Transcriptomics

Dataset Information

301

Transcription profiling by high throughput sequencing of Triticum aestivum, Triticym urartu and Aegilops tauschii to identify homoeologue-specific single nucleotide variants


ABSTRACT: 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 ‘nullisomic-tetrasomic’ 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

INSTRUMENT(S): Illumina Genome Analyzer IIx

SUBMITTER: Lindsey Leach  

PROVIDER: E-MTAB-4223 | ArrayExpress | 2014-04-22

SECONDARY ACCESSION(S): SRP028357

REPOSITORIES: ArrayExpress, ENA

altmetric image

Publications

Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat.

Leach Lindsey J LJ   Belfield Eric J EJ   Jiang Caifu C   Brown Carly C   Mithani Aziz A   Harberd Nicholas P NP  

BMC genomics 20140411


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 homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution 'nullisomic-tetrasomic' lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identif  ...[more]

Similar Datasets

| GSE54398 | GEO
2011-11-01 | GSE33357 | GEO
2016-03-02 | E-GEOD-78784 | ArrayExpress
| PRJNA163531 | ENA
| PRJNA163533 | ENA
| PRJNA15595 | ENA
| PRJNA256105 | ENA
| PRJNA15519 | ENA
| PRJNA417989 | ENA
| PRJNA431830 | ENA