Genetic characterization and authentication of Lonicera japonica Thunb. by using improved RAPD analysis

A lack of population structure characterizes the invasive Lonicera japonica in West Virginia and across eastern North America

Invasive plant species cause massive ecosystem damage globally, yet represent powerful case studies in population genetics and rapid adaptation to new habitats. The availability of digitized herbarium collections data, and the ubiquity of invasive species across the landscape make them highly accessible for studies of invasion history and population dynamics associated with their introduction, establishment, spread, and ecological interactions. Here we focus on Lonicera japonica, one of the most damaging invasive vine species in North America. We leveraged digitized collections data and contemporary field collections to reconstruct the invasion history and characterize patterns of genomic variation in the eastern USA, using a straightforward method for generating nucleotide polymorphism data and a recently published, chromosome-level genome for the species. We found an overall lack of population structure among sites in northern West Virginia, USA, as well as across sites in the central and eastern USA. Heterozygosity and population differentiation were both low based on Fst, analysis of molecular variance, principal components analysis, and cluster-based analyses. We also found evidence of high inbreeding coefficients and significant linkage disequilibrium, in line with the ability of this otherwise outcrossing, perennial species to propagate vegetatively. Our findings corroborate earlier studies based on allozyme data, and suggest that intentional, human-assisted spread explains the lack of population structure, as this species was planted for erosion control and as an ornamental, escaping cultivation repeatedly across the USA. Finally, we discuss how plant invasion genomics can be incorporated into experiential undergraduate education as a way to integrate teaching and research.

Identification of SCAR markers for genetic authentication of Dendrobium nobile Lindl

Dendrobium nobile Lindl. is an orcid plant with important medicinal values. This is a colourful houseplant, and also a popular herb in traditional Chinese medicine (TCM). The variants of this plant from different geographic regions might be high, and in this study, we aimed to develop specific sequence characterized amplified region (SCAR) markers for the identification of specific variant of this plant. Different cultivars of D. nobile were collected from nine different places of China, and one cultivar from Myanmar. DNA materials were extracted from the plant samples, random amplified polymorphic DNA (RAPD) were developed, cloned and sequenced for the development of SCAR markers. We have developed four SCAR markers, which are specific to the cultivar from Luzhou China, and clearly distinguishable (genetically) from other cultivars. These SCAR markers are deposited in GenBank (accession number MZ417502, MZ484089, MZ417504 and MZ417505). Four SCAR markers for D. nobile are effective molecular technique to genetically identify the different cultivars or species, and this method is applicable for genetic characterization and identification of other plant species too.

Fingerprinting, structure, and genetic relationships among selected accessions of blue honeysuckle (Lonicera caerulea L.) from European collections

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Scarcely on December 13, 2018, L. caerulea fruits were included in the list of novel foods in EU.

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Hence, the growing interest in L. caerulea extends to its genome.

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R-ISSR explores other than the RAPD, ISSR, AFLP, and RFLP techniques part of genome and analyze other range of genetic variability.

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R-ISSR markers could be used for Lonicera core germplasm collection, development of SCARs, genetic map construction, barcoding, protection of variety rights, MAS, and genomic selection.

Due to its value and economic importance, the genome of Lonicera caerulea L. has been widely studied in various fields of science. In this study the genetic structure and relationships between 24 accessions of L. caerulea of different origins were assessed. A total of 692, 814, and 258 loci were amplified using 43 RAPD (random amplified polymorphic DNA), 40 ISSR (intersimple sequence repeat), and 20 R-ISSR (RAPD+ISSR) primers, respectively. Among the amplified loci, 66–78% were polymorphic and 12–20% were private. Selected R-ISSR sequences were detected in Lonicera japonica transcripts. Cluster and STRUCTURE analyses performed for each of the techniques revealed the existing differences and unknown similarities between the genotypes. The r-factor values calculated in the Mantel test indicated highly significant positive correlations between the Nei distance matrices, similar to the F_ST values (F_{ST_RAPD} = 0.223, F_{ST_ISSR} = 0.279, F_{ST_R-ISSR} = 0.363) determined in the analysis of molecular variance. It was found that 78%, 72%, and 64% of the genetic variations were related to the differences observed within the populations, which suggest that the variations are mainly reflected in the differences among the genotypes. The principal coordinate analysis showed greater differences between the mean distances of the Lonicera genotype pair and the actual distances of the same pairs on the Nei matrix compared to multidimensional scaling. These differences were 45%, 56%, and 42% higher for RAPD, ISSR and R-ISSR, respectively.

Genetic Analysis of Prunus salicina L. by Random Amplified Polymorphic DNA (RAPD) and Intersimple Sequence Repeat (ISSR)

Background

Prunus salicina L. is an important fruit tree species of great economic value which is mainly distributed in the northern hemisphere.

Methods

25 samples of Prunus salicina L. were collected from 8 provinces in China, Japan, USA, and New Zealand. The genetic variations of these samples were characterized by the random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) technique, respectively, and in combination.

Results

Totally, 257 RAPD bands ranging 200∼2300 bp was found, and 81.59% of these bands were polymorphic. ISSR analysis identified 179 bands ranging 300∼2500 bp, and 87.74% of the bands were polymorphic. ISSR results showed that the similarity coefficient index between samples P10 (Maihuangli in Anhui, Chin) and P13 (Longyuanqiuli in Heilongjiang, China) was lowest, while that between samples P10 (Maihuangli in Anhui, Chin) and P15 (Baili in Japan) was highest. Combined analysis of RAPD and ISSR demonstrated that the similarity coefficient index between samples P4 (Qiepili in Ningbo, Zhejiang, China) and P13 (Longyuanqiuli in Heilongjiang, China) was lowest, while that between samples P19 (Laroda in USA) and P20 (Red heart in USA) was highest.

Conclusion

RAPD combined with ISSR analysis can be used for genetic characterization of Prunus L. species.

SCAR marker for identification and discrimination of specific medicinal Lycium chinense Miller from Lycium species from ramp-PCR RAPD fragments

In the current study, ramp-PCR fragments from improved RAPD (random amplified polymorphic DNA) amplification of Lycium (Goji) species or cultivars were cut and cloned into the vector of pGEM-T. A positive clone 10-5 was screened by PCR amplification, enzymatic digestion, and Sanger sequencing. A SCAR (sequence-characterized amplified region) marker, named Goji 10-5, with 949 nucleotides in length, was identified. Goji 10-5 is specific to Goji species Lycium chinense Miller from Jiangxi in China and Texas in the USA. A BLAST search of this nucleotide sequence in the GenBank database indicated that it shows no identity with any other species, including no any other Lycium species. As a new sequence, we have deposited it in the GenBank database with accession No. MN862323. PCR assays were developed and converted the nucleotide sequence to become a novel molecular marker for Lycium chinense Miller, named Goji 10-5. This marker may be used for the genetic identification of other samples. This study has successfully developed Goji 10-5, a specific SCAR marker to identify L. chinense and distinguish it from other species, including other Lycium species from different locations.

Wound Healing and the Use of Medicinal Plants

Cutaneous wound healing is the process by which skin repairs itself. It is generally accepted that cutaneous wound healing can be divided into 4 phases: haemostasis, inflammation, proliferation, and remodelling. In humans, keratinocytes re-form a functional epidermis (reepithelialization) as rapidly as possible, closing the wound and reestablishing tissue homeostasis. Dermal fibroblasts migrate into the wound bed and proliferate, creating “granulation tissue” rich in extracellular matrix proteins and supporting the growth of new blood vessels. Ultimately, this is remodelled over an extended period, returning the injured tissue to a state similar to that before injury. Dysregulation in any phase of the wound healing cascade delays healing and may result in various skin pathologies, including nonhealing, or chronic ulceration. Indigenous and traditional medicines make extensive use of natural products and derivatives of natural products and provide more than half of all medicines consumed today throughout the world. Recognising the important role traditional medicine continues to play, we have undertaken an extensive survey of literature reporting the use of medical plants and plant-based products for cutaneous wounds. We describe the active ingredients, bioactivities, clinical uses, formulations, methods of preparation, and clinical value of 36 medical plant species. Several species stand out, including Centella asiatica, Curcuma longa, and Paeonia suffruticosa, which are popular wound healing products used by several cultures and ethnic groups. The popularity and evidence of continued use clearly indicates that there are still lessons to be learned from traditional practices. Hidden in the myriad of natural products and derivatives from natural products are undescribed reagents, unexplored combinations, and adjunct compounds that could have a place in the contemporary therapeutic inventory.

SCAR marker for Phytophthora nicotianae and a multiplex PCR assay for simultaneous detection of P. nicotianae and Candidatus Liberibacter asiaticus in citrus

AIMS

This study aimed to develop a random amplified polymorphic DNA (RAPD)-based sequence characterized amplified region (SCAR) marker for species-specific detection of Phytophthora nicotianae, a global plant pathogen. Another objective was to develop a multiplex PCR assay for simultaneous detection of P. nicotianae and huanglongbing-causing bacterium, Candidatus Liberibacter asiaticus (CaLas) in citrus roots using the developed SCAR marker and a previously published 16SrDNA-based CaLas-specific primer set.

METHODS AND RESULTS

The RAPD primer, OPA4, amplified a specific fragment of c. 400 bp only in P. nicotianae isolates. The fragment was eluted, purified, cloned and sequenced. One set of SCAR primers (SCAR4F/SCAR4R1), developed from the sequence information of the fragment, was found specific to P. nicotianae and produced an amplicon of 330 bp size, and was found non-specific to the five Phytophthora species (P. citrophthora, P. palmivora, P. lacustris, P. boehmeriae and P. insolita) and five other pathogens (Mycosphaerella citri, Alternaria alternata, Septobasidium pseudopedicillatum, Phytopythium vexans and Colletotrichum gloeosporioides) isolated from the citrus agroecosystem. The sensitivity of the primer pair was 5 pg µl^-1 of mycelial DNA. Furthermore, the specific SCAR primers coupled with a previously reported CaLas-specific primer set were used effectively in developing a multiplex PCR assay to detect P. nicotianae and CaLas simultaneously in root tissues of citrus plants.

CONCLUSIONS

A rapid method using a RAPD-based SCAR marker for the detection of P. nicotianae was developed. Furthermore, a multiplex PCR assay was established for simultaneous detection of P. nicotianae and CaLas in citrus roots.

SIGNIFICANCE AND IMPACT OF THE STUDY

A RAPD-SCAR marker-based detection system and the one-step multiplex PCR method developed in this study can be applied to index citrus trees infected (individually or conjointly) with P. nicotianae and CaLas. The present technique developed would also be useful in monitoring disease epidemiology and phytosanitary surveillance.

Evaluation of genetic diversity of edible honeysuckle monitored by RAPD in relation to bioactive substances

The aim of this study was clarifying the relation between genetic diversity of edible honeysuckle (Lonicera kamtschatica) and the major group of biologically active substances as total polyphenols content (TPC) including antioxidant activity (AO). Fruits of edible honeysuckle becomes more and more popular, especially in Europe. The current status of research on polyphenolic compounds in the berries of edible honeysuckle and their biological effects, including recommended utilization, are reviewed.The biological material including 14 cultivars of the edible honeysuckle (´Zoluška´, ´Amfora´, ´Pruhonický 44´, ´Vasilijevsky´, ´Moskovskaja´, ´Vojtek´, ´Sinoglaska´, ´Altaj´, ´Lipnická´, ´Kamčadalka´, ´Sinaja Ptica´, ´Fialka´, ´Modrý Triumf´, and ´Leningradský velikán´) originated from Czech republic (Žabcice near Brno). The content of TPC and AO were determined by location and its soil-climatic conditions and these environmental circumstances determines the RAPD profiles of analysed honeysuckle acessions, too. DPPH method was used to analyze AO and Folin-Ciocalteu method was used to determine TPC. The results of experiment showed that the highest value of AO was determined at the cultivars ´Zoluška´ (81.04 mg.L-1) and the lowest was measured in ´Kamčadalka´ (54.122 mg.L-1).  On the contrary, the highest content of TPC was determined at the cultivar ´Kamčadalka´ (51.09 mg.L-1) and the lowest value was measured at the cultivar ´Pruhonický 44´ (21.65 mg.L-1). Phylogenetic trees were similar in genetic distance. The  content of TPC and AO were  not statistically significant in relation to cultivar. The analyzed cultivars of the edible honeysuckle were separated in 4 clusters according to used primers. In both  gel images, the amplicon size ranged from 100 to 1,500 bp. We found that genetic diversity was partially related to content of total polyphenolic substances and antioxidant activity. Based on phylogenetic trees we have stated that variety ´Lipnická´, ´Sinoglaska´, ´Altaj´, ´Leningradský velikán´, ´Modrý Triumf´, ´Sinaja Ptica´ and ´Kamčadalka´ were grouped in the similar cluster. The highest genetic distance was determined at the variety ´Vasilijevskaja´ and ´Amfora´. In the same way, there were variety ´Vojtek´, ´Fialka´ and ´Zoluška´.

Characterization and molecular cloning of novel isoforms of human spermatogenesis associated gene SPATA3

This study aimed to clone and characterize novel isoforms of the human SPATA3 gene. The isoforms of SPATA3 gene was cloned into pGMT vector using human testis cDNA as template, and Sanger sequencing was performed. Their characterizations and tissue-specific expression profiles were analyzed. The two novel isoforms were successfully cloned and deposited into GenBank as MG029442 (AYP71042) and MG029443 (AYP71043) respectively. Isoforms SPATA3-I1 and SPATA3-I2 were found with higher identity, where only 7 amino acids missed at N-terminus in SPATA3-I2, whereas SPATA3-I3 and SPATA3-I4 had more C-terminus deletion but in SPATA3-I3 no amino acid missed at N-terminus. Importantly, we found the characterization of QQPSPESTP domain with two repeats for isoforms SPATA3-I1 and SPATA3-I4, whereas three repeats for isoforms SPATA3-I1 and SPATA3-I2. The SPATA3 family of genes is orthologous conserved; the similar core PEST domain was also revealed with variable repeats, indicating that this domain may pay roles in the spermatogenesis and male development differently. Furthermore, RNA-seq data indicated that the SPATA3 gene is only expressed in testis. This further suggests that SPATA3 plays potential roles only in male development, spermatogenesis or spermatogenesis cell apoptosis. Thus, in this study we cloned the two novel isoforms of SPATA3, SPATA3-I3 and SPATA3-I4, and found interesting characteristic PEST domain (QQPSPESTP) conserved in different isoforms as well as in different species. SPATA3 is an essential gene and may functions in male reproductive system, specifically in spermatogenesis.

Evaluation genotypes of cancer cell lines HCC1954 and SiHa by short tandem repeat (STR) analysis and DNA sequencing

Cancer cell lines are used worldwide in biomedical researches, and data interpretation solely depends on unambiguous attribution of those respective cell lines to its original sources. Approximately one-third of all cell lines have an origin other than that assumed, leading to invalid results. It is necessary to characterize the origin of cell lines. Short-tandem-repeat (STR) fingerprinting (DNA fingerprinting) is the method for characterization of genetic identity in cultured cell lines under certain experimental conditions. We showed the fingerprinting profiles in a summed and unidentified human cancer cell line comparison to HCC1954 cell line, revealing marked alterations in DNA fingerprinting profiles up to fourteen STR loci from 16 loci. Furthermore, Sanger DNA sequencing showed no c.3140A > G heterozygous mutation in the PIK3CA gene of this suspected HCC1954 cell line. In addition, we showed the fingerprinting profiles in an unidentified cancer cell line comparison to SiHa cervical cell line, revealing same DNA fingerprinting profiles. In conclusion, we have successfully authenticated and identified both suspected HCC1954 and SiHa cell lines by STR analysis and DNA sequencing. STR analysis combined DNA sequencing may be very useful to evaluate genotypes of cancer cell lines in our cancer studies, as well as in judicial authentication and forensic sciences.

Molecular authentication of Anthemis deserti Boiss. (Asteraceae) based on ITS2 region of nrDNA gene sequence

The dried plant material of medicinally important Anthemis deserti Boiss. (family: Asteraceae) especially when it remains in the powdered form often look similar to Anthemis melampodina Del.; and therefore, difficult to distinguish, finally lead to chances of adulteration. The adulteration in medicinal plants effects on the efficacy of the drugs. The molecular authentication of herbal plant materials such as based on the internal transcribed spacer 2 (ITS2) sequences of nuclear ribosomal DNA (nrDNA) is considered as more reliable method compared to other the biochemical or histological methods. The present study aims to molecular authentication ofA. deserti based on molecular phylogenetic analyses of ITS2 gene sequence of nrDNA region. The ITS2 region of nrDNA of A. deserti were sequenced, and the molecular phylogenetic analyses were performed together with the GenBank sequences. The Maximum Parsimony tree revealed the close relationships of A. deserti with A. melampodina; however, the Neighbor-Joining and Maximum Likelihood tree clearly revealed that A. deserti is distinct from A. melampodina, which is also supported by the differences in nucleotides at five diffident positions (i.e. 22, 28, 87, 175 and 198) in the DNA sequence alignment.

Development of diagnostic SCAR markers for genomic DNA amplifications in breast carcinoma by DNA cloning of high-GC RAMP-PCR fragments

Cancer is genetically heterogeneous regarding to molecular genetic characteristics and pathogenic pathways. A wide spectrum of biomarkers, including DNA markers, is used in determining genomic instability, molecular subtype determination and disease prognosis, and estimating sensitivity to different drugs in clinical practice. In a previous study, we developed highly effective DNA markers using improved random amplified polymorphic DNA (RAPD) with high-GC primers, which is a valuable approach for the genetic authentication of medicinal plants. In this study, we applied this effective DNA marker technique to generate genetic fingerprints that detect genomic alterations in human breast cancer tissues and then developed sequence-characterized amplified region (SCAR) markers. Three SCAR markers (BC10-1, BC13-4 and BC31-2) had high levels of genomic DNA amplification in breast cancer. The PHKG2 and RNF40 genes are either overlapping or close to the sequences of SCAR marker BC13-4, while SCAR marker BC10-1 is in the intron and overlap the DPEP1 gene, suggesting that alterations in the expression of these genes could contribute to cancer progression. Screening of breast cancer cell lines showed that the mRNA expression levels for the PHKG2 and DPEP1 were lower in non-tumorigenic mammary epithelial cell MCF10A, but elevated in other cell lines. The DPEP1 mRNA level in invasive ductal carcinoma specimens was significantly higher than that of the adjacent normal tissues in women. Taken together, high-GC RAMP-PCR provides greater efficacy in measuring genomic DNA amplifications, deletion or copy number variations. Furthermore, SCAR markers BC10-1 and BC13-4 might be useful diagnostic markers for breast cancer carcinomas.

Evaluation of amplification refractory mutation system (ARMS) technique for quick and accurate prenatal gene diagnosis of CHM variant in choroideremia

Choroideremia is a rare X-linked recessive inherited disorder that causes chorioretinal dystrophy leading to visual impairment in its early stages which finally causes total blindness in the affected person. It is caused due to mutations in the CHM gene. In this study, we have recruited a pedigree with choroideremia and detected a nonsense variant (c.C799T:p.R267X) in CHM of the proband (I:1). Different primer sets for amplification refractory mutation system (ARMS) were designed and PCR conditions were optimized. Then, we evaluated the sequence variant in the patient, carrier, and a fetus by using ARMS technique to identify if they inherited the pathogenic gene from parental generation; we used amniotic fluid DNA for the diagnosis of the gene in the fetus. The primer pairs, WT2+C and MT+C, amplified high specific products in different DNAs which were verified by Sanger sequencing. Based on our results, ARMS technique is fast, accurate, and reliable prenatal gene diagnostic tool to assess CHM variants. Taken together, our study indicates that ARMS technique can be used as a potential molecular tool in the diagnosis of prenatal mutation for choroideremia as well as other genetic diseases in undeveloped and developing countries, where there might be shortage of medical resources and supplies.

Genetic analysis of Canarium album in different areas of China by improved RAPD and ISSR

To lay the foundation of the classification of Canarium album (C. album), and C. album from Terminalia Chebula (T. chebula) in different areas of China, improved RAPD and ISSR analysis were performed to analyze polymorphism and genetic relationship. Ten samples were collected from different locations in China. A total of 221 fragments were detected by improved RAPD, out of which polymorphic fragments accounted for 82.3% with average amplification bands of 10.05 per primer. ISSR markers revealed a total of 147 alleles, where polymorphic fragments accounted for 83.5%, with average amplification bands of 7.35 per primer. The sizes of fragments ranged from 200 to 2500bp and from 150 to 2000bp in RAPD and ISSR markers, respectively. The similarity coefficient ranged from 0.46 to 0.86 with RAPD markers and 0.36 to 0.89 with ISSR markers. The results indicated that improved RAPD and ISSR methods are useful for genetic diversity study of C. album. Thus, this study provides us the theoretical basis for the breeding and classification of C. album in South and Southwest China.

Validation of Suitable Reference Genes for Assessing Gene Expression of MicroRNAs in Lonicera japonica

MicroRNAs (miRNAs), which play crucial regulatory roles in plant secondary metabolism and responses to the environment, could be developed as promising biomarkers for different varieties and production areas of herbal medicines. However, limited information is available for miRNAs from Lonicera japonica, which is widely used in East Asian countries owing to various pharmaceutically active secondary metabolites. Selection of suitable reference genes for quantification of target miRNA expression through quantitative real-time (qRT)-PCR is important for elucidating the molecular mechanisms of secondary metabolic regulation in different tissues and varieties of L. japonica. For precise normalization of gene expression data in L. japonica, 16 candidate miRNAs were examined in three tissues, as well as 21 cultivated varieties collected from 16 production areas, using GeNorm, NormFinder, and RefFinder algorithms. Our results revealed combination of u534122 and u3868172 as the best reference genes across all samples. Their specificity was confirmed by detecting the cycling threshold (C t) value ranges in different varieties of L. japonica collected from diverse production areas, suggesting the use of these two reference miRNAs is sufficient for accurate transcript normalization with different tissues, varieties, and production areas. To our knowledge, this is the first report on validation of reference miRNAs in honeysuckle (Lonicera spp.). Restuls from this study can further facilitate discovery of functional regulatory miRNAs in different varieties of L. japonica.

Authentication of medicinal plants by DNA markers

Medicinal plants have been used worldwide for centuries to maintain health and to treat diseases, more so chronic diseases. However, adulteration and use of spurious materials as substitutes have become a major concern for users and industry for reasons of safety and efficacy. Therefore, authentication of medicinal plants is of utmost importance. Morphological, anatomical, chemical and DNA markers solve the problem by differentiating the genuine material from the adulterants, substitutes and spurious drugs. DNA markers use nucleotide sequences to identify species; it takes preference over the other two markers being not age dependent, tissue specific and having a higher discriminating power. Therefore, characterization of plants with such markers is an ideal approach for identification of medicinal plant species and populations/varieties of the same species. Availability of certified taxonomic specimens in herbaria is certainly required for unambiguous confirmation through final visual comparison and analysis.

Genetic Authentication of Gardenia jasminoides Ellis var. grandiflora Nakai by Improved RAPD-Derived DNA Markers

The evergreen shrub, Gardenia jasminoides Ellis var. grandiflora Nakai is one of the most popular garden-plants, with significant ornamental importance. Here, we have cloned improved random amplified polymorphic DNA (RAPD) derived fragments into T-vector, and developed sequence-characterized amplified region (SCAR) markers. These markers have been deposited in GenBank database with the accession numbers KP641310, KP641311, KP641312 and KP641313 respectively. The BLAST search of database confirmed the novelty of these markers. The four SCAR markers, namely ZZH11, ZZH31, ZZH41 and ZZH51 can specifically recognize the genetic materials of G. jasminoides from other plant species. Moreover, SCAR marker ZZH31 can be used to distinguish G. jasminoides Ellis var. grandiflora Nakai from other G. jasminoides on the market. Together, this study has developed four stably molecular SCAR markers by improved RAPD-derived DNA markers for the genetic identification and authentication, and for ecological conservation of medicinal and ornamental plant G. jasminoides.

Development of SCAR Markers Based on Improved RAPD Amplification Fragments and Molecular Cloning for Authentication of Herbal Medicines Angelica sinensis, Angelica acutiloba and Levisticum officinale

Molecular cloning from DNA fragments of improved RAPD amplification of Angelica sinensis, Angelica acutiloba and Levisticum officinale, provided novel sequence-characterized amplified region (SCAR) markers A13, A23, Al-34 and Al-0 whose sequences were deposited in the GenBank database with the accession numbers KP641315, KP641316, KP641317 and KP641318, respectively. By optional PCR amplification, the SCAR markers A13 and A23 are Levisticum officinale-specific, whereas the SCAR marker Al-34 is Angelica acutiloba-specific, and the SCAR marker Al-0 is Angelica sinensis-specific. These diagnostic SCAR markers may be useful for genetic authentications, for ecological conservation of all three medicinal plants and as a helpful tool for the genetic authentication of adulterant samples.

Genetic analysis of litchi (Litchi chinensis Sonn.) in southern China by improved random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR)

Litchi (Litchi chinensis Sonn., L. chinensis), a type of tree growing in most areas of southern China, produces an edible fruit that is also a source of traditional medicine. Genetic identification of litchi species or cultivars using molecular markers is very important. In this study, a total of six litchi samples from Fujian, Hainan, Guangdong, Guangxi and Sichuan province, as well as one wild Dimocarpus confinis (D. confinis) sample from Guangxi province were collected for genetic analysis. The cluster dendrograms were constructed for genetic analysis on the basis of DNA amplification results by RAPD and ISSR. The improved RAPD amplified DNA with consistent and clear banding patterns. A total of 176 bands were found, indicating a 72.7 % polymorphism in L. chinensis DNA samples. Significant genetic distances were found among the different species or cultivars, with an index of similarity coefficient ranging from 0.59 to 0.87. Similar to RAPD results, ISSR analysis of the L. chinensis DNA samples showed a range of 0.70-0.93 similarity coefficients. The genetic distance between Hainan sample and Sichuan samples was the farthest, which is consistent with their geographic distance. Furthermore, the index of similarity coefficient between D. confinis and L. chinensis was 0.35-0.41 by RAPD and 0.38-0.48 by ISSR, indicating that these two species have significant genetic difference. This study reveals the high level of genetic differences between different litchi species or cultivars, and confirms the significance of the improved RAPD method in genetic characterization of organisms. Taken together, the improved RAPD combined with ISSR analysis can be used frequently for the genetic diversity, germplasm resources preservation, molecular-assisted breeding, and genetic characterization of various organisms.

Molecular cloning and development of RAPD-SCAR markers for Dimocarpus longan variety authentication

As an edible fruit and source of traditional medicine, D. longan is grown in most areas of Southern China. Identification of D. longan cultivars by using molecular markers is important genetically. In this study, we cloned fragments from improved randomly amplified polymorphic DNA (RAPD), and developed stably diagnostic sequence-characterized amplified region (SCAR) markers. The specific RAPD bands of D. longan cultivars from Guangxi, with size ranging from 500 bp to 900 bp were gel-purified, cloned and sequenced. Four clones named LY2-1, LY4-7, LY4-8 and LY5-2 were identified. In order to investigate whether the fragments were specific for the species, four pairs of SCAR primers were then designed. PCR amplifications were conducted to analyze 18 samples including different D. longan cultivars and other species. The specific bands with expected sizes were amplified in five D. longan samples but not in others. To identify and characterize the difference between D. longan and D. confinis, PCR amplifications were performed again. The specific bands with expected sizes were found in D. longan but not in D. confinis by SCAR markers LY2-1, LY4-7 and LY5-2, respectively. These results showed that our developed SCAR markers could be very useful as a specific D. longan variety authentication. Therefore, our study provides an effective and precise PCR-based diagnostic method and markers to identify D. longan species.