Androgenic Switch: Changes in Gene Expression during Early Stages of Androgenesis in the Barley Microspore

Androgenesis exploits the totipotency of haploid immature microspores to regenerate a completely homozygous diploid plant. When exposed to stress, microspores undergo cellular dedifferentiation and embark on the path of embryogenesis. We know little about the gene expression changes that lead to the arrest of pollen development and the switch to the developmental pathway leading to embryos in androgenesis. To measure changes in gene expression that occur during the cellular dedifferentiation and re-differentiation, an RNA-seq analysis was performed on three sets of materials: (1) unstressed immature microspores, (2) microspores two days after the stress treatment that induces embryogenesis and (3) microspores five days after the stress. Expression of 13,262 genes was observed in the immature microspore. Differential expression was detected for 11.8% (day 2 vs 0) and 8.5% (day 5 vs 2) of these genes. Differentially expressed genes were clustered according to their expression profile during microspore development and used to perform a gene set enrichment analysis (GSEA). The set of up-regulated genes was enriched for genes involved in molecular functions governing protein phosphorylation, oxidation-reduction and carbohydrate metabolism. Among down-regulated genes, genes involved in biological processes linked to DNA metabolism such as the regulation of DNA replication and DNA methylation were enriched. In contrast, up-regulated genes linked to the induction of embryogenesis were enriched for DNA-associated processes such as nucleosome assembly, DNA packaging and chromatin assembly or disassembly. In conclusion, this study provides a transcriptomic foundation toward understanding a complex developmental change that underpins androgenesis in barley.