Transcriptome profiles revealed molecular mechanisms of alternating temperatures in breaking the epicotyl morphophysiological dormancy of Polygonatum sibiricum seeds

Abstract

Background To adapt seasonal climate changes under natural environments, Polygonatum sibiricum seeds have a long period of epicotyl morphophysiological dormancy, which limits their wide-utilization in the large-scale plant progeny propagation. It has been proven that the controlled consecutive warm and cold temperature treatments can effectively break and shorten this seed dormancy status to promote its successful underdeveloped embryo growth, radicle emergence and shoot emergence. To uncover the molecular basis of seed dormancy release and seedling establishment, a SMRT full-length sequencing analysis and an Illumina sequencing-based comparison of P. sibiricum seed transcriptomes were combined to investigate transcriptional changes during warm and cold stratifications. Results A total of 87,251 unigenes, including 46,255 complete sequences, were obtained and 77,148 unigenes (88.42%) were annotated. Gene expression analyses at four stratification stages identified a total of 27,059 DEGs in six pairwise comparisons and revealed that more differentially expressed genes were altered at the Corm stage than at the other stages, especially Str_S and Eme. The expression of 475 hormone metabolism genes and 510 hormone signaling genes was modulated during P. sibiricum seed dormancy release and seedling emergence. One thousand eighteen transcription factors and five hundred nineteen transcription regulators were detected differentially expressed during stratification and germination especially at Corm and Str_S stages. Of 1246 seed dormancy/germination known DEGs, 378, 790, and 199 DEGs were associated with P. sibiricum MD release (Corm vs Seed), epicotyl dormancy release (Str_S vs Corm), and the seedling establishment after the MPD release (Eme vs Str_S). Conclusions A comparison with dormancy- and germination-related genes in Arabidopsis thaliana seeds revealed that genes related to multiple plant hormones, chromatin modifiers and remodelers, DNA methylation, mRNA degradation, endosperm weakening, and cell wall structures coordinately mediate P. sibiricum seed germination, epicotyl dormancy release, and seedling establishment. These results provided the first insights into molecular regulation of P. sibiricum seed epicotyl morphophysiological dormancy release and seedling emergence. They may form the foundation of future studies regarding gene interaction and the specific roles of individual tissues (endosperm, newly-formed corm) in P. sibiricum bulk seed dormancy.

Transcriptomics and metabolomics changes triggered by exogenous 6-benzylaminopurine in relieving epicotyl dormancy of Polygonatum cyrtonema Hua seeds

“…When the germination rate reached 60% (30 days), it was sluggish and had a tendency to be more consistent ( Figure 1A ). After that, the seeds stopped growing and entered epicotyl dormancy ( Liao et al, 2021 ). This study found, to release the epicotyl dormancy of P. cyrtonema seeds, the application of a certain concentration of 6-BA could significantly increase the emergence rate then relieved the dormancy of seeds ( Figure 1B ).…”

“…P. cyrtonema seeds began to enter the epicotyl dormancy after the bulb appeared. The dormancy state can be broken effectively by alternating temperatures ( Liao et al, 2021 ). However, other studies have shown that exogenous phytohormones can also relieve dormancy ( Yang et al, 2017 ).…”

“…Seed dormancy is mainly controlled by abscisic acid ABA and GA, and ABA decreased and GA increased during seed dormancy release in Arabidopsis ( Chen H. et al, 2020 ). However, NCED of ABA biosynthetic pathway were upregulated in the three stages of treatment groups, and during the development of P. cyrtonema seed from corm to seedling emergence, the development of embryo needed to transport nutrients from endosperm to new corm tissue and cold stratification before seedling establishment ( Liao et al, 2021 ). This means that seeds are still not fully mature, and there is a direct correlation between ABA excess production and fruit maturity ( Monribot-Villanueva et al, 2022 ).…”

“…The significance of the enriched GO terms and enriched KEGG pathways were separately assessed with the Wallenius non-central hypergeometric distribution test and the hypergeometric distribution test. An adjusted p -value < 0.05 was set as the threshold for significance ( Liao et al, 2021 ).…”

Seed Germination Mechanism of Carex rigescens Under Variable Temperature Determinded Using Integrated Single-Molecule Long-Read and Illumina Sequence Analysis

“…PacBio single molecular real time (SMRT) sequencing can avoid assembly errors and provide complete transcript sequence information for species in case of no or poor reference genomes ( Workman et al, 2018 ). To obtain the full-length transcript information of plants and accurately address biological problems, a method combining PacBio SMRT sequencing with Illumina sequencing has been used in several studies: for example, to determine how alternating temperature breaks the morphophysiological dormancy of Polygonatum sibiricum seeds ( Liao et al, 2021 ), response to drought stress during seed germination of Adzilla beans ( Zhu et al, 2020 ), and potential transcriptional variants of genes involved in oil biosynthesis in Camellia oleifera seeds ( Gong et al, 2020 ). Similar to that in previous studies, this combined method can be used to study C. rigescens seed germination and will provide useful genetic information as well as allow elucidation of germination mechanisms.…”