GSE98338
Dynamic seed transcriptome analysis of japonica to imbibitional tolerance
Seeds experience several stress responses from dry to germinated state. To determine the regulators contributing to imbibitional tolerance, dynamic transcriptome analyses were conducted at dry (0 h), imbibed (24 h) and germinated (48 h) stages in japonica Jiucaiqing in this study. Results showed that the differentially expressed genes (DEGs) were pronounced in the early stage (0-24 h) than the late stage (24-48 h); 1,452 transcripts were differentially expressed (648 up-regulated and 804 down-regulated) in the early stage and 625 transcripts (230 up-regulated and 395 down-regulated) in the late stage. Gene ontology and MapMan analyses confirmed that 391 and 164 DEGs at the early and late stage respectively involved in stress responses pathway. These DEGs included the abiotic stress-, hormone-, peroxidases-, signaling-, transcription-, proteolysis- and cell wall-related genes. Nearly all the heat stress-related DEGs, e.g. hsp20 and DnaK family proteins, were down-regulated with seed germination, while the peroxidases- and signaling-related DEGs, e.g. calcium-binding proteins, were up-regulated. Many auxins-, abscisic acid- and ethylene-related DEGs, e.g. 9-cis-epoxycarotenoid dioxygenase, OsFBL16 and OsSAUR33, were involved in stress responses during seed germination. Meanwhile, several transcription factors of bZIP and MYB, ethylene responsive element binding protein family (ERF), and heat stress transcription factor family (HSF) were identified during seed germination. The proteolysis-related DEGs, e.g. ubiquitin-related proteins, were significantly regulated during seed germination. The uniformity between transcriptome data, quantitative trait loci co-localizations and quantitative RT-PCR results confirm the crucial roles of the cell wall-related genes on seed germination. The identified stress-responsive might be useful for the improvement of imbibitional tolerance in rice. Overall design: mRNA profiles of seeds in the landrace rice Jiucaiqing (Oryza sativa spp. japonica) after 0, 24 and 48 h imbibition were combined respectively from three biological replicates for RNA sequencing.