Meiosis transcriptome and co-expression network in hexaploid wheat
Azahara Carmen Martín, AbdulKader Alabdullah, Philippa Borrill, Ricardo H. Ramírez-González, Janet Higgins, David Swarbreck, Cristobal Uauy, Peter Shaw, Graham Moore
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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