Meiosis transcriptome and co-expression network in hexaploid wheat

Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologs and homoeologs at the onset of meiosis. In turn, these chromatin changes can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-seq data derived from 6 different genotypes: wheat, wheat-rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the Ph1 locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the six genotypes exhibit different levels of synapsis and chromatin structure. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the Ph1 locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. Our knowledge of the genes involved in meiosis in many crop species such as wheat is largely based on studies on model species. Here we used the WGCNA package in R to build a meiotic gene co-expression network in wheat based on 130 wheat RNA-seq samples collected from a range of tissues including meiotic anthers. A set of 50,387 genes were expressed during meiosis and assigned to 66 modules according to their expression patterns. Three of the modules (modules 2, 28 and 41 containing 4940 genes, 544 genes and 313 genes, respectively) were significantly correlated with meiotic tissue samples but not with any other type of tissue. The three meiosis-related modules were highly enriched with GO terms related to cell cycle, DNA replication, chromatin modifications and other processes occurring during meiosis. Wheat orthologs of meiosis genes were found in modules 2, 28 and 41. Module 2, in particular, was significantly enriched possessing 166 meiosis orthologs. The combination of co-expression network analysis in tandem with orthologue information will contribute to enhance wheat meiotic studies, which will lead to better understanding of the regulation of meiosis in wheat (and other polyploid plants) and subsequently improve wheat production. Project Code: BB/J007188/1.
This data is made available under the Toronto Agreement
All of the data listed here is available under the prepublication data sharing principle of the Toronto agreement. By using this data, you agree to:
  • respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.
  • not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories.
  • contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses.
  • fully cite the prepublication data along with any applicable versioning details.
  • understand that this data as accessed is precompetitive and is not patentable in its present state.
This agreement does not expire by time but only upon publication of the first global analysis by the data producers and contributors.

          User details

          You are browsing the public view on the public zone
          iRods Data ObjectFiltered_TPMs_HC_exp_in_meiosis_130samples.csv 60MB2020-08-02 01:03
          iRods Data ObjectFiltered_counts_HC_exp_in_meiosis_130samples.csv 49MB2020-08-02 01:03
          iRods Data Objectdatapackage.json191KB2020-09-16 07:48
          iRods CollectionTablesToUse/2020-08-02 01:03
          iRods CollectionWGCNA/2020-08-02 01:05
          iRods CollectionexpressionValuesPerGene/2020-08-02 01:06
          iRods CollectionexpressionValuesPerTranscript/2020-08-02 01:03
          iRods Collectionexpvip/2020-08-02 01:03