MRNA-Seq for associative transcriptomics in hexaploid wheat
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ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR420126.fastq.gz | Fastqsanger.gz | |||
| ERR420127.fastq.gz | Fastqsanger.gz | |||
| ERR420128.fastq.gz | Fastqsanger.gz | |||
| ERR420129.fastq.gz | Fastqsanger.gz | |||
| ERR420130.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.
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Project description:affy_hexaploid_wheat - hexa - Changes upon polyploidization in hexaploid wheat - transcriptomic changes in synthetic hexaploid derived from a cross between tetraploid and natural diploid. Study aims to understand regulation of gene expression in synthetic and natural wheat allohexaploids (Triticum aestivum), that combines the AB genome of T. turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. We conducted a comprehensive genome-wide analysis of gene expression that allowed us to compare the effect of variability of the D genome progenitor, the trans-generation stability as well as comparison to natural wheat allohexaploid. We used the Affymetrix GeneChip® Wheat Genome Array, on which 55,049 transcripts are represented. Additive expression was shown to represent majority of expression regulation in the synthetic allohexaploids, where expression for more than 93% of transcripts was equal to the one evaluated from equal mixture of parental RNA. This leaves ~2000 (~7%) transcripts, which expression was non-additive. No global gene expression bias or dominance towards any of the progenitor genomes was observed whereas high trans-generational stability and low effect of the D genome progenitor variability were revealed. Our study suggests that gene expression regulation in wheat allohexaploids is early established upon allohexaploidization and highly conserved over generations, as demonstrated by the high similarity of expression with natural wheat allohexaploids. Keywords: genotype and ecotype comparison
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Project description:Hexaploid wheat mitochondrion sequencing
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Project description:affy_hexaploid_wheat - hexa - Changes upon polyploidization in hexaploid wheat - transcriptomic changes in synthetic hexaploid derived from a cross between tetraploid and natural diploid. Study aims to understand regulation of gene expression in synthetic and natural wheat allohexaploids (Triticum aestivum), that combines the AB genome of T. turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. We conducted a comprehensive genome-wide analysis of gene expression that allowed us to compare the effect of variability of the D genome progenitor, the trans-generation stability as well as comparison to natural wheat allohexaploid. We used the Affymetrix GeneChip® Wheat Genome Array, on which 55,049 transcripts are represented. Additive expression was shown to represent majority of expression regulation in the synthetic allohexaploids, where expression for more than 93% of transcripts was equal to the one evaluated from equal mixture of parental RNA. This leaves ~2000 (~7%) transcripts, which expression was non-additive. No global gene expression bias or dominance towards any of the progenitor genomes was observed whereas high trans-generational stability and low effect of the D genome progenitor variability were revealed. Our study suggests that gene expression regulation in wheat allohexaploids is early established upon allohexaploidization and highly conserved over generations, as demonstrated by the high similarity of expression with natural wheat allohexaploids. Keywords: genotype and ecotype comparison 18 arrays - wheat
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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
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2014-10-20 | GSE56587 | GEO
Project description:Plants of two non-restorer varieties of hexaploid winter wheat (Astoria, Grana) and two restorers ones (Patres and Primépi) were used to identify effective Rf (fertility restorer) genes by next generation sequencing on whole transcriptomes (RNA-seq).
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Project description:[hexa-] Transcriptomic changes in synthetic hexaploid wheat
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Project description:Gene expression levels of newly synthetic triploid wheat (ABD), its chromosome-doubled hexaploid (AABBDD), stable synthetic hexaploid (AABBDD), and their parents, Triticum turgidum (accession KU124, AABB) and Aegilops tauschii (accession KU2074, DD) were compared to understand genome-wide change of gene expressions during the course of amphidiploidization and genome stabilization. Stable synthetic hexaploid which were maintained through self-pollinations for 13 generations using the same combinations of the parents for production of synthetic common wheat.
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Project description:Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely-cultivated allohexaploid wheat variety carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity. The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.
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