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.
Project description:Sequencing of 46 maize leaf whole transcriptome revealed 77 differentially expressed genes (DEGs) between Lancaster and Non-Lancaster maize genetic resources under optimal growing conditions. Cold test of the subset of four Lancaster and four Non-Lancaster lines showed that the first were cold sensitive and the later cold tolerant, with the majority of identified DEGs showing FPKM values above the plate mean in Lancaster, but below the plate mean in Non-Lancaster subset. Cold induced expression analysis for revealed that, among seven tested DEGs, ATP-sulfurylase and photosystem II I encoding genes showed responsiveness to low temperatures in a genetic-background-dependent manner, likely contributing to different cold response/adaptability of Lancaster and Non-Lancaster lines.
Project description:The present transcript profiling compares the gene expression during cold-acclimation in different genotypes of barley (Hordeum vulgare L.), wheat (Triticum aestivum L.) and rye (Secale cereale L.) in order to determine factors influencing frost tolerance. Because of its outstanding robustness against adverse environmental conditions rye is considered to be a model species for abiotic stress tolerance. Wheat is moderate frost-tolerant and barley is most sensitive species in this study. The aim of this study elucidate conserved, as well as, species-specific gene regulation across the Triticeae. Furthermore, transcript abundances were correlated between the distinct frost tolerances of genotypes within each species in order to find candidate genes for frost tolerance.
Project description:The effects of temperature stress on transcriptome of purple non sulfur bacterium R. capsulatus were investigated by comparing expression profiles under optimum hydrogen production condition (30°C), heat (42°C) and cold (4°C) stress conditions.
Project description:PARE (parallel analysis of RNA ends) was performed to study the change of uncapped mRNAs before and after cold treatment in Brachypodium. Different change patterns were identified. We have provided a complete view of uncapped transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants.
Project description:To distinguish transcripts expressed from each of the three wheat genomes and those from the rye chromatins, genomic probes generated from diploid progenitors of wheat and rye were synthesized
2015-02-24 | GSE58678 | GEO
Project description:Transcriptome sequencing under cold stress
| PRJNA1035950 | ENA
Project description:Rice under cold stress. Transcriptome
