Yam (Dioscorea alata L.) is an important tuber crop and purple pigmented elite cultivar has recently become popular because of associated health benefits. Identifying candidate genes responsible for flavonoid biosynthesis pathway (FBP) will facilitate understanding the molecular mechanism of controlling pigment formation in yam tubers. Here, we used Illumina sequencing to characterize the transcriptome of tubers from elite purple-flesh cultivar (DP) and conventional white-flesh cultivar (DW) of yam. In this process, we also designed high quality molecular markers to assist molecular breeding for tuber trait improvement. A total of 125,123 unigenes were identified from the DP and DW cDNA libraries, of which about 49.5% (60,020 unigenes) were annotated by BLASTX analysis using the publicly available protein database. These unigenes were further annotated functionally and subject to biochemical pathway analysis. 511 genes were identified to be more than 2-fold (FDR < 0.05) differentially expressed between the two yam cultivars, of which 288 genes were up-regulated and 223 genes were down-regulated in the DP tubers. Transcriptome analysis detected 61 unigenes encoding multiple well-known enzymes in the FBP. Furthermore, the unigenes encoding chalcone isomerase (CHS), flavanone 3-hydroxylase (F3H), flavonoid 3′-monooxygenase (F3’H), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX), and flavonol 3-O-glucosyltransferase (UF3GT) were found to be significantly up-regulated in the DP, implying that these genes were potentially associated with tuber color formation in this elite cultivar. The expression of these genes was further confirmed by qRT-PCR. Finally, 11,793 SSRs were successfully identified with these unigenes and 6,082 SSR markers were developed using Primer 3. This study provides the first comprehensive transcriptomic dataset for yam tubers, which will significantly contribute to genomic research of this and other related species. Some key genes associated with purple-flesh trait were successfully identified, thus providing valuable information about molecular process of regulating pigment accumulation in elite yam tubers. In the future, this information might be directly used to genetically manipulate the conventional white-fleshed tuber cultivars to enable them to produce purple flesh. In addition, our SSR marker sets will facilitate identification of QTLs for various tuber traits in yam breeding programs.

Polygonatum cyrtonema Hua is a traditional Chinese herb propagated using rhizomes, and excessive demand for seedlings and quality deterioration caused by rhizome propagation has highlighted that seed propagation may be an ideal solution to address these issues. However, the molecular mechanisms involved in P. cyrtonema Hua seed germination and emergence stages are not well understood. Therefore, in the present study, we performed transcriptomics combined with hormone dynamics during different seed germination stages, and 54,178 unigenes with an average length of 1390.38 bp (N50 = 1847 bp) were generated. Significant transcriptomic changes were related to plant hormone signal transduction and the starch and carbohydrate pathways. Genes related to ABA(abscisic acid), IAA(Indole acetic acid), and JA(Jasmonic acid) signaling, were downregulated, whereas genes related to ethylene, BR(brassinolide), CTK(Cytokinin), and SA(salicylic acid) biosynthesis and signaling were activated during the germination process. Interestingly, GA biosynthesis- and signaling-related genes were induced during the germination stage but decreased in the emergence stage. In addition, seed germination significantly upregulated the expression of genes associated with starch and sucrose metabolism. Notably, raffinose biosynthesis-related genes were induced, especially during the emergence stage. In total, 1171 transcription factor (TF) genes were found to be differentially expressed. Our results provide new insights into the mechanisms underlying P. cyrtonema Hua seed germination and emergence processes and further research for molecular breeding.

To breed a new yam cultivar of Dioscorea alata, the different and excellent germplasm resources were investigated within artificially cultivated population and some superior individuals, with a higher yield and medicinal properties, were selected. Considering results of the yield and medicinal properties during 2006-2013 cropping season, strains and lines were established and selected. As a result, the yield of the new developed cultivar (Wenshanyao No. 1, WSY01-1) reached 2217. 0 kg per 667 m2 (fresh weight) and 348.3 kg per 667 m2 (dry weight), and increased 23.8% and 23.9% comparing with control cultivars (landraces). Comparing with control cultivars, the level of polysaccharide, allantoin, and dioscin increased 36.9%, 48.3%, 20.9%, and reached 12.2%, 1.30%, 579.7 µg · g(-1), respectively. This result showed that the systematic selection method can significantly improve yield and medicinal properties of D. alata, and the developed " Wenshanyao No. 1" exhibits wide spreading prospects.

Dendrobium officinale is a well-known traditional Chinese medicinal plant in Orchidaceae, and cadmium (Cd) toxicity in the substrate of continuous cultivation has become an important factor limiting cultivation of D. officinale domesticated seedling. Glutathione S-transferase (GSTs) are well-characterized as crucial mediators of plant stress responses. However, their specific functional roles and molecular mechanisms in Cd tolerance remain poorly understood in D. officinale. In this study, we identified a member of the GST gene family, DoGST18, demonstrating its significant involvement in Cd detoxification. DoGST18 expression in yeast increased host tolerance to Cd. In addition, genetic transformation in Arabidopsis revealed that overexpression (OE) lines exhibited enhanced Cd resistance relative to wild-type lines, as evidenced by growth rates and antioxidant enzyme activities. The candidate target S5M5N9/DoHSP70 was identified by pull-down and mass spectrometry. Yeast two-hybrid, bimolecular fluorescence complementation and co-immunoprecipitation experiments confirmed the specific interaction between DoGST18 and S5M5N9 in the plant cytoplasm, which was also proved by further pull-down experiments. Our findings offer a crucial theoretical foundation for revealing the molecular mechanism of DoGST18 in the Cd resistance of D. officinale, and will potentially contribute to cultivating low Cd-accumulating D. officinale germplasm.

Dendrobium officinale is a traditional and valuable medicinal herb, with extensive research conducted on its polysaccharides, alkaloids, and other components, yet studies on anthocyanins remain limited. In this study, we analyzed the expression levels of GST family genes in green and purplish D. officinale and found that DoGSTF11 is highly expressed in the purplish variety. DoGSTF11 is localized to the nucleus and cell membrane but lacks transcriptional activation activity. Overexpression of DoGSTF11 in tomato enhances anthocyanin accumulation, suggesting a role in anthocyanin sequestration or transport. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays further revealed that DoGSTF11 interacts with DoGST31, while DoIDD12 and DoNF-YB3 are potential transcriptional regulators based on promoter-binding assays and expression correlation. In conclusion, our study demonstrates that DoGST11 positively regulates anthocyanin accumulation in D. officinale. These findings provide valuable insights into the metabolic engineering of flavonoids in D. officinale.