Transcriptome and Degradome Sequencing Reveals Dormancy Mechanisms of Cunninghamia lanceolata Seeds

Abstract

Seeds with physiological dormancy usually experience primary and secondary dormancy in the nature; however, little is known about the differential regulation of primary and secondary dormancy. We combined multiple approaches to investigate cytological changes, hormonal levels, and gene expression dynamics in Cunninghamia lanceolata seeds during primary dormancy release and secondary dormancy induction. Light microscopy and transmission electron microscopy revealed that protein bodies in the embryo cells coalesced during primary dormancy release and then separated during secondary dormancy induction. Transcriptomic profiling demonstrated that expression of genes negatively regulating gibberellic acid (GA) sensitivity reduced specifically during primary dormancy release, whereas the expression of genes positively regulating abscisic acid (ABA) biosynthesis increased during secondary dormancy induction. Parallel analysis of RNA ends revealed uncapped transcripts for ∼55% of all unigenes. A negative correlation between fold changes in expression levels of uncapped versus capped mRNAs was observed during primary dormancy release. However, this correlation was loose during secondary dormancy induction. Our analyses suggest that the reversible changes in cytology and gene expression during dormancy release and induction are related to ABA/GA balance. Moreover, mRNA degradation functions as a critical posttranscriptional regulator during primary dormancy release. These findings provide a mechanistic framework for understanding physiological dormancy in seeds.

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

“…Its targets, the plant GAMyb TFs, have been shown to activate gibberellin-responsive gene expression of α-amylase in barley [94,95]. Our degradome data indicate the possible cleavage of various mRNA isoforms encoding nuclear transcription factor Y subunit A-4 (NFYA4, HORVU4Hr1G005670, TargetSeek: score = 3, MFE = -27.6, PAREsnip2: score = 2, MFE = -28.1) mediated by miR169d (20 nt, id = 84) (Table 1), what is consistent with previous studies on Cunninghamia lanceolata L. showing that NFYA4 mRNA is targeted by miR169d (authors used PAREsnip approach) [96]. The NFYA4 protein is involved in many abiotic stress responses and may regulate the timing of transition from vegetative to reproductive phase [97].…”

Exploring the fate of mRNA in aging seeds: protection, destruction, or slow decay?

“…Mature, dry seeds often serve as the final time point in transcriptomic studies of seed development ( Jones et al , 2010 ; Pereira Lima et al , 2017 ) or the initial time point in seed germination series ( Nakabayashi et al , 2005 ; Bellieny-Rabelo et al , 2016 ; Bai et al , 2017 ). Analyses of transcriptome changes during seed storage are rare and focused on dormancy relief in dry after-ripened or hydrated seeds ( Johnson and Dyer, 2000 ; Bazin et al , 2011 ; Gao et al , 2013 ; El-Maarouf-Bouteau et al , 2013 ; Cao et al , 2016 ) or following artificial aging of seeds exposed for a short time to warm, wet conditions ( Chen et al , 2013 ). Both physiological transitions presume degradation of specific transcript targets.…”

Illumina‐based transcriptomic analysis on recalcitrant seeds of Panax notoginseng for the dormancy release during the after‐ripening process

“…H). The changes of phytohormones concentration in physiology dormancy (PD) and PD release of Cunninghamia lanceolata seeds, a woody species, were similar with P. notoginseng seeds (Cao et al ). In addition, compared with the significant morphological changes during seed germination in P. Polyphylla (Qi et al ), similar changes occur during dormancy release in P. notoginseng seeds, implying that the seeds of P. notoginseng need to go through a phase of morphological post‐ripeness and a phase of physiological post‐ripeness to break dormancy.…”