Parallel selection of loss-of-function alleles of Pdh1 orthologous genes in warm-season legumes for pod indehiscence and plasticity is related to precipitation.

Pod dehiscence facilitates seed dispersal in wild legumes but results in yield loss in cultivated legumes. The evolutionary genetics of the legume pod dehiscence trait remain largely elusive. We characterized the pod dehiscence of chromosome segment substitution lines of Glycine max crossed with Glycine soja and found that the gene underlying the predominant quantitative trait locus (QTL) of soybean pod-shattering trait was Pod dehiscence 1 (Pdh1). A few rare loss-of-function (LoF) Pdh1 alleles were identified in G. soja, while only an allele featuring a premature stop codon was selected for pod indehiscence in cultivated soybean and spread to low-precipitation regions with increased frequency. Moreover, correlated interactions among Pdh1's haplotype, gene expression, and environmental changes for the developmental plasticity of the pod dehiscence trait were revealed in G. max. We found that orthologous Pdh1 genes specifically originated in warm-season legumes and their LoF alleles were then parallel-selected during the domestication of legume crops. Our results provide insights into the convergent evolution of pod dehiscence in warm-season legumes, facilitate an understanding of the intricate interactions between genetic robustness and environmental adaptation for developmental plasticity, and guide the breeding of new legume varieties with pod indehiscence.

Pharmacokinetics, tissue distribution and excretion of a novel long-acting human insulin analogue - recombinant insulin LysArg in rats.

As a novel long-acting recombinant human insulin analogue, it is necessary to carry out the preclinical research for insulin LysArg. The purpose of this study was to characterise the pharmacokinetic, tissue distribution and excretion of insulin LysArg and provide a reference for its development. Three methods were used to measure the content of insulin LysArg in biological samples after a single subcutaneous administration in rats, including radioassay, radioassay after precipitation with TCA and separation by HPLC. After Subcutaneous administration of recombinant insulin LysArg 1, 2, 4 U/kg in rats, it showed both Cmax and AUC0-t were positively correlated with the dose. In the meanwhile, after a single subcutaneous administration of recombinant insulin LysArg at 2 U/kg in rats, the amount of radioactivity in most organs was highest at 1.5 h and then decreased gradually, no accumulation was found. The highest level of insulin LysArg was observed in the kidney. Like other macromolecules, insulin LysArg was mainly excreted from urine. The study fully illustrated the pharmacokinetic pattern of insulin LysArg, provided valuable informations to support its further development about safety and toxicology.

Bioactive compounds induced in Physalis angulata L. by methyl-jasmonate: an investigation of compound accumulation patterns and biosynthesis-related candidate genes.

KEY MESSAGE: We employed both metabolomic and transcriptomic approaches to explore the accumulation patterns of physalins, flavonoids and chlorogenic acid in Physalis angulata and revealed the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Physalis angulata L. is an annual Solanaceae plant with a number of medicinally active compounds. Despite the potential pharmacological benefits of P. angulata, the scarce genomic information regarding this plant has limited the studies on the mechanisms of bioactive compound biosynthesis. To facilitate the basic understanding of the main chemical constituent biosynthesis pathways, we performed both metabolomic and transcriptomic approaches to reveal the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Untargeted metabolome analysis showed that most physalins, flavonoids and chlorogenic acid were significantly upregulated. Targeted HPLC-MS/MS analysis confirmed variations in the contents of two important representative steroid derivatives (physalins B and G), total flavonoids, neochlorogenic acid, and chlorogenic acid between MeJA-treated plants and controls. Transcript levels of a few steroid biosynthesis-, flavonoid biosynthesis-, and chlorogenic acid biosynthesis-related genes were upregulated, providing a potential explanation for MeJA-induced active ingredient synthesis in P. angulata. Systematic correlation analysis identified a number of novel candidate genes associated with bioactive compound biosynthesis. These results may help to elucidate the regulatory mechanism underlying MeJA-induced active compound accumulation and provide several valuable candidate genes for further functional study.

An innovative procedure of genome-wide association analysis fits studies on germplasm population and plant breeding.

KEY MESSAGE: The innovative RTM-GWAS procedure provides a relatively thorough detection of QTL and their multiple alleles for germplasm population characterization, gene network identification, and genomic selection strategy innovation in plant breeding. The previous genome-wide association studies (GWAS) have been concentrated on finding a handful of major quantitative trait loci (QTL), but plant breeders are interested in revealing the whole-genome QTL-allele constitution in breeding materials/germplasm (in which tremendous historical allelic variation has been accumulated) for genome-wide improvement. To match this requirement, two innovations were suggested for GWAS: first grouping tightly linked sequential SNPs into linkage disequilibrium blocks (SNPLDBs) to form markers with multi-allelic haplotypes, and second utilizing two-stage association analysis for QTL identification, where the markers were preselected by single-locus model followed by multi-locus multi-allele model stepwise regression. Our proposed GWAS procedure is characterized as a novel restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS, https://github.com/njau-sri/rtm-gwas ). The Chinese soybean germplasm population (CSGP) composed of 1024 accessions with 36,952 SNPLDBs (generated from 145,558 SNPs, with reduced linkage disequilibrium decay distance) was used to demonstrate the power and efficiency of RTM-GWAS. Using the CSGP marker information, simulation studies demonstrated that RTM-GWAS achieved the highest QTL detection power and efficiency compared with the previous procedures, especially under large sample size and high trait heritability conditions. A relatively thorough detection of QTL with their multiple alleles was achieved by RTM-GWAS compared with the linear mixed model method on 100-seed weight in CSGP. A QTL-allele matrix (402 alleles of 139 QTL × 1024 accessions) was established as a compact form of the population genetic constitution. The 100-seed weight QTL-allele matrix was used for genetic characterization, candidate gene prediction, and genomic selection for optimal crosses in the germplasm population.

Advances in Dendrobium molecular research: Applications in genetic variation, identification and breeding.

Orchids of the genus Dendrobium are of great economic importance in global horticultural trade and in Asian traditional medicine. For both areas, research yielding solid information on taxonomy, phylogeny, and breeding of this genus are essential. Traditional morphological and cytological characterization are used in combination with molecular results in classification and identification. Markers may be useful when used alone but are not always reliable in identification. The number of species studied and identified by molecular markers is small at present. Conventional breeding methods are time-consuming and laborious. In the past two decades, promising advances have been made in taxonomy, phylogeny and breeding of Dendrobium species due to the intensive use of molecular markers. In this review, we focus on the main molecular techniques used in 121 published studies and discuss their importance and possibilities in speeding up the breeding of new cultivars and hybrids.

Detecting the QTL-allele system of seed isoflavone content in Chinese soybean landrace population for optimal cross design and gene system exploration.

KEY MESSAGE: Utilizing an innovative GWAS in CSLRP, 44 QTL 199 alleles with 72.2 % contribution to SIFC variation were detected and organized into a QTL-allele matrix for cross design and gene annotation. The seed isoflavone content (SIFC) of soybeans is of great importance to health care. The Chinese soybean landrace population (CSLRP) as a genetic reservoir was studied for its whole-genome quantitative trait loci (QTL) system of the SIFC using an innovative restricted two-stage multi-locus genome-wide association study procedure (RTM-GWAS). A sample of 366 landraces was tested under four environments and sequenced using RAD-seq (restriction-site-associated DNA sequencing) technique to obtain 116,769 single nucleotide polymorphisms (SNPs) then organized into 29,119 SNP linkage disequilibrium blocks (SNPLDBs) for GWAS. The detected 44 QTL 199 alleles on 16 chromosomes (explaining 72.2 % of the total phenotypic variation) with the allele effects (92 positive and 107 negative) of the CSLRP were organized into a QTL-allele matrix showing the SIFC population genetic structure. Additional differentiation among eco-regions due to the SIFC in addition to that of genome-wide markers was found. All accessions comprised both positive and negative alleles, implying a great potential for recombination within the population. The optimal crosses were predicted from the matrices, showing transgressive potentials in the CSLRP. From the detected QTL system, 55 candidate genes related to 11 biological processes were χ (2)-tested as an SIFC candidate gene system. The present study explored the genome-wide SIFC QTL/gene system with the innovative RTM-GWAS and found the potentials of the QTL-allele matrix in optimal cross design and population genetic and genomic studies, which may have provided a solution to match the breeding by design strategy at both QTL and gene levels in breeding programs.

Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China.

Dendrobium plants are important commercial herbs in China, widely used in traditional medicine and ornamental horticulture. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to molecular phylogeny analysis and species identification of 31 Chinese Dendrobium species. Fourteen SRAP primer pairs produced 727 loci, 97% of which (706) showed polymorphism. Average polymorphism information content of the SRAP pairs was 0.987 (0.982-0.991), showing that plenty of genetic diversity exists at the interspecies level of Chinese Dendrobium. The molecular phylogeny analysis (UPGMA) grouped the 31 Dendrobium species into six clusters. We obtained 18 species-specific markers, which can be used to identify 10 of the 31 species. Our results indicate the SRAP marker system is informative and would facilitate further application in germplasm appraisal, evolution, and genetic diversity studies in the genus Dendrobium.

Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome.

This study was designed to reveal the genome-wide distribution of presence/absence variation (PAV) and to establish a database of polymorphic PAV markers in soybean. The 33 soybean whole-genome sequences were compared to each other with that of Williams 82 as a reference genome. A total of 33,127 PAVs were detected and 28,912 PAV markers with their primer sequences were designed as the database NJAUSoyPAV_1.0. The PAVs scattered on whole genome while only 518 (1.8%) overlapped with simple sequence repeats (SSRs) in BARCSOYSSR_1.0 database. In a random sample of 800 PAVs, 713 (89.13%) showed polymorphism among the 12 differential genotypes. Using 126 PAVs and 108 SSRs to test a Chinese soybean germplasm collection composed of 828 Glycine soja Sieb. et Zucc. and Glycine max (L.) Merr. accessions, the per locus allele number and its variation appeared less in PAVs than in SSRs. The distinctness among alleles/bands of PCR (polymerase chain reaction) products showed better in PAVs than in SSRs, potential in accurate marker-assisted allele selection. The association mapping results showed SSR + PAV was more powerful than any single marker systems. The NJAUSoyPAV_1.0 database has enriched the source of PCR markers, and may fit the materials with a range of per locus allele numbers, if jointly used with SSR markers.

Whole-Transcriptome Sequencing Reveals the Global Molecular Responses and NAC Transcription Factors Involved in Drought Stress in Dendrobium catenatum.

Dendrobium catenatum is a highly drought-tolerant herb, which usually grows on cliffs or in the branches of trees, yet the underlying molecular mechanisms for its tolerance remain poorly understood. We conducted a comprehensive study utilizing whole-transcriptome sequencing approaches to investigate the molecular response to extreme drought stress in D. catenatum. A large number of differentially expressed mRNAs, lncRNAs, and circRNAs have been identified, and the NAC transcription factor family was highly enriched. Meanwhile, 46 genes were significantly up-regulated in the ABA-activated signaling pathway. In addition to the 89 NAC family members accurately identified in this study, 32 members were found to have different expressions between the CK and extreme drought treatment. They may regulate drought stress through both ABA-dependent and ABA-independent pathways. Moreover, the 32 analyzed differentially expressed DcNACs were found to be predominantly expressed in the floral organs and roots. The ceRNA regulatory network showed that DcNAC87 is at the core of the ceRNA network and is regulated by miR169, miR393, and four lncRNAs. These investigations provided valuable information on the role of NAC transcription factors in D. catenatum's response to drought stress.

Development of Chloroplast Microsatellite Markers and Evaluation of Genetic Diversity and Population Structure of Cutleaf Groundcherry (Physalis angulata L.) in China.

Cutleaf groundcherry (Physalis angulata L.), an annual plant containing a variety of active ingredients, has great medicinal value. However, studies on the genetic diversity and population structure of P. angulata are limited. In this study, we developed chloroplast microsatellite (cpSSR) markers and applied them to evaluate the genetic diversity and population structure of P. angulata. A total of 57 cpSSRs were identified from the chloroplast genome of P. angulata. Among all cpSSR loci, mononucleotide markers were the most abundant (68.24%), followed by tetranucleotide (12.28%), dinucleotide (10.53%), and trinucleotide (8.77%) markers. In total, 30 newly developed cpSSR markers with rich polymorphism and good stability were selected for further genetic diversity and population structure analyses. These cpSSRs amplified a total of 156 alleles, 132 (84.62%) of which were polymorphic. The percentage of polymorphic alleles and the average polymorphic information content (PIC) value of the cpSSRs were 81.29% and 0.830, respectively. Population genetic diversity analysis indicated that the average observed number of alleles (Na), number of effective alleles (He), Nei's gene diversity (h), and Shannon information indices (I) of 16 P. angulata populations were 1.3161, 1.1754, 0.1023, and 0.1538, respectively. Moreover, unweighted group arithmetic mean, neighbor-joining, principal coordinate, and STRUCTURE analyses indicated that 203 P. angulata individuals from 16 populations were grouped into four clusters. A molecular variance analysis (AMOVA) illustrated the considerable genetic variation among populations, while the gene flow (Nm) value (0.2324) indicated a low level of gene flow among populations. Our study not only provided a batch of efficient genetic markers for research on P. angulata but also laid an important foundation for the protection and genetic breeding of P. angulata resources.

Development and characterization of 110 novel EST-SSR markers for Dendrobium officinale (Orchidaceae).

PREMISE OF THE STUDY: Expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers were developed in Dendrobium officinale by screening a cDNA library. The loci were verified by sequencing and explored for polymorphism among 19 genotypes and transferability among 30 other distantly related Dendrobium species. • METHODS AND RESULTS: One hundred ten EST-SSRs were developed, and a set of 20 amplified two to six nucleotide repeats with a mean number of 2.5 alleles per locus and with an observed heterozygosity and polymorphism information content per locus ranging from 0.3463 to 0.9003 and 0.0997 to 0.6537 in 19 D. officinale genotypes, respectively. Furthermore, 92 of these markers have cross-taxa transferability, ranging from 6.45% to 100% among 30 other distantly related Dendrobium species. • CONCLUSIONS: The developed markers have potential for application in germplasm appraisal, genetic diversity study, genetic mapping, and molecular breeding in D. officinale and other congeneric species.

Ultraviolet-B Irradiation Increases Antioxidant Capacity of Pakchoi (Brassica rapa L.) by Inducing Flavonoid Biosynthesis.

As an important abiotic stress factor, ultraviolet-B (UV-B) light can stimulate the accumulation of antioxidants in plants. In this study, the possibility of enhancing antioxidant capacity in pakchoi (Brassica rapa L.) by UV-B supplementation was assessed. Irradiation with 4 µmol·m-2·s-1 UV-B for 4 h or 2 µmol·m-2·s-1 UV-B for 24 h significantly increased the 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging activity and total reductive capacity, as a result of inducing a greater accumulation of total polyphenols and flavonoids without affecting the plant biomass. A high performance liquid chromatography (HPLC) analysis showed that the concentrations of many flavonoids significantly increased in response to UV-B treatment. The activities of three enzymes involved in the early steps of flavonoid biosynthesis, namely phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), and 4-coumarate: coenzyme A (CoA) ligase (4CL), were significantly increased after the corresponding UV-B treatment. Compared with the control, the expression levels of several flavonoid biosynthesis genes (namely BrPAL, BrC4H, Br4CL, BrCHS, BrF3H, BrF3'H, BrFLS, BrDFR, BrANS, and BrLDOX) were also significantly up-regulated in the UV-B treatment group. The results suggest that appropriate preharvest UV-B supplementation could improve the nutritional quality of greenhouse-grown pakchoi by promoting the accumulation of antioxidants.

GlioMarker: An integrated database for knowledge exploration of diagnostic biomarkers in gliomas.

Gliomas are the most frequent malignant and aggressive tumors in the central nervous system. Early and effective diagnosis of glioma using diagnostic biomarkers can prolong patients' lives and aid in the development of new personalized treatments. Therefore, a thorough and comprehensive understanding of the diagnostic biomarkers in gliomas is of great significance. To this end, we developed the integrated and web-based database GlioMarker (http://gliomarker.prophetdb.org/), the first comprehensive database for knowledge exploration of glioma diagnostic biomarkers. In GlioMarker, accurate information on 406 glioma diagnostic biomarkers from 1559 publications was manually extracted, including biomarker descriptions, clinical information, associated literature, experimental records, associated diseases, statistical indicators, etc. Importantly, we integrated many external resources to provide clinicians and researchers with the capability to further explore knowledge on these diagnostic biomarkers based on three aspects. (1) Obtain more ontology annotations of the biomarker. (2) Identify the relationship between any two or more components of diseases, drugs, genes, and variants to explore the knowledge related to precision medicine. (3) Explore the clinical application value of a specific diagnostic biomarker through online analysis of genomic and expression data from glioma cohort studies. GlioMarker provides a powerful, practical, and user-friendly web-based tool that may serve as a specialized platform for clinicians and researchers by providing rapid and comprehensive knowledge of glioma diagnostic biomarkers to subsequently facilitates high-quality research and applications.

Phytochemistry, pharmacology, and potential clinical applications of saffron: A review.

ETHNOPHARMACOLOGICAL RELEVANCE: Saffron, the dried red stigma of the perennial herb Crocus sativus L. (Iridaceae), is one of the most important and expensive spices in the world. It is used as a traditional Chinese medicine with demonstrated effects in promoting blood circulation and suppressing blood stasis, cooling blood detoxification, and relieving depression. It is mainly used for the treatment of depression, irregular menstruation, postpartum thrombosis, and bruises. AIM OF THE STUDY: This review aims to provide a systematic and up-to-date overview of the phytochemistry, pharmacology, and clinical applications of saffron. We hope it could provide useful references and guidance for the future directions of research on saffron. MATERIALS AND METHODS: The online database, such as Web of Science, Google Scholar, Science Direct, PubMed, SpringerLink, Wiley Online Library, SciFinder and Chemical book, and CNKI were used to collect relevant literature. And the classic books about Chinese herbal medicine were also being referenced. RESULTS: More than 150 chemical compounds, including carotenoids, flavonoids and flavonoid glycosides, monoterpenes and monoterpenoid derivatives, monocyclic aromatic hydrocarbons, amino acids, alkaloids and others, were revealed. The pharmacological activities study of saffron were focused on the antioxidant, anti-inflammatory, antitumor, antidepressant, hypoglycemic, hypolipidemic, memory-enhancing, and so on. Currently, saffron is mainly used for the treatment of diabetes, Alzheimer's disease, depression, anxiety disorders, cardiovascular diseases, learning and memory disorders, cancer, and other conditions. CONCLUSIONS: Phytochemical and pharmacological analyses of saffron have been revealed in recent studies. However, clinical studies have focused mainly on AD, depression and anxiety disorders. Therefore, a large number of clinical trials are needed to study the efficacy of saffron and its major chemical components against other diseases including hypertension, hyperlipidemia, and cancer. Further studies of the mechanism of action and toxicological properties of saffron are also required, especially research to establish an effective dose of saffron and its long-term toxicity in vivo.

Development, Identification, and Application of a Germplasm Specific SCAR Marker for Dendrobium officinale Kimura et Migo.

The stems of Dendrobium officinale have been used as a rare and valuable Chinese tonic medicine, known as "Tiepi Fengdou", since the Qing dynasty. Because of the increased market demand and continued exploitation of this plant, the reserves of wild D. officinale resources have been depleted, and D. officinale products on the market are being increasingly adulterated. Such changes have strongly affected the sustainable utilization of this valuable medicinal plant resource and the development of related industries. In this study, a species-specific DNA marker was developed for the rapid and accurate authentication of D. officinale. In total, 36 start codon-targeted (SCoT) polymorphism primers were screened in 36 definite Dendrobium species, and a distinct species-specific DNA amplicon (SCoT13-215) for D. officinale was obtained. After the sequence was cloned and sequenced, a sequence-characterized amplified region marker was developed (named SHF/SHR) and validated through PCR amplification of all 38 Dendrobium samples. The marker's specificity for D. officinale was confirmed through the consistent amplification of a clear 197-bp band. This SCAR marker can be used to rapidly, effectively, and reliably identify D. officinale among various Dendrobium species and may play an important role in ensuring the quality of medicinal preparations and protecting the germplasm of this important medicinal species.

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits.

The fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

Pharmacodynamics and pharmacokinetics of a new type of recombinant insulin Lisargine injection.

BACKGROUND: Recombinant insulin Lisargine is a new type of insulin. In this study, we aimed to compare its pharmacodynamic (PD) and pharmacokinetic (PK) with Lantus. METHODS: The PD test was performed by exploring the effect of single administration on blood glucose of normal rats and STZ-induced diabetic rats, and the effect of multiple administrations on blood glucose of STZ-induced diabetic rats. Further PD tests include receptor affinity test, receptor autophosphorylation test and adipocyte glucose uptake test. Four IU and 8 IU per dog Lisargine was used for PK test, insulin was measured and area under curve (AUC) was calculated. RESULTS: With single injection, Lisargine 1.5 IU/kg had significant hypoglycemic effects at 1 and 2 h, similar to that of Lantus. Lisargine 5 IU/kg and 10 IU/kg lowered the blood glucose of STZ-induced diabetic rats at 1, 2, 4 & 6 h significantly. With multiple injections, Lantus lowered blood glucose at 2, 4 & 6 h, Lisargine 2.5 IU/kg, 5 IU/kg, and 10 IU/kg lowered blood glucose at 2 & 4 h significantly, compared with vehicle. There was no difference for receptor affinity test, receptor autophosphorylation test and adipocyte glucose uptake test between Lisargine and Lantus. The PK of Lisargine and Lantus of healthy Beagle dogs was very similar. CONCLUSIONS: This animal study demonstrated that PK and PD of Lisargine and Lantus were similar, suggesting the bioequivalence of these products.

A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data.

Dendrobium huoshanense is used to treat various diseases in traditional Chinese medicine. Recent studies have identified active components. However, the lack of genomic data limits research on the biosynthesis and application of these therapeutic ingredients. To address this issue, we generated the first chromosome-level genome assembly and annotation of D. huoshanense. We integrated PacBio sequencing data, Illumina paired-end sequencing data, and Hi-C sequencing data to assemble a 1.285 Gb genome, with contig and scaffold N50 lengths of 598 kb and 71.79 Mb, respectively. We annotated 21,070 protein-coding genes and 0.96 Gb transposable elements, constituting 74.92% of the whole assembly. In addition, we identified 252 genes responsible for polysaccharide biosynthesis by Kyoto Encyclopedia of Genes and Genomes functional annotation. Our data provide a basis for further functional studies, particularly those focused on genes related to glycan biosynthesis and metabolism, and have implications for both conservation and medicine.

Molecular diversity and relationships among Cymbidium goeringii cultivars based on inter-simple sequence repeat (ISSR) markers.

Spring orchid (Cymbidium goeringii) is a popular flowering plant species. There have been few molecular studies of the genetic diversity and conservation genetics on this species. An assessment of the level of genetic diversity in cultivated spring orchid would facilitate development of the future germplasm conservation for cultivar improvement. In the present study, DNA markers of intersimple sequence repeats (ISSR) were identified and the ISSR fingerprinting technique was used to evaluate genetic diversity in C. goeringii cultivars. Twenty-five ISSR primers were selected to produce a total of 224 ISSR loci for evaluation of the genetic diversity. A wide genetic variation was found in the 50 tested cultivars with Nei's gene diversity (H = 0.2241) and 93.75% of polymorphic loci. Fifty cultivars were unequivocally distinguished based on ISSR fingerprinting. Cultivar-specific ISSR markers were identified in seven of 50 tested cultivars. Unweighted pair-group mean analysis (UPGMA) and principal coordinates analysis (PCA) grouped them into two clusters: one composed the cultivars mainly from Japan, and the other contained three major subclusters mainly from China. Two Chinese subclusters were generally consistent with horticultural classification, and the third Chinese subcluster contained cultivars from various horticultural groups. Our results suggest that the ISSR technique provides a powerful tool for cultivar identification and establishment of genetic relationships of cultivars in C. goeringii.

Transcriptome-wide identification of microRNAs and functional insights inferred from microRNA-target pairs in Physalis angulata L.

Physalis angulata L., a member of the family Solanaceae, is widely used as the folk medicine in various countries. Continuous research efforts are devoted to the discovery of the effective medicinal ingredients from Physalis angulata. However, due to the limited resources of genome and transcriptome sequencing data, only a few studies have been performed at the gene regulatory level. In this study, the transcriptomes of five organs (roots, stems, leaves, flowers and fruits) of Physalis angulata were reported. Based on the transcriptome assembly containing 196,117 unique transcripts, a total of 17,556 SSRs (simple sequence repeats) were identified, which could be useful RNA-based barcoding for discrimination of the plants closely relative to Physalis angulata. Additionally, 24 transcripts were discovered to be the potential microRNA (miRNA) precursors which encode a total of 31 distinct mature miRNAs. Some of these precursors showed organ-specific expression patterns. Target prediction revealed 116 miRNA-target pairs, involving 31 miRNAs and 83 target transcripts in Physalis angulata. Taken together, our results could serve as the data resource for in-depth studies on the molecular regulatory mechanisms related to the production of medicinal ingredients in Physalis angulata.