RNA-Seq screening of differentially-expressed genes during somatic embryogenesis in Fragaria × ananassa Duch. ‘Benihopp’

Abstract

SUMMARYSomatic embryogenesis is an important model system for studies on embryo development. In order to gain a better understanding of the molecular mechanisms underlying somatic embryogenesis, RNA-Seq data were generated from non-embryogenic callus, embryogenic callus, somatic embryos, early-germinated somatic embryos, and late-germinated somatic embryos of Fragaria X ananassa Duch. ‘Benihopp’. Totals of 21 x 106–34 x 106 high-quality reads were obtained from the various RNA-seq libraries, with average lengths of 87–94 base pairs. A total of 81% of the reads were mapped to the reference Fragaria vesca genome and 946 differentially-expressed genes were identified, most of which were associated with non-embryonic callus. An analysis of the expression data using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database indicated that the gene ontology (GO) classes with the highest representation were ‘metabolic process’ and ‘metabolism’. In total, 38 transcription factors were identified, including members of the AP2/EREBP and MYB families. Three genes related to hormone signalling pathways were identified: one gene encoding the AUXIN RESISTANT 1 (AUX1) protein and two genes encoding pathogenesis- related 1 (PR1) proteins. During somatic embryogenesis, levels of transcripts corresponding to the AUX1 protein increased, while those corresponding to PR1 decreased. Non-embryogenic callus showed the greatest difference in transcriptome profile compared with the other samples, and the GO annotation term ‘metabolism pathways’ was particularly common in the data associated with strawberry somatic embryogenesis. Based on the RNA-seq data, we speculate that the phytohormones auxin and salicylic acid may play important roles during somatic embryogenesis. Our transcriptome dataset represents a valuable resource for researchers studying somatic embryogenesis and has the potential to provide new insights into the underlying mechanisms of molecular regulation.