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Differential chromatin accessibility landscape reveals the structural and functional features of the allopolyploid wheat chromosomes

ABSTRACT: We have a limited understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes. Using a differential nuclease sensitivity (DNS) assay, we investigated the chromatin states in the coding and transposon element (TE) -rich repetitive regions of the allopolyploid wheat genome.

ORGANISM(S): Triticum aestivum

PROVIDER: GSE153289 | GEO | 2020/06/26

REPOSITORIES: GEO

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Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid 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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Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower

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