Inter-simple Sequence Repeat Molecular Markers Research Articles

Molecular and mycotoxin characterization of Fusarium graminearum isolates obtained from wheat at a single field in Argentina

Fusarium graminearum is the primary causal agent of Fusarium head blight of wheat in Argentina. This disease affects yield losses and quality of grains, reducing the wheat end-use, also causing mycotoxin contamination. In this study, the genetic variability and deoxynivalenol (DON) potential/production of F. graminearum sensu stricto (s.s.) isolates obtained from wheat samples of the 2009, 2010, and 2011 growing seasons from a single location in Argentina were evaluated. The genetic variability detected using inter-simple sequence repeat (ISSR) was analyzed in relation to the in vitro deoxynivalenol production, the main monitored and quantified mycotoxin according to the current regulations for the international marketing of cereals. Of the 68 F. graminearum s.s. isolates obtained in this study, 95 % showed a different banding pattern with ISSR molecular markers and a high variability was detected within the population. However, no clustering was found in relation with year or DON production. All isolates amplify for the DON-related gene and a high variability in DON production was observed among the isolates, with production values between non-producers and 1741 μg/g. The results suggest that the F. graminearum s.s. population varies significantly in both genetic structure and toxin production in a limited sampled area.

English

Jatropha belonging to Euphorbiaceae family has around 170 species distributed throughout tropical semi-arid regions of Africa and the Americas. Some of its species include Jatropha curcas L. (Physic Nut), Jatropha pohliana Müll.Arg. (Brazilian Purging Nut) and Jatropha gossypiifolia L. (Black Physic Nut). Phenotypic and genetic studies of a population are important for plant improvements, helping in the characterization of accesses, as well as facilitating selection of parental for directed crossings. Thus, the present study aimed to evaluate accesses of three Jatropha species from different regions of Brazil, through morphological characters and ISSR molecular markers, in order to group them according to the existing degree of divergence. A higher interspecific variability, rather than intraspecific, was observed among accesses, for morphological as well as molecular characters. Qualitative and quantitative characters showed variability between accesses and may serve as reference for future genetic studies. There was no relation between similarity patterns and geographical origin of accesses in the group analysis. Average percentage of polymorphism found for inter-simple sequence repeat (ISSR) markers between the studied accesses was 40.6%. A higher genetic variability interspecific was observed than intraspecific, suggesting the search for genetic variability among species Jatropha through interspecific crosses.   Key words: Germplasm, Jatropha curcas, Jatropha gossypiifolia, Jatropha pohliana, variability.

Towards the identification of retrotransposon-based and ISSR molecular markers associated with populations resistant to ZYMV in melon

Melon (Cucumis melo L.) is one of the most important commercial vegetable crops grown in Iran. Very few studies on the genetic structure and diversity of melon landraces of Iran are available in the literature. In addition, it is susceptible to a number of diseases causing reduction in both productivity and quality of the crop. In this study we applied inter retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and inter simple sequence repeat (ISSR) molecular markers to investigate genetic diversity and its association with populations resistant to ZYMV in 11 Iranian melon populations and 12 commercial lines. Significant differences (P≤0.01) were detected among populations for reaction to ZYMV infection. No symptoms observed on inbred line PI414723, while variety Charentais T showed the highest value of virus infection (1.87). Based on five IRAP, 15 REMAP and 20 ISSR primers, a total of 656 reproducible and scorable loci were generated, among them 75.41% were polymorphic. Population structure analysis using STRUCTURE software identified K=10 as the reliable value for the number of clusters. Associations between molecular markers and populations resistant to ZYMV were tested using mixed linear model (MLM) approach that accounts for population structure. Highly significant associations were found for seven REMAP and four ISSR markers affecting ZYMV resistance (P≤0.01). This study provides evidence that using natural germplasms, the diversity can be enhanced for marker-trait associations that can be validated in segregating populations and exploited through marker-assisted selection.

<b>Analysis of the genetic diversity of <i>Eucalyptus cladocalyx</i> (sugar gum) using ISSR markers

Eucalyptus cladocalyx F. Muell is a tree endemic to southern Australia and is distributed across four isolated regions: Kangaroo Island, southern Flinders Ranges, and two geographical zones in Eyre Peninsula. E. cladocalyx is capable of growing under extreme environmental conditions, including dry and saline soils. The objective of this study was to analyze genetic diversity in 45 half-sib families planted in northern Chile that are distributed across five different zones (provenances). Genetic variability was assessed using ISSR (Inter Simple Sequence Repeat) molecular markers. The results showed low levels of genetic diversity within populations (He = 0.113 to 0.268) in contrast with other Eucalyptus species. In addition, there was a significant genetic differentiation among provenances (Φst = 0.14); populations from the Kangaroo Island provenance showed more differentiation than any other population. These results are in agreement with previous studies of the species. Our study revealed that Chilean resources are a representative sample of Australian populations; therefore, the germplasm planted in northern Chile would be sufficient for the development of improvement programs. ISSR-Marker technology could be an alternative to identify genotypes of interest in material selection.

Genetic diversity and taxonomic status of Pinus tabulaeformis f. shekanensis revealed by ISSR markers

Pinus tabulaeformis f. shekanensis is a rare taxon endemic in the Ziwuling Loess Plateau, of which only one population is known. Inter-simple sequence repeat molecular markers were employed to compare the taxon's genetic diversity with its 4 nearest wild relatives (P. tabulaeformis, P. tabulaeformis var. mukdensis, P. massoniana, and P. henryi) to assess the taxonomic status of P. tabulaeformis f. shekanensis. Inter-simple sequence repeat marker data revealed higher genetic diversity in the P. tabulaeformis f. shekanensis population than in the other populations. Population genetic analysis (neighbor-joining cluster analysis, principal coordinate analysis, and structure clustering) revealed that P. tabulaeformis f. shekanensis and P. tabulaeformis are likely conspecific (the former may be a variety of the latter). Strategies are also proposed for the conservation of P. tabulaeformis f. shekanensis.

Population structure and genetic diversity in Gynaikothrips uzeli (Thysanoptera: Phlaeothripidae): is there a correlation between genetic and geographic proximity?

Gynaikothrips uzeli (Thysanoptera: Phlaeothripidae) is a minuscule insect species, which forms galls, is subsocial, and parthenogenetic. It is associated with Ficus benjamina L. (Moraceae) and has a pantropical occurrence. The paucity of genetic studies on the order Thysanoptera led us to use inter-simple sequence repeat molecular marker to assess intra- and inter-gall, as well as intra- and inter-site, genetic variability and population structure of G. uzeli. Analyses indicated low genetic variability, probably related to haplodiploidy, genetic drift, the galling habit, and the low dispersal ability of G. uzeli. Populations were highly structured, with higher variation within populations than among them. Geographic distance does not appear to affect structure and genetic diversity, the latter being influenced by G. uzeli's bioecological traits, by numerous introductions during a short period, and by a possible recent, common ancestry.

Molecular tracing of white muscardine in Asian corn borer using inter-simple sequence repeat (ISSR) analysis

Beauveria bassiana is a soil fungus that parasitizes arthropod species, and is used to control the Asian corn borer in Northeast China. In this study, B. bassiana was investigated in Xiaoxian County and Baicheng City, and the results were compared with those of Gongzhuling City, where the fungus was not applied. Using the inter-simple sequence repeat (ISSR) molecular marker technique, 198 isolates were extracted from Asian corn borer and other insect cadavers, and soil and air, and two released strains were analyzed to trace the infection source. In Xiaoxian and Baicheng populations, artificially released B. bassiana subpopulations were more abundant than indigenous fungi, and the released strains were the main cause of disease in those areas. Artificial B. bassiana displayed positive effect on overwintering of Asian corn borers in corn straw stacks in Xiaoxian County. Indigenous populations in Gongzhuling City showed higher genetic variation. In summary, we identified a significant correlation between genetic distance and geographic distance (P < 0.01).

Fragmentation effects and genetic diversity of the key semidecidual forest species Metrodorea nigra in Southwestern Brazil.

Studies of genetic diversity in plant species present in the remaining fragments of the Atlantic Forest are very important for understanding their resilience to such a degraded ecosystem. We analyzed the genetic diversity of 3 populations of the high-density understory species Metrodorea nigra St. Hill. (Rutaceae) located in forest remnants in the region of Ribeirão Preto, SP, Brazil (M13-Rib, BSQ-Rib, and FAC-Crav), by using simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) molecular markers for conservation purposes. A total of 133 polymorphic loci were observed in 136 inter-simple sequence repeat loci (average of 17 per primer). The Nei genetic diversity (HE) was relatively high considering all populations (0.31). The BSQ-Rib population exhibited the highest value (0.27), followed by the M13-Rib (0.26) and FAC-Crav (0.24) populations. The simple sequence repeat markers analyzed showed a high number of alleles (K = 104), with an average of 14.85 alleles per locus. The average observed heterozygosity was 0.516 and the average expected heterozygosity was 0.771, ranging from 0.688 (FAC-Crav) to 0.765 (BSQ-Rib). The fixation indexes showed positive and significant differences from zero for all sample sets, indicating inbreeding, which may have resulted from the species' mating patterns and the barochoric seed dispersal system of M. nigra. Both markers indicated differentiation among populations, with higher values observed for inter-simple sequence repeat markers. No significant differences between juvenile and adult generations in any of the fragments were observed, indicating the resilience of M. nigra to the effects of fragmentation and reduced habitat.

Genetic stability of micropropagated plants of Crambe abyssinica Hochst using ISSR markers.

Crambe (Crambe abyssinica) is a non-edible annual herb, which was first cultivated to extract oil for industry, and now has great potential for biodiesel production. The objective of this investigation was to evaluate the genetic stability of micropropagated plants of the C. abyssinica Hochst cultivar 'FMS brilhante' using polymerase chain reaction techniques based on inter-simple sequence repeat (ISSR) molecular markers. The aim was to develop a protocol for the in vitro regeneration of these plants with low genetic variation as compared to the donor plant. For micropropagation, shoot tips from in vitro germinated seedlings were used as explants and were initially cultivated for 90 days on MS medium with 5.0 μM 6-benzylaminopurine (BAP), which at 90 days, led to the highest number of shoots per explant (NSE) (12.20 shoots) being detected. After 120 days, the interaction between BAP concentration and naphthalene acetic acid (NAA) was tested, and the highest NSE was observed following exposure to 0.0/0.5 μM BAP/NAA (11.40 shoots) and 1.0/0.0 μM BAP/NAA (11.00 shoots). The highest proportion of rooting phase were observed following exposure to 0.5 μM NAA (30%). The 13 ISSR primers used to analyze genetic stability produced 91 amplification products, of which only eight bands were polymorphic and 83 were monomorphic for all 10 regenerated crambe plants, compared to the donor plant explant. These results indicate that crambe shoot tips are a highly reliable explant that can be used to micropropagate genetically true-to-type plants or to maintain genetic stability, as verified using ISSR markers.

Genetic diversity of the Neotropical tree Hancornia speciosa Gomes in natural populations in Northeastern Brazil.

Mangabeira (Hancornia speciosa Gomes) is a fruit tree of the Apocynaceae family, which is native to Brazil and is a very important food resource for human populations in its areas of occurrence. Mangabeira fruit is collected as an extractive activity, and no domesticated varieties or breeding programs exist. Due to a reduction in the area of ecosystems where it occurs, mangabeira is threatened by genetic erosion in Brazil. The objective of this study was to characterize and evaluate the genetic diversity of 38 mangabeira individuals collected from natural populations in Pernambuco State using inter-simple sequence repeat (ISSR) molecular markers. The ISSR methodology generated a total of 93 loci; 10 were monomorphic and 83 were polymorphic. The average number of loci per primer was 15.5, ranging from 9 (#UBC 866) to 21 (#UBC 834). The results showed a high level of genetic diversity (0.30), and found that only around 30% of genetic variability is distributed among populations (GST = 0.29, ФST = 0.30), with the remainder (ФCT = 70%) found within each population, as expected for forest outcrossing species. Estimates for historic gene flow (1.18) indicate that there is some isolation of these populations, and some degree of genetic differentiation.

Hybridization in Capparis spinosa L.: Molecular and morphological evidence from a Mediterranean island complex

Inter-Simple Sequence Repeat (ISSR) molecular markers and morphological analysis were used in order to characterize wild populations and cultivated forms of orphan crop species Capparis spinosa L. in a Mediterranean island complex. Nineteen wild populations belonging to two different subspecies, C. spinosa subsp. spinosa and subsp. rupestris, were sampled in different environments in Sicily and the surrounding islets Lampedusa, Pantelleria and Salina. Different biotypes cultivated in Pantelleria and Salina were analysed. Six ISSR primers were selected for genetic characterization, and all clear and reproducible bands were scored and analysed. Among the 47 ISSR bands obtained, 97.5% were polymorphic. Results of AMOVA and STRUCTURE analysis suggested a clear genetic distinctness between subspecies at the regional level and suggested the existence of two taxonomic groups among wild populations, with different ecological preferences and distinctive morphological characters. Cultivated forms showed genetic affinity to subsp. rupestris. ISSR analysis not only provided specific molecular markers to discriminate the taxa, but also proved useful in supporting the hypothesis of a hybrid origin of the intermediate phenotypes found in overlapping distribution areas. The identified molecular markers provided a basic tool for the DNA fingerprinting of wild and commercial capers in the Mediterranean region and nearby territory.

Exploration of Genetic Variability of Bean (Phaseolus vulgaris L.) Landraces through ISSR Markers

In this study, 30 bean landraces collected from three Mexican states, namely Puebla, Zacatecas and Oaxaca, were evaluated in order to estimate genetic diversity among them through their genomic fingerprints obtained from ISSR (Inter Simple Sequence Repeat) markers. Genetic variability of semi-domesticated bean populations is a valuable resource for plant breeding programs as a source of stress-tolerant genes that were lost during the selection process of commercial cultivars. In this study, ten ISSR primers produced a total of 92 bands, 82 of which were polymorphic (representing 89 percent of polymorphism). Jaccard's distances between pairs of accessions were used to define four groups according to their molecular diversity. The results obtained from this study proved the existence of important genetic variability among bean landraces collected at distinct geographical locations, establishing the basis for conservation and utilization of evaluated materials for breeding purposes. ISSR molecular markers were able to genetically differentiate bean accessions despite their expected high genetic homogeneity due to their self-pollinating nature.

In Vitro Mass Multiplication and Assessment of Genetic Stability of In Vitro Raised Artemisia absinthium L. Plants Using ISSR and SSAP Molecular Markers

The present investigations were made attempting to develop a rapid, reliable, and reproducible in vitro regeneration protocol for Artemisia absinthium L., a medicinal plant of Kashmir Himalayas. Out of several auxin-cytokinin combinations tested, Murashige and Skoog’s (MS) medium supplemented with 0.5 mgL−1 2,4-dichlorophenoxyacetic acid (2,4-D) and 0.5 mgL−1 kinetin (Kn) was found to be the best for the callus induction. On the other hand, 4.5 mgL−1 6-benzylaminopurine (BAP) and 0.5 mgL−1 1-α-naphthaleneacetic acid (NAA) in the medium resulted in maximum shoot induction from the callus. Similarly, BAP and NAA at a concentration of 1.5 mgL−1 and 0.5 mgL−1, respectively, proved to be the best for the multiple shoot induction from nodal explants. Numerous shoots were obtained from nodal explants after third subculture. In vitro rooting was maximum on medium containing indole-3-butyric acid (IBA) at 0.5 mgL−1. The genetic stability of the in vitro raised plants of Artemisia absinthium was assessed using the intersimple sequence repeat (ISSR) and sequence-specific amplification polymorphism (SSAP) molecular markers. Both markers were able to detect the somaclonal variations in the callus regenerated plants, while no variation was detected in the plants regenerated from the nodal explants. SSAP has been found to be more useful in detection of variability as compared to ISSR molecular marker. The results of present study concluded that the direct regeneration protocol will be useful for the production of true to type plants of this medicinally important plant. This will go a long way in reducing the pressure on the natural populations for the secondary metabolite production, especially for extraction of essential oils.

Molecular diversity and hypoglycemic polypeptide-P content of Momordica charantia in different accessions and different seasons.

Momordica charantia (MC) has been used for treating diabetes mellitus from ancient times in Asia, Africa and South America. There are many MC accessions in local markets. Polypeptide-P as a main hypoglycemic component in MC was first studied in this experiment to illustrate the different contents in MC of different accessions and different harvesting times. Nineteen MC accessions collected from different regions were clustered into three groups using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers. Content of polypeptide-P in the tested MC accessions was detected by western blot (WB) method. The WB results revealed that polypeptide-P was detected in MC accessions harvested in June and July but not in September and October. Furthermore, Polypeptide-P content corresponded well with the MC accessions. Our results suggest that the MC accessions and the harvesting times or the weather during harvest play significant roles in high content of polypeptide-P.

A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments.

BackgroundCommon wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat varieties that maintain yield (YD) under moderate or even intense nitrogen (N) deficiency can adapt to low input management systems. A detailed genetic map is necessary for both wheat molecular breeding and genomics research. In this study, an F6:7 recombinant inbred line population comprising 188 lines was used to construct a novel genetic map and subsequently to detect quantitative trait loci (QTL) for YD and response to N stress.ResultsA genetic map consisting of 591 loci distributed across 21 wheat chromosomes was constructed. The map spanned 3930.7 cM, with one marker per 6.7 cM on average. Genomic simple sequence repeat (g-SSR), expressed sequence tag-derived microsatellite (e-SSR), diversity arrays technology (DArT), sequence-tagged sites (STS), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeat (ISSR) molecular markers were included in the map. The linear relationships between loci found in the present map and in previously compiled physical maps were presented, which were generally in accordance. Information on the genetic and physical positions and allele sizes (when possible) of 17 DArT, 50 e-SSR, 44 SRAP, five ISSR, and two morphological markers is reported here for the first time. Seven segregation distortion regions (SDR) were identified on chromosomes 1B, 3BL, 4AL, 6AS, 6AL, 6BL, and 7B. A total of 22 and 12 QTLs for YD and yield difference between the value (YDDV) under HN and the value under LN were identified, respectively. Of these, QYd-4B-2 and QYddv-4B, two major stable QTL, shared support interval with alleles from KN9204 increasing YD in LN and decreasing YDDV. We probe into the use of these QTLs in wheat breeding programs. Moreover, factors affecting the SDR and total map length are discussed in depth.ConclusionsThis novel map may facilitate the use of novel markers in wheat molecular breeding programs and genomics research. Moreover, QTLs for YD and YDDV provide useful markers for wheat molecular breeding programs designed to increase yield potential under N stress.

Somaclonal Variation in Habanero Pepper (Capsicum chinense Jacq.) as Assessed ISSR Molecular Markers

Intersimple sequence repeat (ISSR) markers were used to evaluate the effects of in vitro culture on genetic variation in Habanero pepper (Capsicum chinense Jacq.) regeneration protocols. A total of 219 ISSR clear and reproducible fragments were generated with 13 ISSR primers in direct organogenesis, direct and indirect somatic embryos, and the embryogenic callus system. A cluster analysis was performed to express in the form of dendrogram the relationships among different regeneration systems and the genetic variability detected. Genetic distance analysis indicated that our regeneration protocols are inappropriate for micropropagation, conservation, or genetic transformation; however, they may be applicable to breeding. This is the first report on the use of molecular analysis to evaluate genetic variation of in vitro-regenerated plants of Habanero pepper using ISSR markers.

Local adaptation and phenotypic plasticity both occurred in Wedelia trilobata invasion across a tropical island

The role of the local adaptation and phenotypic plasticity of invasive species in their invasion of new environments has historically been a debatable issue, particularly at small spatial scales (e.g., different habitats within an island). We selected seven field sites across Hainan Island, Hainan Province, China, to investigate the role of local adaptation and/or phenotypic plasticity in the successful invasion of Wedelia trilobata by a field survey, molecular marker analysis, and common garden experiment. In the field survey, the clonal growth characteristics of W. trilobata showed significant differences among the seven sites, suggesting that the species was able to adapt to different environments. The mean phenotypic plasticity index of W. trilobata was higher than that of other invasive plant species (0.61 vs 0.48). The analysis of the inter-simple sequence repeat molecular markers of 420 individuals from the seven sites revealed a Shannon’s index that was similar to those of other invasive plants (0.29 vs 0.25). The nested analysis of the molecular variance in the genetic diversity of the population showed significant differences among the sites. In the common garden experiment, the growth characteristics of plants grown from the seven sites were significantly affected by light and density treatments but not by soil moisture. However, the responses of plants grown from different sites to light treatment varied. Plants from sunny sites had greater clonal traits than those from shady sites, indicating that local adaptation occurred in plant populations grown at some sites. Overall, our results implied that both phenotypic plasticity and local adaptation contributed to the successful invasion of W. trilobata across Hainan Island.

Molecular characterization of aflatoxigenic and non-aflatoxigenic Aspergillus flavus isolates collected from corn grains.

Twelve species from six fungal genera were found to be associated with corn (Zea mays L.) grain samples collected from three main regions of Saudi Arabia. The average frequencies of the most common genera were Aspergillus (11.4%), Fusarium (9.5%), Penicillium (5.1%), and Alternaria (5.8%). Fifteen isolates of Aspergillus flavus were screened by HPLC for their ability to produce aflatoxins (AF). The percentage of aflatoxigenic A. flavus isolates was 53%. Eight isolates produced AF, at concentrations ranging 0.7-2.9 ppb. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers were used to genetically characterize isolates of A. flavus and to discriminate between the aflatoxigenic and non-aflatoxigenic isolates. RAPD and ISSR analysis revealed a high level of genetic diversity in the A. flavus population, which was useful for genetic characterization. The clustering in the RAPD and ISSR dendrograms obtained was unrelated to geographic origin. The RAPD and ISSR markers could not discriminate between aflatoxigenic and non-aflatoxigenic isolates, but the ISSR primers were somewhat better.

Characterization of Aegilops kotschyi Boiss. x Triticum aestivum L. hybrid lines

A study of four F5 and one BC1F1 &lt;em&gt;Aegilops kotschyi &lt;/em&gt;Boiss. x &lt;em&gt;Triticum aestivum &lt;/em&gt;L. hybrid lines was conducted to determine their quantitative morphological and qualitative features as well as a molecular investigation was carried out. Observations of ten quantitative traits showed that the F5 hybrid lines exhibited intermediate values between &lt;em&gt;Ae. kotschyi &lt;/em&gt;Boiss. and &lt;em&gt;T. aestivum &lt;/em&gt;L., or had similar traits to one of the parents. These hybrid lines had a significantly lower number and weight of grains per main spike, main spike fertility and 1000-grain weight than &lt;em&gt;T. aestivum &lt;/em&gt;L. cv. ‘Rusałka’. The BC1F1 hybrid line was characterized by wheat-like fertility and phenotype. The F5 hybrid lines were characterized by much higher variability of the analysed morphological traits than &lt;em&gt;T. aestivum &lt;/em&gt;L. cv. ‘Rusałka’. Grains of the hybrid lines had higher protein and micronutrient (iron and zinc) content than wheat grains. The presence of DNA fragments specific to &lt;em&gt;Ae. kotschyi &lt;/em&gt;Boiss. in the genotypes of the hybrid lines was confirmed by seven ISSR (Inter Simple Sequence Repeats) molecular markers. Two ISSR markers – ISSR23690 and ISSR33650 – were the most effective for germplasm analysis of the hybrid lines. The analysed lines can become a source material for improvement of common wheat &lt;em&gt;T. aestivum &lt;/em&gt;L. in crossing programs.

Genetic diversity of wild Auricularia auricula-judae revealed by ISSR analysis

Abstract Auricularia auricula-judae is an edible and medicinal jelly mushroom, and it is widely cultivated in China. In the present study, inter-simple sequence repeat (ISSR) molecular marker was employed to assess the genetic diversity of 22 wild strains and two cultivars of A. auricula-judae obtained from many ecological regions of China. With the use of 11 ISSR primers, a total of 368 (99.7%) and 81 (71.7%) polymorphic loci in wild and cultivated strains were detected, respectively. The mean genetic similarity of A. auricula-judae was 0.75, based on the dendrogram generated via similarity coefficient, all the tested strains were classified into six groups at a similarity level of 76%, and the two cultivated strains consisted of one group alone. The results of principal coordinate analysis were in accordance with UPGMA clustering, and the first most informative coordinate accounted for 75.9% of the variations, indicated a high level of genetic diversity among wild A. auricula-judae strains. In general, ISSR marker was an effective method to discriminate the A. auricula-judae stains and to evaluate their genetic diversity.