Recombination landscape of hexaploid bread wheat
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB28231 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2744330_1.fastq.gz | Fastqsanger.gz | |||
| ERR2744330_2.fastq.gz | Fastqsanger.gz | |||
| ERR2744321_1.fastq.gz | Fastqsanger.gz | |||
| ERR2744321_2.fastq.gz | Fastqsanger.gz | |||
| ERR2744331_1.fastq.gz | Fastqsanger.gz |
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Project description:Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoalleles, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution ânullisomic-tetrasomicâ lines) with next generation deep sequencing of gene transcripts (RNA-seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative homoeoallelic contribution to gene expression. We obtained mRNA-Seq datasets from non-normalized cDNA libraries created from shoot and root tissues of the euploid bread wheat cultivar Chinese Spring, from which the nullitetra lines are derived, from complete sets of chromosome 1 and 5 nullitetras, and from extant relatives of the diploid A (Triticum urartu) and D (Aegilops tauschii) genome donors, herein referred to as A and D genome diploids
2014-04-22 | E-MTAB-4223 | biostudies-arrayexpress
Project description:Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact. We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChip® aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350 transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation,recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to known sequences in NCBI and TIGR databases. This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat. Keywords: Time course
2006-10-14 | GSE6027 | GEO
Project description:Allohexaploid bread wheat (Triticum aestivum, L.) provides ~ 20% of calories consumed by humans. Hitherto lack of genome sequence for the three homoelogous and highly similar bread wheat genomes (A, B and, D) impeded expression analysis of the grain transcriptome. We used novel genome information to analyze the cell type specific expression of homeologous genes in the developing wheat grain.
2014-07-18 | E-MTAB-2137 | biostudies-arrayexpress
Project description:Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact. We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChip® aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350 transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation,recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to known sequences in NCBI and TIGR databases. This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat. Experiment Overall Design: The seven stages collected were pre-meiosis (PM), leptotene to pachytene (LP), diplotene to anaphase I (DA), telophase I to telophase II (TT), tetrads (T), immature pollen (IP) and mature anthers (MAN). Immediately after determining the stage, the remaining two anthers from the floret were placed into liquid nitrogen. After collecting at least 25 staged anthers for each time point from several biological samples, anthers from the respective stages were pooled. Leaf material used in this study was collected from glasshouse-grown plants (six weeks) and total RNA isolated using Trizol® (Gibco BRL, Australia) according to the manufacturerâs protocol. Experiment Overall Design: Twenty micrograms of aRNA of from each of the seven samples were fragmented for hybridization to each microarray. In total three technical replicates were conducted for each of the seven stages examined. Affymetrix GeneChip® Wheat Genome Arrays were used for all samples. The arrays were hybridized and processed according to the manufacturerâs specifications. Experiment Overall Design: Normalization of the microarray data was conducted using RMA. The software package Acuity 4 (Molecular Devices, CA, USA) was then used to analyze the microarray data.
2008-06-14 | E-GEOD-6027 | biostudies-arrayexpress
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:Hexaploid wheat mitochondrion sequencing
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Project description:Transcriptome of South Australian bread wheat under salt stress
2017-07-02 | E-MTAB-3270 | biostudies-arrayexpress
Project description:Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal.
| PRJEB5135 | ENA
Project description:BACKGROUND:Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations. RESULTS:We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. CONCLUSIONS:This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions.
| S-EPMC6463664 | biostudies-literature
Project description:One week old bread wheat plantlets were artifically infected with Puccinia triticinae (the causal organism of wheat leaf rust) and samples were collected after one week from infection. Samples were collected after one week from infection, non infected as well. Two loacl varities were used MISR 1 and GEMMZA 7.
2014-07-20 | GSE55297 | GEO