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

Abstract

Panax notoginseng (Burk) F.H. Chen is an economically and medicinally important plant of the family Araliacease, with seed dormancy being a key factor limiting the extended cultivation of P. notoginseng. The seeds belong to the morphophysiological dormancy (MPD) group, and it has also been described as the recalcitrant seed. To date, the molecular mechanism of dormancy release in the recalcitrant seed of P. notoginseng is unknown. In the present study, the transcript profiles of seeds from different after-ripening stages (0, 20, 40 and 60 days) were investigated using Illumina Hiseq 2500 technology. 91 979 946 clean reads were generated, and 81 575 unigenes were annotated in at least one database. In addition, the differentially expressed genes (DEGs) were identified by the pairwise comparisons. We screened out 2483 DEGs by the three key groups of 20 days vs 0 d, 40 d vs 0 d and 60 d vs 0 d. The DEGs were analyzed by gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway annotation. Meanwhile, we obtained 78 DEGs related to seeds dormancy release at different after-ripening stages of P. notoginseng, of which 15 DEGs were associated with abscisic acid and gibberellin. 26 DEGs that encode late embryogenesis abundant protein and antioxidant enzyme were correlated with desiccation tolerance in seeds. In summary, the results obtained here showed that PECTINESTERASE-2-LIKE, PROTEIN PHOSPHATASE 2C, SUPEROXIDE DISMUTASE, CATALASE, LATE EMBRYOGENESIS ABUNDANT PROTEIN DC3 and DEHYDRIN 9 were potentially involved in dormancy release and desiccation sensitivity of P. notoginseng seeds. The data might provide a basis for researches on MPD.

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

“…In addition to ABA and GA, which are two major hormones that respectively induce and break seed dormancy in most plants, other phytohormones, such as cytokinins, jasmonic acid, strigolactones, brassinosteroids, ethylene, salicylic acid, and auxin, may also regulate seed dormancy and germination in a plant species-dependent manner. Their contents in dormant and germinating seeds are partly regulated by the expression of genes related to hormone metabolism and signaling [ 40 , 46 ]. In this study, we identified 475 putative hormone metabolism-related unigenes and 510 putative hormone signaling genes that were differentially expressed during P. sibiricum seed dormancy and seedling and shoot emergence (Figs.…”

“…ABI3 and ABI5 are two ABA signaling-related genes that positively control seed dormancy [ 43 ]. ABI5 is found highly expressed in dormant seeds of several plant species [ 19 , 46 ]. Their homologous genes in P. sibiricum were expressed at higher levels in the Seed and Corm stages than in the cold-stratified germinated seeds and seedlings, implying ABA may have accumulated during the Seed and Corm stages under warm conditions, leading to the dormancy of the Seed and Corm stages.…”

The dehiscence process in Panax ginseng seeds and the stigmasterol biosynthesis pathway in terms of metabolomics

“…Transcriptomic analysis on Panax notoginseng (Burk) F.H. Chen seeds revealed 78 differentially expressed genes associated with seed dormancy; of these, 15 genes were involved in the abscisic acid and GA 3 pathways [ 37 ].…”

Stigmasterol Biosynthesis Pathway is Associated With the Dehiscence Process in Panax Ginseng Seeds

“…In addition, enrichment pathway analysis revealed pathways potentially associated with seed dormancy releases, such as steroid biosynthesis, avonoid biosynthesis, avone and avonol biosynthesis, and starch and sucrose metabolism [29], and a transcriptomic analysis on Panax notoginseng (Burk) F.H. Chen seeds revealed 78 differentially expressed genes (DEGs) associated with seed dormancy, and among them, 15 DEGs were involved in abscisic acid (ABA) and GA 3 pathways [35].…”