Amplified Fragment Length Polymorphism Primer Pairs Research Articles

Genetic variation of Anoectochilus formosanus revealed by ISSR and AFLP analysis

Anoectochilus formosanus is an expensive medicinal folk herb in Taiwan. The plant has been used to treat hypertension, diabetes, and hepatitis by native people for a long time. In this study, 4 typical lines of A. formosanus, red-stem, green-stem, narrow-leaf, and round-leaf, were collected and screened to identify the line-specific SSR (single sequence repeat) markers. In addition, we found the narrow-leaf line exhibited the highest polysaccharide content (3.39 ± 0.74%, polysaccharide wt/plant dried wt) which is more than twofold of the lowest content of the red-stem line (1.27 + 0.41%). In the culture program construction, the extent of the somaclonal variation among 20 regenerated shoots from the same parental individual of a narrow-leaf line was revealed using the amplified fragment length polymorphism (AFLP) technique. The aim of this study is to preliminarily investigate the genetic variation of A. formosanus through polymorphic marker screening, which will benefit to the cultivation of A. formosanus with high polysaccharide content in future work. The results showed that 6 out of 81 primers screened, generating a total of 26 markers, were able to differentiate the 4 lines in the inter single sequence repeat (ISSR) analysis. On the other hand, 17 sets of AFLP primers were chosen to detect the somatic variation among the excised shoots derived from the same individual. The genetic variation among the regenerated shoots ranged from 0.00% to 5.43%. The primer pair B6 exerts the most powerful selection ability in the AFLP analysis among 20 somaclonal samples used, whereas the E4 primer pair the lowest. The AFLP primer pairs become useful tools for selecting the lowest somaclonal variation from the regenerated shoots of A. formosanus under the tissue culture program.

Biodiversity status of Tulipa (Liliaceae) in Iran inferred from molecular characterization

Here, we used data generated from amplified fragment length polymorphism (AFLP) analysis to address the biodiversity status and taxonomic relationships among 47 wild accessions representing 9 species of the genus Tulipa in Iran. A high level of genetic diversity within the genus was observed; the most distant taxa were T. humilis and T. schrenkii, while the highest degree of similarity was found between T. montana and T. biflora. Twelve AFLP primer sets amplified 342 fragments, of which 304 were polymorphic (88.1%). The average number of polymorphic bands per AFLP primer pair was 28.5. A hierarchical cluster analysis was carried out on the genetic profile of the taxa, and the results mostly reconfirmed the recognized taxonomy of the genus. However, we found evidence for recognition of a new subgenus for T. biebersteiniana.

Genetic diversity and population structure of endangered Glehnia littoralis (Apiaceae) in China based on AFLP analysis

Genetic diversity studies of endangered plants help to understand the endangering causes and evolutionary history of species. To provide reliable data on the protection of the endangered species Glehnia littoralis, we assessed its genetic diversity and genetic structure based on amplified fragment length polymorphism (AFLP). A total of 127 individuals from 9 wild populations were detected by 10 pairs of AFLP primers. The results showed high levels of genetic diversity in G. littoralis. Ten primer combinations produced a total of 1929 DNA bands with a polymorphic frequency of 100%. The overall gene diversity (Ht) was 0.182, average gene diversity within populations (Hw) was 0.168, Nei’s genetic diversity (Hj) of different populations ranged from 0.142 (Zh15) to 0.1908 (Gld15), and Shannon’s information index (I) was 0.238. The analysis of molecular variance (AMOVA) revealed that the variation within populations accounted for 84.2% of the total variation, indicating the differentiation mainly existed within populations. The gene flow (Nm) among populations was 2.665, revealing more gene communication between populations. The UPGMA cluster analysis, the principal coordinate analysis (PCoA), and the result of mantel test (r = −0.0898, p = 0.259) all showed that there was no obvious correlation between genetic distance and geographical distribution. In conclusion, we speculate that the endangered status of this species could be attributed to the destruction of wildlife habitats rather than to the loss of genetic diversity. Therefore, we suggest strengthening the germplasm resources conservation and doing ecological conservation and restoration work to protect the wild populations of G. littoralis.

Genetic diversity and relationship of sainfoin (Onobrychis viciifolia Scop.) germplasm as revealed by amplified fragment length polymorphism markers

Sainfoin (Onobrychis viciifolia Scop.) is a perennial forage legume widely distributed in the northern temperate regions of the world. Its genetic improvement has been relatively slow due, in part, to the lack of genetic information including molecular characterization of sainfoin germplasm. An attempt was made to evaluate genetic diversity and relationships among 38 sainfoin accessions collected from different regions of the world using amplified fragment length polymorphism (AFLP) markers. Five AFLP primer pairs were used to assess 367 individual plants, which produced 1042 polymorphic AFLP bands. The frequencies of the scored bands in all assayed individuals ranged from 0.003 to 0.973, with a mean value of 0.165. The analysis of molecular variance revealed higher within-accession (84.3%) genetic variation than among accessions (15.7%). The genetic distance based on inter-accession distance matrices was significant for most accessions but was not significant for accessions sharing similar parents. A dendrogram of the collected accessions showed two clusters at an inter-accession genetic distance coefficient of 0.36. The revealed information on genetic distance and genetic diversity of the sainfoin accessions is useful for selecting genetically diverse germplasms for sainfoin genetic improvement efforts.

Genetic structure of phenotypic variants and somaclones of the genus Cereus (Cactaceae) as revealed by AFLP markers

ABSTRACTThe amplified fragment length polymorphism (AFLP) technique was used to investigate the genetic relationship among somaclonal variants and cultivated varieties of Cereus at the molecular level. Samples of tortuosus and monstruosus varieties, as well as cacti with typical erect shoots, monstruosus somaclones, and somaclones with erect shoots were analyzed using six AFLP primer pairs. The highest value for genetic diversity was detected among the monstruosus somaclones. High identity values were detected among erect, monstruosus, and tortuosus varieties as well as among erect and monstruosus somaclones. The AFLP markers revealed divergences in the in vitro cultures and in the natural environment (in vivo), and also illustrated the potential of the monstruosus and tortuosus varieties as well as the Cereus somaclones for generating new varieties of ornamental value.

Genotyping of Individually Isolated gametes from Gossypium hirsutum Chromosome Substitution Lines

As an important crop for US agricultural security and sustainable agriculture, cotton genetic improvement requires development of innovative analytical tools. Genetic analyses based on individual gametes provide several advantages including minimum sample requirement, genetic identification of male parent and overcoming the complexity of polyploidy due to haploid nature of microspores. This research used tetraploid cotton (G. hirsutum x G. barbadense) chromosome substitution (CS) lines with G. barbadense chromosomes 17 and 25 in G. hirsutum background. The individually isolated pollen grains were germinated to release their DNAs and genomic DNA was increased by modified primer extension pre-amplification (PEP) using MasterAmp™ Extra-Long PCR Kit (EPICENTRE®, Madison, WI). Also from select cotton lines, microspores just released from tetrad developmental stage were individually isolated and gamete DNA was extracted as well as amplified through multiple displacement amplification (MDA) using REPLI-g Single Cell Kit (QIAGEN, Valencia, CA). The parental samples along with PEP and MDA amplified individual gamete DNAs were then analyzed using simple sequence repeat (SSR) as well as IRD800 and IRD-700 labeled (Li-Cor, Lincoln, NE) amplified fragment length polymorphism (AFLP) methods. Nineteen SSR and 28 AFLP primer pairs were used to analyze TM-1, 3-79, CS-B17 and CS-B25 cotton lines. The amplification of parental SSR and AFLP markers from both mature pollen as well as early free microspore samples provided unique tools for comparative genetic studies using agarose and polyacrylamide gel electrophoresis, respectively.

Assessment of genetic diversity among six populations of Rhododendron triflorum in Tibet using ISSR and AFLP markers

In order to assess genetic variations among Rhodendron trifolium populations sampled from Tibet and determine the correlation among genetic variations, the geographic location of a population, and factors that influence high-level genetic diversity, in total of 107 R. triflorum samples using inter simple sequence repeats (ISSR) and amplified fragment length polymorphisms (AFLP). All genotypes were collected from six different areas. Eleven ISSR primers and five AFLP primer pairs were screened, and 118 and 169 amplification products were produced, of which, 96.61% in ISSR and 95.27% in AFLP were polymorphic. High genetic diversity was observed at the species level: Nei's genetic diversity (H) was 0.3382 and 0.306, and Shannon's information index (I) was 0.5085 and 0.4642 in ISSR and AFLP, respectively. Both the coefficient of gene differentiation (GST 0.3752 in ISSR, 0.31 in AFLP) and AMOVA analysis (75% in ISSR, 71% in AFLP) indicated that most genetic diversity was distributed within populations. Gene flow (Nm) was 0.8326 in ISSR and 1.1127 in AFLP. The analyze of unbiased genetic distances determined by an unweighted pair group method using arithmetic mean (UPGMA) phonograms indicated that there was a certain degree correlation between the genetic distance and the geographic distance, which was confirmed by a principal coordinate analysis. The results maybe indicated that difference of geographical environment and variation of habitat types caused the genetic differentiation of R. triflorum. At last, some conservation strategies for R. triflorum germplasm were put forward according to these results.

Assessment of genetic relationship among Rhododendron cultivars using amplified fragment length polymorphism and inter-simple sequence repeat markers.

Genetic relationships of 17 Rhododendron cultivars, China, were assessed using inter-simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) markers. A total of 133 bands were obtained using nine selected ISSR primers, 129 (96.99%) of which were polymorphic; 267 bands were amplified by four AFLP primer pairs, 251 (94.01%) of which exhibited polymorphism. Based on these polymorphic products, a cluster analysis revealed similarities between the results of the ISSR and AFLP. All of the cultivars were clustered into two major branches; one branch contained the same four cultivars, and the other cultivars were separated into different groups in the other branch. The cluster results showed that the genetic relationships of the 17 cultivars were partly related to their morphological characteristics, particularly the flowering phase. Therefore, the results of this study support the classification of Rhododendron cultivars according to flowering phase. In addition, the cluster results can be used to select suitable parents for breeding.

Analysis of Genetic and Epigenetic Changes in Potato Somatic Hybrids Between Solanum tuberosum and S. etuberosum by AFLP and MSAP Markers

In this study, 26 mother plants and their respective 26 regenerants (30th cycles sub-cultured plants) of potato interspecific somatic hybrids were examined for genetic and epigenetic changes by amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) markers, respectively. Eight AFLP primer pair combinations yielded 78 polymorphic bands out of 353 scorable bands. Cluster analysis based on the Jaccard’s similarity coefficient exhibited 100 % similarity between the mother plant and their regenerants, whereas eight MSAP markers detected epigenetic variation (2–6 %) in the regenerants. Out of total 6411 MSAP sites in the regenerants, 6133 unmethylated, 132 (2 %) fully methylated, and 143 (2.2 %) hemi-methylated sites were detected. This study shows that a minimum epigenetic variation (2–6 %) was induced in the regenerants as compared to the mother plants of potato somatic hybrids during tissue culture process.

DNA damage and genetic methylation changes caused by Cd in Arabidopsis thaliana seedlings.

Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MASP) techniques are sensitive to deoxyribonucleic acid (DNA) damage and genetic methylation, respectively. Using these 2 techniques, Arabidopsis thaliana cultured with 0 mg/L (control), 0.5 mg/L, 1.5 mg/L, and 5.0 mg/L Cd(2+) for 16 d was used to analyze the DNA damage and methylation changes as a result of cadmium (Cd). The DNA was amplified by 14 AFLP primer pairs and 13 MSAP primer combinations. In the AFLP experiment, 62 polymorphic sites were found in the patterns of 11 primer combinations and a total of 1116 fragments were obtained in these patterns. There were no polymorphic bands in the remaining 3 pairs. The proportions of polymorphic sites in the 0.5-mg/L Cd(2+) and 5.0-mg/L Cd(2+) treatments were significantly different. Seven polymorphic fragments were then separated and successfully sequenced, yielding 6 nucleobase substitutions and 1 nucleobase deletion. Similarly, in the MSAP experiment, the MSAP% and number of demethylated-type bands were unchanged after Cd treatment, but the number of methylated-type bands was increased significantly in the 5.0-mg/L Cd(2+) treatment group, a finding that may be associated with the AFLP results. The polymorphic bands were also sequenced and the functions of their homologous genes were determined. The DNA damage and methylation changes may be the primary cause of certain pathology changes as a result of Cd uptake in plants.

Genetic and phenotypic diversity for drought tolerance in perennial ryegrass (Lolium perenne L.)

Perennial ryegrass (Lolium perenne L.) is a widely grown species in temperate regions as forage grass as well as for recreational and bioenergy production purposes. Information on perennial ryegrass genetic background facilitates breeding programs by providing an assessment of genetic diversity in exotic material. Genetic diversity of 104 genotypes of perennial ryegrass was evaluated using phenotypic drought traits and amplified fragment length polymorphism (AFLP) data. A high variation was observed for the drought tolerance traits. Chlorophyll fluorescence (F v /F m ) explained 88.8% of the whole variation observed in the collection, while re-growth accounted for 9.1% of all variation. A principal component analysis on the basis of phenotypic drought tolerance traits classified perennial ryegrass collection into three clusters. Three AFLP primer pairs produced a total of 210 fragments, 202 of which were polymorphic among all accessions. The genetic diversity of the collection was high with an average similarity coefficient of 0.46 and the average polymorphic information content of 0.29. The principal component analysis based on AFLP data did not cluster genotypes into any major group. A total of six AFLP fragments, identified as being prevalent in drought tolerant genotypes, together with the high degree of genetic homogeneity found, could provide a choice of selecting genotypes from this perennial ryegrass collection for a drought tolerance breeding program.

Isolation and DNA-Marker Based Genotyping of Individual Pollen Grains

Dry pollen of diploid Solanum clone 9507-04, Cotton chromosomal substitution line and Echinacea purpurea „Magnus‟ were isolated and their cells contents released in individual tubes containing water or pollen germination media, respectively.Six polymorphic markers from individual pollen grains of the diploid potato were amplified using two random amplified polymorphic DNA (RAPD) primers, i.e., UBC291 and UBC504. The procedures for primer extension pre-amplification (PEP) for genome and subsequent amplified fragment length polymorphism (AFLP) analysis with 13 primers pairs were tested on the upland cotton line. The cotton parental AFLP markers were scored for their presence or absences in the 35 pollen samples and majority of the markers were found monomorphic as expected from the gametes of a near isogenic line.PEP and AFLP procedures for linkage mapping were standardized usingpurpleconeflower pollen grains. From 64 possible AFLP primer pairs,37.5% amplified 104 markers for coneflowerthat were linked in 11 linkage groupsranging from 13 to 134 centimorgans (cM). The 409 cM sizedlinkage map constructed forE. purpurea „Magnus‟genome had average distance of 2.4 cM to 22 cMfor the two to 55 polymorphic markers identifiedwithin the 11 groups.The protocols described in this report would serve to enhance breeding efficiencies in plantsimportant for food,fiber, ornamental and medicinal industries.

GENETIC DIVERSITY OF OKRA (<i>ABELMOSCHUS ESCULENTUS</i> L.) GENOTYPES FROM DIFFERENT AGRO-ECOLOGICAL REGIONS REVEALED BY AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS

This study was carried out to assess the genetic diversity in 48 genotypes and accessions using eight Amplified Fragment Length Polymorphism (AFLP) primer-pairs. The eight selected AFLP primer-pairs generated a total of 150 polymorphic loci. Using the generated AFLP data, the Un-Weighted Pair Group Method with Arithmetic Average (UPGMA) ordered the genotypes into six groups based on Dice similarity coefficient. The range in taxonomic distance was from 0.23 to 1.0. Each cluster was found to have genotypes and accessions from different regions and climate and sometimes different continents. The size range of the loci ranged from 87-662 bp. Great variation between the genotypes and accessions in the different cluster could be of high value as the genetically diverse okra genotypes represent a potentially valuable source for improved pathogen and pest resistance.

Cold-induced genetic instability in micropropagated Pistacia lentiscus L. plantlets

Genetic stability of plants during in vitro propagation and conservation is one of the important aspects of plant biotechnology. In the present study, micropropagated P. lentiscus L. shoot cultures, which are cultivated for the mastic resin, have been cold stored up to 12 months at 4 °C in the dark for different durations (2, 4, 6, 8, 10 and 12 months) and genetic alterations in cold storage conditions were evaluated. Growth parameters such as proliferation rate, shoot numbers per explant, shoot lengths and shoot forming capacity were also calculated. Since the highest proliferation rate (100 %) was obtained in 6 month-stored shoot cultures without any severe influence of cold stress on proliferation ability, amplified fragment length polymorphism (AFLP) and inter-retrotransposon amplified polymorphism (IRAP) marker systems were used to determine genetic stability in the plantlets after this storage period. Totally, 702 scorable bands were produced by 10 AFLP primer pairs. Genetic similarity value of the non-stored (control) plant and cold-stored clones ranged from 0.66 to 0.84 with a mean of 0.74. In the case of IRAP, 159 bands were produced by 8 IRAP primers. Genetic similarity value of the non-stored plant and cold-stored clones varied from 0.65 to 0.83 and the average genetic similarity value was determined as 0.72. The genetic similarity indices revealed that genetic variability was similar in both techniques. Our results showed that tissue culture and especially cold storage of P. lentiscus L. may result transposons activation, thus could cause genetic instability.

Genetic relationship among wild, landraces and cultivars of hazelnut (Corylus avellana) from Portugal revealed through ISSR and AFLP markers

The genus Corylus, a member of the birch family Betulaceae, includes several species that are widely distributed throughout temperate regions of the Northern Hemisphere. This study assesses the genetic diversity in 26 international cultivars and 32 accessions of Corylus avellana L. from Portugal: 13 wild genotypes and 19 landraces. The genetic relationships among the 58 hazelnuts (Corylus avellana L.) were analyzed using inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) markers. Eighteen ISSR primers and seven AFLP primer pairs generated a total of 570 unambiguous and repeatable bands, respectively, from which 541 (95.03 %) were polymorphic for both markers. Genetic similarity index values ranged from 0.239 for wild types and cultivars to 0.143 for landraces and wild types. The genetic relationships were presented as a Neighbor-Joining method dendrogram and a two-dimensional principal coordinate analysis (PCoA) plot. The Neighbor-Joining dendrogram showed three main clusters, and the PCoA analysis has shown to be congruent with the hierarchical analysis. Bayesian analysis clustered all individuals into three groups showing a good separation among wild genotypes, landraces and cultivars. The genetic diversity found on wild genotypes and Portuguese landraces may provide relevant information for the diversity conservation and it will be useful in breeding programs and to identify local selections for preservation.

Genetic diversity of side-oats grama [Bouteloua curtipendula(Michx.) Torr.] populations as revealed by amplified fragment length polymorphism markers

Biligetu, B., Schellenberg, M. P. and Fu, Y.B. 2013. Genetic diversity of side-oats grama [Bouteloua curtipendula (Michx.) Torr.] populations as revealed by amplified fragment length polymorphism markers. Can. J. Plant Sci. 93: 1105–1114. Side-oats grama [Bouteloua curtipendula (Michx.) Torr.] is a warm-season grass widely distributed in North America and is considered as an important grass for reclamation and summer forage production in drier regions. This study assessed genetic diversity of nine wild populations of side-oats grama grass, their corresponding balanced multiple-site composite (BMSC), and a population selected for forage type (FT), using the amplified fragment length polymorphism (AFLP) technique. Five AFLP primer pairs were employed to genotype 157 plants, and 312 polymorphic AFLP bands were detected. The frequencies of AFLP bands ranged from 0.01 to 0.99, and averaged 0.39. The AFLP analysis revealed 6% of the total AFLP variation present among the nine wild populations and 94% of variation within populations. The Minto population had the largest within-population diversity, while the FT population the lowest based on AFLP band richness and polymorphic loci. The BMSC population displayed significant genetic differentiation from the wild populations, but still captured substantial genetic diversity. Bayesian cluster analysis using BAPS and STRUCTURE programs revealed three and four optimal clusters of populations that explained 9.8 and 9.5% of the total AFLP variation, respectively. A genetic clustering of individual plants displayed no clear genetic separations among wild, FT, and BMSC populations, but the FT population showed some level of genetic shift, indicating the initial impact of artificial selection. These findings are significant for our understanding of the genetic diversity of side-oats grama. Large genetic variation present within populations provides a potential for further genetic enhancement.

Evaluating genetic variation and relationships amongPuccinellia nuttallianapopulations using amplified fragment length polymorphism markers

Liu, Y., Fu, Y.-B. and Coulman, B. E. 2013. Evaluating genetic variation and relationships among Puccinellia nuttalliana populations using amplified fragment length polymorphism markers. Can. J. Plant Sci. 93: 1097–1104. Nuttall's salt-meadow, or alkali grass [Puccinellia nuttalliana (Shultes) Hitchc.], is a native grass species in North America, well known for its salt tolerance. Little information is available about the genetic diversity of natural populations of this species. Amplified fragment length polymorphism (AFLP) markers were used to examine the inter-population relationships and to compare variances within and among 23 populations collected from the Canadian Great Plains. Five AFLP primer pairs were employed to screen 15 genotypes (five sets of three half-sib plants) from each population, and 185 polymorphic AFLP bands were scored for each sample. The frequencies of these scored bands ranged from 0.02 to 0.99 with a mean of 0.60. The analysis of molecular variance revealed more than 96% of the total AFLP variation resided within populations. Populations were not highly differentiated with only 4% of the total AFLP variation residing among populations. A Mantel test revealed a significant but low correlation between genetic and geographic distances (r=0.29, P=0.024). Implications for P. nuttalliana conservation, germplasm sampling, and cultivar development are discussed.

Evaluating genetic variation and relationships among Puccinellia nuttalliana populations using amplified fragment length polymorphism markers

Liu, Y., Fu, Y.-B. and Coulman, B. E. 2013. Evaluating genetic variation and relationships amongPuccinellia nuttallianapopulations using amplified fragment length polymorphism markers. Can. J. Plant Sci. 93: 1097-1104. Nuttall's salt-meadow, or alkali grass [Puccinellia nuttalliana (Shultes) Hitchc.], is a native grass species in North America, well known for its salt tolerance. Little information is available about the genetic diversity of natural populations of this species. Amplified fragment length polymorphism (AFLP) markers were used to examine the inter-population relationships and to compare variances within and among 23 populations collected from the Canadian Great Plains. Five AFLP primer pairs were employed to screen 15 genotypes (five sets of three half-sib plants) from each population, and 185 polymorphic AFLP bands were scored for each sample. The frequencies of these scored bands ranged from 0.02 to 0.99 with a mean of 0.60. The analysis of molecular variance revealed more than 96% of the t...

Genetic diversity analysis of hulless barley from Shangri-la region revealed by SSR and AFLP markers

For adding the hulless barley resources of Shangri-la region to the global barley resource library, a basic work was done by us to assess their genetic diversity of this region. The genetic diversity of 60 hulless barley samples collected from three counties in Shangri-la region of Yunnan Province, were studied using SSR (simple sequence repeats) and AFLP (amplified fragment length polymorphism) markers. A total of 70 alleles were detected for 19 pairs of SSR primers, and 525 band containing 464 polymorphic bands were revealed for 5 pairs of AFLP primers. The value of polymorphism information content (PIC) ranged from 0.03 to 0.86 for SSR primers. The total numbers of alleles were 51, 55, 43 in three populations and the polymorphic bands were 188, 205 and 141. The genetic distances and genetic identity among the three populations showed their close relationship. The gene diversity among populations relative to the total population diversity (Gst) was 0.13 for SSR markers and 0.02 for AFLP markers and indicated that just 13 and 2% variations were among populations, respectively. The UPGMA cluster analysis revealed that all of the samples grouped randomly rather than clustered into distinct groups corresponding to their populations, row types and spring/fall types. We concluded that there was high genetic diversity in the population of Shangri-la region and the formation of diversity was related to complex environment and inhabitants' traditional practices.

Population structure of Euodia rutaecarpa in China revealed by amplified fragment length polymorphism (AFLP) and sequence-related amplified polymorphism (SRAP)

In the present paper, experimental materials of 33 accessions representative of the Euodia rutaecarpa from four Chinese provinces were analyzed using the sequence-related amplified polymorphism (SRAP) and amplified fragment length polymorphism (AFLP) techniques, focusing on their molecular discrimination and the assessment of their genetic relatedness. For the analysis, we optimized 10 pairs of SRAP primers and 6 pairs of AFLP primers, (The software package NTSYS-pc 2.1 was applied to analyze the data matrix) and cluster analysis distributed samples into two clusters, one with E. rutaecarpa var. officinalis (Dode) Huang and the other with E. rutaecarpa (Juss.) Benth by SRAP+AFLP markers in the same similarity coefficient of 0.53 (Genetic parameters also analyzed using POPGENE version 1.31). Genetic diversity in the species was detected with SRAP (H = 0.2260, I = 0.3341) and AFLP (H = 0.1665; I = 0.2518) markers. Genetic variability levels of E. rutaecarpa var.officinalis (Dode) Huang was higher than genetic variability levels of E. rutaecarpa (Juss.) Benth. Our study shown that both SRAP and AFLP molecular markers are in high efficiency in detecting the genetic diversity of E. rutaecarpa. Key words: Euodia rutaecarpa, variety amplified fragment length polymorphism (AFLP) markers, sequence-related amplified polymorphism (SRAP) markers, genetic diversity.