Random Amplified Polymorphic DNA Method Research Articles

Genetic diversity of maize resources revealed by different molecular markers

AbstractMaize (Zea mays L.) is the third most important cereal crop in the world because of its nutritional value and industrial benefits. Molecular markers are used mainly by the breeders to study the genetic variability of genotypes and its application in the breeding process. Two types of molecular markers, 10 random amplified polymorphic DNA (RAPD) primers and 10 start codon target (SCoT) primers, were assayed to determine the genetic diversity of 25 Slovak maize lines and 25 maize cultivars. A high level of polymorphism was found with both RAPD and SCoT markers, which was confirmed by high average polymorphism information content (PIC) values using both techniques. The efficiency of individual marker techniques in the detection of genotype diversity can be compared by calculating the marker index (MI), detecting diversity index (DDI), discriminating power, resolving power (RP) and other indices. A higher MI (11.788), DDI (2.358) and RP (53.08) value was achieved by the SCoT technique compared to the RAPD method. Three joint dendrograms and PCoA plots constructed based on RAPD, SCoT and both methods combined confirmed the unambiguous separation of maize lines and cultivars from each other. The results obtained from the RAPD and SCoT analysis can be used for the selection of potentially suitable biological sources for further marker-assisted breeding.

Estimating the Genetic Diversity of Oranges Citrus spp. in South Sulawesi, Indonesia, Using RAPD Markers

Oranges hold significant economic importance, being cultivated extensively worldwide and having a large global market. Indonesia, ranked eighth globally as a producer of oranges, is one of the countries with high genetic diversity of oranges. This diversity is distributed across various regions of Indonesia, including South Sulawesi. Despite the advancements in DNA-based molecular marker techniques for assessing genetic diversity, information on orange diversity in South Sulawesi is currently unavailable and under-researched. In this study, random amplified polymorphic DNA (RAPD) markers were utilized to analyze the genetic diversity of oranges in five production centers in South Sulawesi. Leaf samples of 13 orange varieties were collected from the five production centers: Pangkep, Sidrap, Bantaeng, North Luwu, and Selayar in South Sulawesi, Indonesia. Genomic DNA extraction from the orange leaves followed the protocol of the DNA Mini Kit Geneaid. DNA amplification was carried out using the RAPD method with 14 primers: OPE-04, OPH-04, OPH-15, OPN-14, OPN-16, OPR-08, OPR-20, OPW-06, OPW-09, OPX-07, OPX-11, OPX-17, UBC-18, and UBC-51. The RAPD primers yielded 109 amplified fragments ranging in size from 200 to 2000 base pairs (bp), and all RAPD primers showed 100% polymorphism. The genetic diversity value (He) of oranges in South Sulawesi was moderate (0.236). Cluster analysis based on a similarity coefficient of 77% divided the 175 orange genotypes into five groups. The most closely related genotypes were SB6 and SB7, exhibiting 100% similarity, followed by genotypes JS8 and JS9 and JS13 and JS17, with genetic similarities exceeding 99% for each pair. Genotypes P9 and SI5 displayed the highest genetic distance, with a similarity coefficient of 57%. The dendrogram diagram can serve as a basis for selecting desired plant traits in the improvement of plant characteristics through both conventional breeding and genetic engineering activities.

Impact of Iron Nanoparticles Application on Date Palm In-vitro Regeneration Stability

The use of nanoparticles is critical in a number of industries, including manufacturing, healthcare, and agriculture. Iron nanoparticles (Fe NPs) are one of the main sources of plant nutrition because they are effective in releasing a variety of pH values. To study the effect of different concentrations of Fe NPs (0, 0.5, 1.0, 2.0, 4.0 ml/l) on the regeneration and rooting of Bartamoda cv. date palm, as well as to ascertain the content of carbohydrates and chlorophyll in shoots, an experiment was conducted at the Central Laboratory for Research and Development of Date Palm, Agricultural Research Center Giza, Egypt. Adding treatments of Fe NPs at 1.0 and 2.0 ml/l to MS medium containing BA at 2.0 mg/l and NAA at 0.5 mg/l significantly enhanced growth (number of shoots/cluster, number of leaves/cluster, and leaf length), according to Results. MS medium supplemented with NAA at 1.0 mg/l and Fe NPs at 1.0 ml/l showed the highest rooting percentage (89.0%). Treating the shoots with varying doses of iron nanoparticles led to a significantly higher iron content compared to the untreated control shoots. The carbohydrate content improved steadily and significantly with increasing Fe NP concentration. Compared with the control group, treatments with Fe NPs at 1.0 and 2.0 ml/l enhanced the levels of chlorophyll a, chlorophyll b, and carotenoids.
 Through the use of random amplified polymorphic DNA (RAPD) profiles, the somaclonal variation in shoots that can be caused by Fe NPs during the multiplication stage was examined. To amplify DNA from various shoots, seven random 10-mer primers were applied. The shoots' RAPD patterns matched those of the original plant mother, proving that Fe NPs did not cause somaclonal variation that could be seen using the RAPD method.

Improved RAPD Method for Candida parapsilosis Fingerprinting

Recently, methods based on the analysis of arbitrarily amplified target sites of genome microorganisms have been extensively applied in microbiological studies, and especially in epidemiological studies. The range of their application is limited by problems with discrimination and reproducibility resulting from a lack of standardized and reliable methods of optimization. The aim of this study was to obtain optimal parameters of the Random Amplified Polymorphic DNA (RAPD) reaction by using an orthogonal array as per the Taguchi and Wu protocol, modified by Cobb and Clark for Candida parapsilosis isolates. High Simpson's index values and low Dice coefficients obtained in this study indicated a high level of interspecies DNA polymorphism between C. parapsilosis strains, and the optimized RAPD method proved useful in the microbiological and epidemiological study.

GENETIC VARIATIONS OF TWO Anguilla SPECIES IN THE WEST COAST OF WEST SUMATRA AND MENTAWAI USING RAPD

Research on the genetic variation of Anguilla spp. in the waters of the West Coast of West Sumatra was carried out from February to June 2022. This study used the RAPD (random amplified polymorphic DNA) method. In this study, two Anguilla species were found, namely A. marmorata and A. bicolor bicolor. The highest heterozygosity value of A. marmorata in the Tarusan River was 0,2018, and A. bicolor bicolor in Mentawai was 0,2340. The values of gene flow (Nm) in A. marmorata and A. bicolor bicolor were 0.7592 and 1.6318. The values of genetic differentiation (GST) in A. marmorata and A. bicolor bicolor were 0.3971 and 0.2345, respectively. This shows that the value of genetic variation of A. marmorata and A. bicolor bicolor in several rivers on the west coast of West Sumatra is low.

Phylogeny Study of 20 Selected Species of Zingiberaceae from Ex situ Collections in Peninsular Malaysia

Zingiberaceae is widely distributed in Malaysia, with 750 species and 31 genera. This family comprises a different number of subfamilies and genera according to different taxonomic classification methods — classical taxonomy: one subfamily and four tribes vs molecular taxonomy: four subfamilies and six tribes. However, the taxonomic classification of Zingiberaceae is still debated, especially the classical taxonomy. It is due to some Zingiberaceae species showing cryptic morphologies that make it difficult to classify them through classical taxonomy, which refers to the unique morphological characteristics of a tribe/species. Therefore, accurate taxonomic classification is required by using a molecular approach. In this study, 20 selected species of Zingiberaceae collected from the Agricultural Conservatory Park, Institute of Bioscience (IBS), Universiti Putra Malaysia (UPM) were taxonomically classified using a molecular method with the help of three random amplified polymorphic DNA (RAPD) and three inter simple sequence repeat (ISSR) markers until the tribe level. The combined RAPD and ISSR unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree was comparable to Zingiberaceae’s current molecular and classical taxonomy. The 20 selected species were grouped into three tribes (Alpinieae, Zingiberaceae, and Globbeae). This finding has contributed additional biological information to better manage the 20 Zingiberaceae species in the Agricultural Conservatory Park, IBS, UPM. Further studies are needed to explore the genetic diversities and properties of Zingiberaceae species.

Development of a SCAR marker linked to fungal pathogenicity of rice blast fungus Magnaporthe Oryzae.

PCR-based molecular approaches including RAPD (random amplified polymorphic DNA), ISSR (inter-simple sequence repeat), and SRAP (sequence-related amplified polymorphism) are commonly used to analyze genetic diversity. The aims of this study are to analyze genetic diversity of M. oryzae isolates using PCR-based molecular approaches such as RAPD, ISSR, and SRAP and to develop SCAR marker linked to the pathogenicity of rice blast fungus. Twenty Magnaporthe oryzae isolates were collected mainly from the south of Vietnam and assessed for genetic variation by RAPD, ISSR, and SRAP methods. The comparison of those methods was conducted based on the number of polymorphic bands, percentage of polymorphism, PIC values, and phylogenetic analysis. Then, sequenced characterized amplified region (SCAR) markers were developed based on specific bands linked to fungal pathogenicity of rice blast fungus, M. oryzae. The results indicated that SRAP markers yielded the greatest number of polymorphic bands (174) and occupied 51.7% with polymorphism information content (PIC) value of 0.66. Additionally, the SRAP approach showed stability and high productivity compared with RAPD and ISSR. The SCAR marker developed from the SRAP method identified the presence of the avirulence AVR-pita1 gene involving fungal pathogenicity that can break down blast resistance in rice cultivars. The consistency of SCAR marker obtained in this study showed its efficiency in rapid in-field detection of fungal pathogenicity. SCAR marker developed from SRAP technique provides a useful tool for improving the efficiency of blast disease management in rice fields.

Microbial community diversity in the soil of Barrientos Island estimated by RAPD and Biolog Ecoplate methods

The diversity of soil microbial communities at Barrientos Island with differents soil characteristics were evaluated using PCR-based method random amplified polymorphic DNA (RAPD) and community level physiological profiles (CLPP) of Biolog Ecoplate. The soils were selected from 17 different locations around Barrientos Island inhabited by different breeders. Shannon-Weaver index and multivariate analysis were performed to characterize variations of soil microbial communities. Both RAPD and CLPP methods exhibited that most soils with different type of rookery and characteristics could possibly affect the DNA sequence diversity and soil microbial diversity. The abandoned type of rookery had the highest Shannon-Weaver index as exhibited by soil sample 445 (3.4 for RAPD) and 450 (3.09 for CLPP). Higher coefficients of DNA sequence similarity were found in soil samples colonized by similar breeders, like soil 442 and 446 (both were active Chinstrap rookery) shared highest similarity in DNA sequences (73.53). The cluster analysis of RAPD profiles by UPGMA and principle component analysis (PCA) of Biolog Ecoplate exhibited similar influence of type of rookery and soil condition towards soil microbial community diversity. The results may suggest that the change in microbial community DNA composition is accompanied with the change in microbial functional properties.

Genetic Kinship of Nilem Fish Strains (Osteochillus hasselti)

The research aims to analyze the kinship of nilem fish strains using RAPD (Random Amplified Polymorphic DNA). This research used exploratory method with descriptive analysis. The primers used in the RAPD method are OPA-02 (5'-TGCCGAGCTG-3 '), OPA-03 (5'-AGTCAGCCAC-'3), OPA-05 (5'-AGGGGTCTTG-3') and OPA-11 (5) 5'- CAATCGCCGT-3 '). The primary optimization results showed that OPA-02 and OPA-11 were the primary primers for detecting polymorphic and monomorphic fragments of the nilem fish genome. Phenograms from the RAPD method that were processed through the NTSYS-pc program showed that the OPA-02 primer was the best primer for nilem kinship analysis. Relationship between red nilem with green nilem is 92%, red nilem and green nilem with mangot nilem are 72% and the three nilem with beureum panon are 12%.

Plant regeneration from hypocotyls of black carrot via direct somatic embryogenesis and determination of its genetic stability by RAPD and iPBS methods

A study was carried out to investigate plant regeneration from hypocotyls of black carrot (Daucus carota spp. sativus), an industrially and medicinally important plant via somatic embryogenesis, and the genetic stability of obtained plantlets with the random amplified polymorphic DNA (RAPD) and inter primer binding sites (iPBS) methods. Hypocotyl explants isolated from in vitro germinated seeds were incubated initially at Murashige and Skoog (MS) medium containing 0.5 mg/L or 1 mg/L 2,4-D for 2 weeks and then at hormone-free MS medium in order to obtain somatic embryos, which were observed after 15 days on the explants. Performed molecular analyses showed that all bands obtained from plantlets through micropropagation were monomorphic. This protocol where black carrot was determined to be clonally reproduced through somatic embryogenesis may lead the way for further research regarding germplasm conservation and breeding studies.

Genetic diversity of pigeon pea (Cajanus cajan (l.) Millsp.) based on molecular characterization using randomly amplified polymorphic DNA (RAPD) markers

Pigeon pea (Cajanus cajan (L.) Millsp.) is an annual leguminous crop (perennial) which has advantages over other local leguminous crops as drought resistant, hold collapsed and strong pods. The research on drought resistance plant is very important to adapt to climate change adverse impact to support food security. The potential of pigeon pie has not been supported by accurate data. To explore the potential of pigeon pea, it is necessary to record the important properties by characterization, one of which is molecular. Increasing genetic diversity can be done through mutation which widely used gamma ray for the induction. The purpose of this study was to identify the genetic diversity of pigeon pea of black, white and brown seeds type resulted by gamma-ray irradiation with a wavelength of 100, 200 and 300 grays by using RAPD method. The experiment resulted 14 bands, 12 of them are polymorphic bands and 2 of them are monomorphic with size varied from 300 bp to 1.3 kbp. The dendrogram showed from 30 accessions are divided into two main clusters, B shows clear genetical divergence from other clusters and some others split randomly. The range of similarity coefficient is from 0.43 to 1.00

Randomly primed improved PCR approach for genetic characterization and identification of Cymbopogon germplasms

Among monocots forming the grass family (Poaceae), Cymbopogon is one of the most important aromatic essential oil yielding genera. Genetic characterization is very important for proper utilization and improvement of the oil grasses. An improved random amplified polymorphic DNA (RAPD) analysis where touchdown polymerase chain reaction with prolonged RAMP time has been used to characterize the genetic variation in ten Indian elite cultivars of Cymbopogon aromatic grasses of essential oil trade types of Citronella, Palmarosa and Lemongrass. The total of 203 amplification products was scored using 23 RAPD primers, exhibiting an overall 92.61% polymorphism. Polymorphic information content (PIC), effective multiplex ratio (EMR), marker index (MI) and resolving power (RP) averaged 0.374, 7.69, 2.92 and 5.15 per primer, respectively, showing the high efficiency and reliability of the markers used. Also, RAPDs of diagnostic and curatorial importance were discerned as ‘stand alone’ molecular descriptors for cultivar and species (biotype) identification. The order of the average value of Jaccard’s coefficient of similarity was found to be C. winterianus (0.890) > C. flexuosus (0.657) > C. martinii (0.425). The present study confirms the significance of the improved RAPD method in genetic characterization of Cymbopogon sp. and can be employed for efficient identification, conservation and utilization of germplasm resources for plant improvement through conventional as well as molecular breeding approaches.

Molecular typing and virulence analysis of multidrug resistant Klebsiella pneumoniae clinical isolates recovered from Egyptian hospitals

Klebsiella pneumonia infection rates have increased dramatically. Molecular typing and virulence analysis are powerful tools that can shed light on Klebsiella pneumonia infections. Whereas 77.7% (28/36) of clinical isolates indicated multidrug resistant (MDR) patterns, 50% (18/36) indicated carpabenem resistance. Gene prevalence for the AcrAB efflux pump (82.14%) was more than that of the mdtK efflux pump (32.14%) in the MDR isolates. FimH-1 and mrkD genes were prevalent in wound and blood isolates. FimH-1 gene was prevalent in sputum while mrkD gene was prevalent in urine. Serum resistance associated with outer membrane protein coding gene (traT) was found in all blood isolates. IucC, entB, and Irp-1 were detected in 32.14%, 78.5% and 10.7% of MDR isolates, respectively. We used two Polymerase Chain Reaction (PCR) analyses: Enterobacterial Repetitive Intergenic Consensus (ERIC) and Random Amplified Polymorphic DNA (RAPD). ERIC-PCR revealed 21 and RAPD-PCR revealed 18 distinct patterns of isolates with similarity ≥80%. ERIC genotyping significantly correlated with resistance patterns and virulence determinants. RAPD genotyping significantly correlated with resistance patterns but not with virulence determinants. Both RAPD and ERIC genotyping methods had no correlation with the capsule types. These findings can help up better predict MDR Klebsiella pneumoniae outbreaks associated with specific genotyping patterns.

English

In this study, the genetic diversity of 6 oak species known as Quercus coccifera L., Q. robur L., Q. infectoria Oliver, Q. cerris L., Q. ithaburensis subsp. macrolepsis (Kotschy) Hedge and Yalt. and Q. trojana P.B. Webb  in 18 populations was screened using the randomly amplified polymorphic DNA method (RAPD).  10 RAPD primers giving the best results produced 262 total loci. The highest and lowest band sizes were between 125 and 1800 bp, respectively. The binary RAPD data was computed using the Statistica version 8.0 and Popgene 32, genetic data analysis software program. The principal component analysis and cluster analysis displayed the seperation of populations based on genetic distances. The genetic similarity and distance matrix using Popgene 32 based on Nei (1972) revealed the genetic relations between studied populations. As a result of this study, it may be expressed that genetic relationships are more similar in the species belonging to same section and especially the relationships between Quercus cerris and Quercus trojana in the section Cerris attracts quite attention. Key words: Cerris, genetic relationships, Quercus, randomly amplified polymorphic DNA method (RAPD).

Molecular characterization of Pasteurella multocida isolates obtained from poultry, ruminant, cats and dogs using RAPD and REP-PCR analysis.

In the present study, Randomly Amplified Polymorphic DNA (RAPD) and Repetitive Extragenic Palindromic sequence-based Polymerase Chain Reaction (REP- PCR) were used to characterize 131 isolates of Pasteurella multocida, originating from different healthy and diseased animal species obtained from several geographical regions of Iran. The RAPD and REP-PCR generated amplified products in the range of 300 to 3400 bp and 200 to 2850 bp, respectively. Among all of the P. multocida isolates, cluster analysis revealed that 63 clusters and nine untypable isolates and 81 clusters and six untypable isolates were produced with RAPD and REP-PCR methods, respectively. The results indicated that the REP-PCR method showed a slightly higher level of discrimination power in differentiating of P. multocida isolates as compared with RAPD. The results showed that a considerable level of genetic diversity exists among P. multocida isolates even in the isolates with the same animal or geographical origins. There was no host- and region-specific pattern. In addition, the isolates obtained from the healthy and diseased animal did not reveal any correlation genotypic profiles, which could be supported by the hypothesis that P. multocida is a strictly opportunistic pathogen. In conclusion, because of a large amount of genetic heterogeneity in the P. multocida isolates, Pasteurellosis may be caused by different clones in the same herd or animal.

Genetic Variability of Macrophomina phaseolina Isolates from Dry Beans in Turkey

Charcoal rot is a soil and seed borne, economically important fungal disease on dry bean in Turkey. Twenty bean isolates of M. phaseolina collected from different locations in Turkey during 2008 and 2012 years were studied for genetic variability using random amplified polymorphic DNA (RAPD) assay, chlorate sensitivity on medium supplemented with 120mM of potassium, phenotype of colony, and pathogenicity. Isolates were identified as M. phaseolina based on morhological features and PCR assays using species-specific primers (MPKF1and MPKR1). Isolates of M. phaseolina were analysed for their aggressiveness on the susceptible bean cv. Akman 98, by soil inoculation method. Isolates exhibiting a dense chlorate phenotype were chlorate-resistant, while those possessing feathery and restricted chlorate phenotypes were chlorate-sensitive. More than half of the isolates (55%) were resistant to chlorate and produced dense phenotype, while 35% isolates showed feathery and two isolates (10%) showed restricted growth. DNA from 20 isolates was subjected to genetic diversity analysis by the RAPD method using 14 randomly chosen 10-base random primers, and low genetic diversity (33.3%) was observed among the tested isolates.

An improved DNA marker technique for genetic characterization using RAMP-PCR with high-GC primers.

Random amplified polymorphic DNA (RAPD) is a widely used molecular marker technique. As traditional RAPD has poor reproducibility and productivity, we previously developed an improved RAPD method (termed RAMP-PCR), which increased the reproducibility, number of bands, and efficiency of studies on polymorphism. To further develop the efficiency of this method, we used high-GC content primers for improved RAMP-PCR with DNA samples from Lonicera japonica. Comparison of amplification profiles obtained by standard RAPD primers with those obtained by regular PCR and RAMP-PCR, and high-GC primers with regular PCR and RAMP-PCR showed that the average number of bands and polymorphisms per primer gradually and significantly increased (from 6.4 to 15.0 and from 4.6 to 10.2, respectively). Cluster dendrograms showed similar results, indicating that this new method is consistent and reproducible. A total of 22 samples from different species, including plants, animals, and humans, were used for RAMP-PCR with high-GC primers. Multiple bands were successfully amplified from all samples, demonstrating that this method is a reliable technique with consistent results and may be of general interest in studies on different genera and species. We developed highly effective DNA markers, which can provide a more effective and potentially valuable approach than traditional RAPD for the genetic identification of various organisms, particularly of medicinal plants.

Direct detection of Burkholderia pseudomallei and biological factors in soil

Burkholderia pseudomallei, a Gram-negative saprophytic bacillus, is a severe infectious agent that causes melioidosis and soil is the most important reservoir. One hundred and forty soil samples were tested for pH, moisture content and total C and N measurements and used for DNA extraction and culture for B. pseudomallei. The quantitative real-time PCR (qPCR) targeting wcbG, a putative capsular polysaccharide biosynthesis protein gene of B. pseudomallei, was developed to detect the bacterium, and random amplified polymorphic DNA (RAPD) was used to detect the microbial diversity in soil. The acidic pH was correlated with the presence of the bacterium. Forty-four soil sites (44/140, 31.4%) were positive for B. pseudomallei by qPCR, of which 21 were positive by culture. The limit of detection is 32 fg of DNA (about 4 genomes). The RAPD method could classify the soil samples into low diversity (LD) and high diversity (HD) sites. The trend of LD was found with B. pseudomallei positive soil sites. The acidity of the soil or metabolites from organisms in the sites may contribute to the presence of the bacterium. Further investigation of microbes by a more robust method should elucidate biological factors that promote the presence of B. pseudomallei and may be used for controlling the bacterium in the environment.

High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers

The genetic diversity in Zanthoxylum species viz. Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r=0.65612).

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.