AS) and long (5AL) arm-specific BAC libraries, were fingerprinted and assembled into contigs by complementary analytical approaches based on FingerPrinted Contigs and Linear Topological Contig. Combined anchoring approaches based on PCR marker screening, microarray and BlastN searches, applied to interlinked genomic tools, that is genetic maps, deletion bin map, high-density neighbor map, BAC end sequences, genome zipper and chromosome survey sequences, allowed the development of a high quality physical map, with an anchored physical coverage of 75% for 5AS and 53% for 5AL, with high portions (64 and 48%, respectively) ordered along the chromosome. The gene distribution along the wheat chromosome 5A compared with the closest related genomes showed a pattern of syntenic blocks belonging to different chromosomes of Brachypodium, rice and sorghum and regions involving translocations and inversions. The physical map presented here is currently the most comprehensive map for 5A chromosome and represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits, and a reference for the 5A sequencing projects. 55 DNA pools of short arm of chromsome 5A and 63 DNA pools of long arm of 5A. The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.
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