Chinese cork oak (Quercus variabilis) is a widely distributed and highly valuable deciduous broadleaf tree from both ecological and economic perspectives. Seeds of this species are recalcitrant, i.e., sensitive to desiccation, which affects their storage and long-term preservation of germplasm. However, little is known about the underlying molecular mechanism of desiccation sensitivity of Q. variabilis seeds. In this study, the seeds were desiccated with silica gel for certain days as different treatments from 0 (Control) to 15 days (T15) with a gradient of 1 day. According to the seed germination percentage, four key stages (Control, T2, T4, and T11) were found. Then the transcriptomic profiles of these four stages were compared. A total of 4,405, 4,441, and 5,907 differentially expressed genes (DEGs) were identified in T2 vs. Control, T4 vs. Control, and T11 vs. Control, respectively. Among them, 2,219 DEGs were overlapped in the three comparison groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these DEGs were enriched into 124 pathways, such as “Plant hormone signal transduction” and “Glycerophospholipid metabolism”. DEGs related to hormone biosynthesis and signal transduction (ZEP, YUC, PYR, ABI5, ERF1B, etc.), stress response proteins (LEA D-29, HSP70, etc.), and phospholipase D (PLD1) were detected during desiccation. These genes and their interactions may determine the desiccation sensitivity of seeds. In addition, group specific DEGs were also identified in T2 vs. Control (PP2C62, UNE12, etc.), T4 vs. Control (WRKY1-like, WAK10, etc.), and T11 vs. Control (IBH1, bZIP44, etc.), respectively. Finally, a possible work model was proposed to show the molecular regulation mechanism of desiccation sensitivity in Q. variabilis seeds. This is the first report on the molecular regulation mechanism of desiccation sensitivity of Q. variabilis seeds using RNA-Seq. The findings could make a great contribution to seed storage and long-term conservation of recalcitrant seeds in the future.

Background: Chinese cork oak (Quercus variabilis) is a widely distributed and highly valuable deciduous broadleaf tree from both ecological and economic perspectives. Seeds of Q. variabilis are recalcitrant, i.e., sensitive to desiccation, which affects their storage and long-term preservation of germplasm. However, little is known about the underlying mechanism of desiccation sensitivity of Q. variabilis seeds. Results: In this study, the seeds were desiccated with silica gel for 0 day (control, CK), one day (T1) to 15 days (T15). After desiccation, the transcriptomic profiles of these different desiccation stages were compared using the Quercus suber genome as a reference, as well four key stages (CK, T2, T4 and T11) of desiccation sensitivity of Q. variabilis seeds through germination test were identified. A total of 4405, 4441, and 5907 differentially expressed genes (DEGs) were identified in T2 vs CK, T4 vs CK, and T11 vs CK, respectively. Among them, 2219 DEGs were overlapped in the three comparison groups. KEGG (Kyoto Encyclopaedia of Genes and Genomes) enrichment analysis showed that these DEGs were enriched into 124 pathways, such as "plant hormone signal transduction" and "glycerophospholipid metabolism". DEGs related to hormone synthesis and signal transduction (ZEP, YUC, PYR, ABI5, ERF1B, etc), stress response proteins (LEA D-29, HSP70, etc), and phospholipase D (PLD1) were detected during seed desiccation. These genes and their interactions may regulate the desiccation sensitivity of Q. variabilis seeds. Finally, a possible work model was proposed to show the molecular regulation mechanism of desiccation sensitivity in recalcitrant Q. variabilis seedsConclusions: Our study is the first on the molecular regulation mechanism of desiccation sensitivity of Q. variabilis seeds by using RNA-Seq and propose a possible work model. Our findings could make a great contribute to seed storage and long-term conservation of germplasm resources of recalcitrant seeds in the future.