Caicai Lin’s research while affiliated with Dezhou University and other places

In plants, flowering is crucial to reproductive success. Receiving limited attention in apple research is the function of WRKY transcription factors in regulating flowering time. We characterized a WRKY transcription factor, MdWRKY71, from red-fleshed apple in this study, and ectopically expressed it in Arabidopsis thaliana, which revealed its role in flowering. The sequence of MdWRKY71 exhibited similarity to that of AtWRKY71, and its protein comprised a WRKY domain and a C2H2 zinc finger-like motif, placing it within subgroup IIc of the WRKY family. The similar changing trends demonstrated a significant positive correlation between the expression level of MdWRKY71 and the key flower transition genes in apical buds of apple in flower transition stage. Overexpression of MdWRKY71 promoted the upregulation of certain flower transition genes in apple calli. The ectopic expression of MdWRKY71 in A. thaliana was observed to induce early flowering. Additionally, MdWRKY71 could bind to the promoters of several floral pathway integrators directly and interact with them to enhance their expression levels. These results contribute to our understanding of the molecular mechanism through which MdWRKY71 regulates the flowering process in fruit trees, such as red-fleshed apple.

Potatoes are a critical staple crop worldwide, yet their yield is significantly constrained by salt stress. Understanding and enhancing salt tolerance in potatoes is crucial for ensuring food security. This study evaluated the salt tolerance of 17 diverse potato varieties using principal component analysis, membership function analysis, cluster analysis, and stepwise regression analysis. Comprehensive evaluation based on morphological, physiological, and biochemical indicators divided the varieties into three categories, identifying Z1264-1, Z700-1, Z943-1, Z1266-1, Z510-1, and Z1076-1 as having strong salt tolerance. Regression equations established stem thickness, root length, and catalase activity as rapid identification markers for salt tolerance in tetraploid potatoes. Transcriptome analysis of the highly tolerant variety Z1076-1 identified 68 differentially expressed miRNAs (DE miRNAs). qRT-PCR validation for eight randomly selected DE miRNAs confirmed consistent expression trends with transcriptome data. Predicted target genes of these miRNAs are involved in calcium channel signaling, osmotic regulation, plant hormone signaling, and reactive oxygen species clearance. Our findings provide valuable insights for the identification and screening of salt-tolerant potato germplasms. The findings also lay the foundation for studying molecular mechanisms of salt tolerance and advancing genetic breeding efforts to cultivate more resilient potato varieties.

Background Developing and enriching genetic resources plays important role in the crop improvement. The flag leaf affects plant architecture and contributes to the grain yield of wheat (Triticum aestivum L.). The genetic improvement of flag leaf traits faces problems such as a limited genetic basis. Among the various genetic resources of wheat, Thinopyrum intermedium has been utilized as a valuable resource in genetic improvement due to its disease resistance, large spikes, large leaves, and multiple flowers. In this study, a recombinant inbred line (RIL) population was derived from common wheat Yannong15 and wheat-Th. intermedium introgression line SN304 was used to identify the quantitative trait loci (QTL) for flag leaf-related traits. Results QTL mapping was performed for flag leaf length (FLL), flag leaf width (FLW) and flag leaf area (FLA). A total of 77 QTLs were detected, and among these, 51 QTLs with positive alleles were contributed by SN304. Fourteen major QTLs for flag leaf traits were detected on chromosomes 2B, 3B, 4B, and 2D. Additionally, 28 QTLs and 8 QTLs for flag leaf-related traits were detected in low-phosphorus and drought environments, respectively. Based on major QTLs of positive alleles from SN304, we identified a pair of double-ended anchor primers mapped on chromosome 2B and amplified a specific band of Th. intermedium in SN304. Moreover, there was a major colocated QTL on chromosome 2B, called QFll/Flw/Fla-2B, which was delimited to a physical interval of approximately 2.9 Mb and contained 20 candidate genes. Through gene sequence and expression analysis, four candidate genes associated with flag leaf formation and growth in the QTL interval were identified. Conclusion These results promote the fine mapping of QFll/Flw/Fla-2B, which have pleiotropic effects, and will facilitate the identification of candidate genes for flag leaf-related traits. Additionally, this work provides a theoretical basis for the application of Th. intermedium in wheat breeding.

The red root of Salvia miltiorrhiza Bunge, a famous traditional Chinese medicine (TCM), was caused by tanshinone in epidermis cells. In order to study the biological function of ncRNAs in the tanshinone synthesis, the expression patterns of mRNA and ncRNAs were comprehensively analyzed in red (high tanshinone content) and white root (low tanshinone content) tissues derived from the same plant. A total of 731 differentially expressed genes (DEGs) were mainly enriched in primary metabolic pathways such as galactose and nitrogen, and some secondary metabolic pathways such as phenylpropanoid and terpenoids. A total of 70 miRNAs, 48 lncRNAs, and 26 circRNAs were identified as differentially expressed (DE) ones. The enrichment pathway of the targets of DE-lncRNA were mainly in ribosome, carbon metabolism, plant hormone signal transduction, and glycerophospholipid metabolism. The function of the targets genes of 59 miRNAs combined with DE-circRNAs was mainly involved in plant–pathogen interaction, endocytosis, phenylpropanoid biosynthesis, and sesquiterpenoid and triterpenoid biosynthesis pathways. Most genes of the tanshinone synthesis pathway had a higher expression. Some ncRNAs were predicted to regulate several key enzyme genes of the tanshinone synthesis pathway, such as SmDXS2, SmGGPPS1, SmKSL. Furthermore, most target genes were related to the resistance of pathogens. The present study exhibited the tissue-specific expression patterns of ncRNAs, which would provide a basis for further research into the regulation mechanism of ncRNAs in the tanshinone synthesis process.

Tanshinones are the bioactive constituents of Danshen (Salvia miltiorrhiza Bunge), which is used in Traditional Chinese Medicine to treat cardiovascular and other diseases, and they synthesize and accumulate in the root periderm of S. miltiorrhiza. However, there is no relevant report on the initial stage of tanshinone synthesis, as well as the root structure and gene expression characteristics. The present study aims to provide new insights into how these bioactive principles begin to synthesize by characterizing possible differences in their biosynthesis and accumulation during early root development from both spatial and temporal aspects. The morphological characteristics and the content of tanshinones in roots of S. miltiorrhiza were investigated in detail by monitoring the seedlings within 65 days after germination (DAGs). The ONT transcriptome sequencing was applied to investigate gene expression patterns. The periderm of the S. miltiorrhiza storage taproot initially synthesized tanshinone on about 30 DAGs. Three critical stages of tanshinone synthesis were preliminarily determined: preparation, the initial synthesis, and the continuous rapid synthesis. The difference of taproots in the first two stages was the smallest, and the differentially expressed genes (DEGs) were mainly enriched in terpene synthesis. Most genes involved in tanshinone synthesis were up regulated during the gradual formation of the red taproot. Plant hormone signal transduction and ABC transport pathways were widely involved in S. miltiorrhiza taproot development. Five candidate genes that may participate in or regulate tanshinone synthesis were screened according to the co-expression pattern. Moreover, photosynthetic ferredoxin (FD), cytochrome P450 reductase (CPR), and CCAAT binding transcription factor (CBF) were predicted to interact with the known downstream essential enzyme genes directly. The above results provide a necessary basis for analyzing the initial synthesis and regulation mechanism of Tanshinones.

Main conclusion SmANS deletion leads to white flower mutation in Salvia miltiorrhiza. Abstract SmANS deletion leads to white flower mutation in Salvia miltiorrhiza. Abstract Salvia miltiorrhiza is an essential traditional Chinese medicine (TCM) with purple flowers, and S. miltiorrhiza Bge. f. alba is a unique intraspecific variation with white flowers. The molecular mechanism of flower color formation in S. miltiorrhiza will provide vital information for the variation and evolution. Here, we performed HPLC, transcriptomic, and re-sequencing analyses of purple-flowered S. miltiorrhiza line ‘Zihua105’ (ZH105) and white-flowered S. miltiorrhiza Bge. f. alba line ‘Baihua18’ (BH18). Delphinidin was the most anthocyanidin in ZH105, which become the main different between ZH105 vs. BH18 flowers. Transcriptome analysis revealed 299 differentially expressed genes (DEGs). SmANS, the anthocyanidin synthase gene in the down-stream anthocyanin biosynthesis pathway, was significantly expressed in ZH105 corollas, suggesting it might play a key role in white petal formation. Whole-genome re-sequencing revealed that a 6.75 kb segment located on chromosome 5, which contains the complete sequence of the SmANS genes, was lost in BH18 and another S. miltiorrhiza Bge. f. alba line. In contrast, the other five purple-flowered S. miltiorrhiza lines both possessed this segment. Further molecular marker identification also confirmed that wild S. miltiorrhiza Bge. f. alba lines lost regions that contained a complete or important part of SmANS sequences. Subsequently, the research showed that the deletion mutant of SmANS genes resulted in the natural white flower color variant of S. miltiorrhiza.

Salvia miltiorrhiza is a traditional Chinese medicinal plant of Labiatae, which has been widely utilized to treat a variety of cardiovascular and cerebrovascular diseases. However, due to the long growth cycle, low content of active ingredients, and serious quality deterioration of S. miltiorrhiza, the use of biotechnology to improve S. miltiorrhiza to meet the growing demand for clinical applications has become a research hotspot. In this study, a novel one-step hairy root regeneration method was developed, which could rapidly obtain hairy roots and regenerated plants with high tanshinone content. By optimizing the parameters of Agrobacterium rhizogenes transformation in S. miltiorrhiza, it was finally established that the explants were infected in Ar.qual (OD600 = 0.6) for 10 min, co-cultured for 3 days, and then screened on the screening medium containing 7.5 mg/l hygromycin, the maximum transformation frequency can reach 73.85%. GFP and PCR detection yielded a total of 9 positive transgenic hairy root lines and 11 positive transgenic regenerated plants. SmGGPPS1 was successfully overexpressed in positive transgenic regenerated plants, according to the results of qRT-PCR. The content of tanshinone IIA and cryptotanshinone were dramatically enhanced in transgenic regenerated plants and hairy roots by Ultra Performance Liquid Chromatography analysis. Based on the Agrobacterium-mediated transformation of S. miltiorrhiza, this study developed a new method for regenerating plants with transgenic hairy roots. This method provides a foundation for the breeding of S. miltiorrhiza and the sustainable development of medicinal plant resources, as well as provides a useful reference for the application of other species.

Background: Salvia miltiorrhiza is an important traditional Chinese medicinal (TCM) plant and a model plant in the genetic study of TCM. A series of omics related to Danshen have been published. Integrating, managing, storing, and sharing data has become an urgent problem to be solved in S. miltiorrhiza genetic studies. Objectives: The genome database is the link for the exchange, acquisition, and use of different omics data between data producers and users, maximizing value and utilization of data. Methods: The genome database included DSS3 genome and five RNA-Seq data. The back-end performs data search and retrieval through the LAMP (Linux, Apache, MySQL, PHP) framework. Results: Here, we present SmGDB (S. miltiorrhiza genome database; http://8.140.162.85/ ), which houses the latest version of genome sequence and annotation data for S. miltiorrhiza, combining three unpublished RNA-Seq data from our group and two released RNA-Seq data. We also identified a novel gene cluster including seven CYP71D genes involved in the tanshinone synthesis pathway based on genome sequences and expression data. Besides, SmGDB provides user-friendly web interfaces for querying and browsing gene annotation, structure, location, and expression profiles for concerned genes. Popular bioinformatics tools such as 'BLAST', 'Search', 'Heatmap', 'JBrowse', etc., were also provided in SmGDB. Conclusions: SmGDB will provide utility for characterizing the structure of the S. miltiorrhiza genome and better understanding gene functions and biological processes underlying complex secondary metabolism in Danshen.

Background: Long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have been shown to play fundamental roles in plant development. However, the information of these noncoding RNAs (ncRNAs) in Salvia miltiorrhiza remains largely unexplored. In this study, the expression pattern of ncRNAs in six tissues from the same strain of S. miltiorrhiza was analyzed to study the biological function of ncRNAs on active ingredients synthesis. Methods: Analysis of tanshinone content differences of two root simples was carried out on high-performance liquid chromatography (HPLC). RNA sequencing, GO and KEGG enrichment analysis were applied to analyzing the targets of diferentially expressed ncRNAs in different organs. Results: A total of 6,929 lncRNAs, 6,239 circRNAs, and 360 miRNAs were identified. Forty-eight lncRNAs, 70 miRNAs, and 26 circRNAs expressed differentially between red and white root tissues with significantly different tanshinone content. GO and KEGG pathway analysis of target genes of differently expressed ncRNAs indicated that some target genes are involved in the synthesis pathway of terpene, including diterpene and sesquiterpene. We also found many target genes related to secondary metabolites, including 2-C-Methyl-d-erythritol 2,4-cyclodiphosphate Synthase (SmMCS) and several CYP450s. Furthermore, most target genes may be related to the resistance of pathogens, such as receptor kinases, disease-resistant proteins, and pentatricopeptide repeat-containing proteins. Conclusions: The present study exhibited the tissue-specific expression patterns of ncRNAs preliminarily in S. miltiorrhiza, which may reflect that the formation of white root or red root is related to regulation by ncRNAs. It would provide a basis for further research about the regulation mechanism in the tanshinone synthesis process.

Background: Cassia tora L. is an annual leguminous plant. Its seeds had wide utility in herbal medicine in Asian, but is usually regard as a potent, invasive weed which even helps farmers eliminate other parasitic weed species. However, compared with other important legume crops, C. tora is far from fully developed and the genetic basis is greatly lacking. A reference genome sequence will be great valuable resource for its genome evolution, genetic breeding and development. Results: Here, we de novo assembled a chromosome-scale genome for C. tora by combining PacBio sequencing technology with chromatin interaction mapping, resulting in 621-Mb genome with a contig N50 of 2.5 Mb, of which 77.44% was ordered and oriented on 13 pseudochromosomes. The genome contained 32,361 protein-coding genes with a repetitive DNA content of approximately 58.15%. Gypsy-type LTRs constituted the largest subfamily. LTR insertion events seldom occurred in this genome over the past 10 million years. Comparative genomic analyses showed that C. tora diverged ~95 million years ago (MYA), which revealed it has the most distant genetic relationship with 11 other legumes. Compared with other legume crops, Cassia tora is maybe an ancient species in Leguminosae. Conclusions: The high-quality reference genome sequence reported here furnishes unprecedented insights into genome dynamics and provides an important basis for future research on legume genome evolution.