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.
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          iRods Data ObjectFiltered_TPMs_HC_exp_in_meiosis_130samples.csv 60MB2020-08-02 01:03f69d8803b0a01baede4f6f714e18664f
          iRods Data ObjectFiltered_counts_HC_exp_in_meiosis_130samples.csv 49MB2020-08-02 01:038aa41f285743480a89cc4ee61831e95e
          iRods Data Objectdatapackage.json191KB2020-09-16 07:48e15955c96fe1b95e0f6f098d499182a8
          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
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