Inter-simple Sequence Repeat Fingerprinting Research Articles

Conservation Strategies for Aquilaria sinensis: Insights from DNA Barcoding and ISSR Markers.

The evergreen tree species Aquilaria sinensis holds significant economic importance due to its specific medicinal values and increasingmarket demand. However, the unrestricted illegal exploitation of its wild population poses a threat to its survival. This study aims to contribute to the conservation efforts of A. sinensis by constructing a library database of DNA barcodes, including two chloroplast genes (psbA-trnH and matK) and two nuclear genes (ITS and ITS2). Additionally, the genetic diversity and structure were estimated using inter-simple sequence repeats (ISSR) markers. Four barcodes of 57 collections gained 194 sequences, and 1371 polymorphic bands (98.63%) were observed using DNA ISSR fingerprinting. The Nei's gene diversity (H) of A. sinensis at the species level is 0.2132, while the Shannon information index (I) is 0.3128. The analysis of molecular variance revealed a large significant proportion of total genetic variations and differentiation among populations (Gst = 0.4219), despite a relatively gene flow (Nm = 0.6853) among populations, which were divided into two groups by cluster analysis. There was a close genetic relationship among populations with distances of 0.0845 to 0.5555. This study provides evidence of the efficacy and dependability of establishing a DNA barcode database and using ISSR markers to assess the extent of genetic diversity A. sinensis. Preserving the genetic resources through the conservation of existing populations offers a valuable proposition. The effective utilization of these resources will be further deliberated in subsequent breeding endeavors, with the potential to breed agarwood commercial lines.

Assessment of genotoxic effects of wastewater of Kitchener pool, Nile Delta Region, North Egypt, using Allium test

BackgroundIn the present study, Allium test bioassay was utilized to evaluate the effects of mixed wastewater of agricultural and sewage effluents at Kitchener pool, Gharbia governate, Middle Delta region, North Egypt. Germination indices, mitotic index and aberrations, α, β-esterase isozymes and inter-simple sequence repeat (ISSR) fingerprinting were tested by different concentrations of the wastewater (tap water as control, 25%, 50% and 100% wastewater).ResultsWater analysis recorded high levels of electrical conductivity, cations and anions compared to control, but were in the permitted limits according to FAO (Food and Agricultural Organization) except Mg2+ and K1+ were above the limits. P, N and heavy metals as Pb, Mn and Ni were also higher than the control. Germination indices showed reduction for all parameters studied (root and shoot lengths, root and shoot fresh and dry weights, and tolerance index). Mitotic index decreased, and the percentage of mitotic aberrations increased as the concentration of treatments increased and the time prolonged. Different types of aberrations were recorded in all treatments and its percentage is time and dose independent. Goat cells are the most common type recorded after different times in all treatments. The expression of α, β-esterase enzymes showed variation in different treatments compared to control and ISSR profiles showed considerable polymorphism. Concentration of 25% mixed water induced different profiles for expression of both α- and β-esterase from other treatments, and the cluster analysis based on polymorphism in ISSR fingerprinting revealed the distinction of plants treated with this concentration and the control plants from those treated with high concentrations.ConclusionIt was suggested that concentration of 25% mixed water may be suitable for growth and act as fertilizer. Mixed water from this pool may be genotoxic for Allium cepa plants at early growth if it is used for irrigation in its present form and usage of this wastewater for agricultural purposes may be harmful and must be partially treated and biologically tested before use.

Genetic diversity of toxigenic Fusarium verticillioides associated with maize grains, India.

In the present investigation, prevalence, genetic diversity, and mycotoxin producing potential of Fusarium species associated with maize grain samples were studied from different geographical regions of India. The highest prevalence of Fusarium verticillioides was recorded as 88.52%, followed by F. coffeatum, F. foetens, and F. euwallaceae, 6.55%, 3.27%, and 1.63%, respectively. We isolated 54 strains of F. verticillioides, and their genetic diversity was studied by inter simple sequence repeats (ISSR). The ISSR fingerprints (AG) 8C and (AG) 8G showed 252 and 368 microsatellite sites in the genome of F. verticillioides and resulted in 99-100% repeatability and reproducibility. The Simpson (SID) and Shannon (H) indices (0.78 and 2.36) suggest that F. verticillioides strains exhibit moderate to high diversity. Molecular detection of fumonisin B1 (FB1) biosynthetic genes (FUM1 and FUM13) involved in FB1 production in F. verticillioides was confirmed by polymerase chain reaction (PCR). Furthermore, 91% of the strains were positive for FB1 production, which was affirmed by liquid chromatography with tandem mass spectrometry (LC-MS-MS). In-vitro appurtenance of F. verticillioides spores exhibited a high to moderate effect on the growth and development of the maize. The current finding demonstrated that most F. verticillioides strains showed a wide range of genetic diversity with varied toxigenic and pathogenic potentials. In conclusion, for the first time, F. coffeatum, F. foetens, and F. euwallaceae species were reported from maize grain samples in India. They were positive for FB1 and negatively affecting grain quality, which is a major concern in food safety.

Comparative assessment of SCoT and ISSR markers for analysis of genetic diversity and population structure in some Aegilops tauschii Coss. accessions

AbstractAegilops tauschii, the diploid progenitor of the wheat D-genome, is a valuable genetic resource for wheat breeders. In this study, we compared the efficiency of inter-simple sequence repeat (ISSR) (as an arbitrary technique) and start codon targeted (SCoT) (as a gene-targeting technique) markers in determining the genetic diversity and population structure of 90 accessions of Ae. tauschii. SCoT markers indicated the highest values for polymorphism information content, marker index and effective multiplex ratio compared to ISSR markers. The total genetic diversity (Ht) and genetic diversity within populations (Hs) parameters were comparably modest for the two marker systems. The results of the analysis of molecular variance showed that the genetic variation within populations was significantly higher than among them (ISSR: 92 versus 8%; SCoT: 88 versus 12%). Furthermore, SCoT markers discovered a high level of genetic differentiation among populations than ISSRs (0.19 versus 0.05), while the amount of gene flow detected by ISSR was higher than SCoT (2.13 versus 8.62). Cluster analysis and population structure of SCoT and ISSR data divided all investigated accessions into two and four main clusters, respectively. Our results revealed that SCoT and ISSR fingerprinting could be used to further molecular analysis in Ae. tauschii and other wild species. The high-genetic variability found in this study also indicates the valuable genetic potential present in the investigated Ae. tauschii germplasm, which could be utilized for future genetic analysis and linkage mapping in breeding programmes.

Keragaman Genetik Kultivar Pisang Diploid (AA) Koleksi Cibinong Science Center Berdasarkan Marka RAPD dan ISSR

The banana (Musa acuminata Colla) is considered as an important crop plant due to its high economic value which also has good dietary source. Here, the genetic variation of 20 diploid (AA) banana cultivars from Cibinong Science Center collection were analyzed. Random amplified polymorphic DNAs (RAPDs) and Inter Simple Sequence Repeats fingerprinting of these banana cultivars were carried out by four primers of RPDSs and two primers of inter simple sequence repeats (ISSRs) led to DNA amplification. The amplification products of RPADs and ISSRs were polymorphic, 97.83% and 95%, respectively. Size of the bands was varied from 350bp to 2.0 kbp. The range of genetic distance was from 0.06 to 0.07. The molecular data showed that these banana varieties were diverse collection.

Germination of Persian Walnut Somatic Embryos and Evaluation of their Genetic Stability by ISSR Fingerprinting and Flow Cytometry

Somatic embryos (SEs) can play important roles in genetic manipulation and breeding. They can be used as targets for induced mutagenesis, as material for cryopreservation and germplasm conservation, and for transformation or gene editing in support of plant improvement and proof of gene function. However, germination rates of walnut (Juglans regia) SEs are low, and the genetic stability of plantlets regenerated from them has not been explored. Here, we studied first the effects of gibberellic acid (GA3) and low temperature storage (LTS) on germination of walnut somatic embryos. Second, we assessed the genetic fidelity of plantlets regenerated from these SEs by comparing them to each other and to their cultivar of origin. Results showed that GA3 and LTS increased the walnut SE germination rate. The best rate was observed when SEs were subjected to LTS for 60 d followed by culture on a medium with either 1 or 3 mg·L−1 GA3 (56.6% and 46.6% germination respectively). Genetic stability was evaluated, using flow cytometry and 15 sets of ISSR primers. Flow cytometry indicated that all samples (i.e., regenerated and parental counterpart) showed the same peak. Amplified fragments of inter simple sequence repeats (ISSR) primers ranged in size from ≈200 to 1800 bp. All ISSR profiles of regenerants were monomorphic. Results did not show any genetic differences among plantlets regenerated from SEs or from their parental counterpart. Due to this apparent genetic stability, walnut SEs can be useful for genetic transformation and germplasm conservation.

Molecular and Morpho‐Agronomic Characterization among Introduced Bristle Oat Collection Using ISSR Fingerprinting

Core Ideas The genetic diversity of Avena strigosa was examined in order to clarify its phylogenic relationships and analyze the domestication of these well‐adapted ecotypes in the Tunisian environment. The analysis of molecular variance revealed that the 91% of the variation was within groups of accessions according to their geographic origins and only 9% appeared among groups. Three analyses revealed a scattered distribution, independent of the geographic origin. Knowledge about the genetic variation of bristle oat (Avena strigosa Schreb.) cultivars is helpful for the development of conservation strategies to molecularly assist selection to improve the introduced germplasm in the Tunisian environment. The present study examines the genetic diversity among 22 accessions of A. strigosa and clarifies its phylogenic relationships to analyze the domestication of these well‐adapted ecotypes. Twenty‐two accessions of diploid A. strigosa sampled from 22 various geographical locations were analyzed with 20 universal inter‐simple sequence repeat (ISSR) primers. Twelve morpho‐agronomic traits were scored and all data were compiled to establish the repartition of the total ISSR variation and to analyze the genetic structure of the accessions under study. Out of 275 bands, 252 were recorded as polymorphic. The analysis of molecular variance revealed that 91% of the variation was within groups of accessions according to their geographic origins. In addition, three analyses (Bayesian, principal component analysis, and unweighted pair group method with arithmetic mean) revealed a confused distribution, independent of the geographic origin. Therefore, it may be concluded that the bristle oat accessions are interrelated in spite of their agronomic divergence. Avena strigosa may be a potential forage crop that is suited to marginal Tunisian environments.

ASSESSMENT OF GENETIC COMPONENTS AND GENETIC DIVERSITY OF SIX EGYPTIAN CLOVER (Trifolium alexandrinum L.) GENOTYPES USING ISSR AND URP MARKERS

Six Egyptian clover genotypes, i.e., Helaly, Sakha 4, Gemmeiza 1, Serw1, Giza6 and Sakha composite were used in this study. Data was calculated on four cuts and seasonal yield for fresh and dry forage yield. The results indicated that the mean square values were highly significant for genotypes for all studied traits. Helaly cultivar gave the highest values in four cuts and seasonal yield for fresh forage yield. High heritability values were recorded for all studied traits except 1st fresh yield which recorded moderate value. Phenotypic coefficient of variability (PCV) was higher than genotypic coefficient of variability (GCV) in all cuts and seasonal yields. Genetic variations among the six Egyptian clover cultivars were evaluated using universal rice primers (URP) and inter simple sequence repeat (ISSR) markers. URP fingerprinting detected more polymorphic loci (90%) than the ISSR fingerprinting (77.55%). Mean PIC (polymorphism information content) and band informativness (Ib) for each of these marker systems were (0.21, 0.26 for ISSR and 0.32, 0.46 for URP) respectively, suggested that URP marker systems were effective than ISSR in determining polymorphisms. Pairwise similarity index values ranged from 0.37 to 0.72 for ISSR, 0.23 to 0.62 for URP and 0.29 to 0.65 for combined ISSRs and URP indicated the genetic distinctness among the studied genotypes.

INTRA SPECIFIC ANALYSIS OF GLORIOSA SUPERBA (L) THROUGH ISSR FINGER PRINTING AND DNA SEQUENCING OF ECOTYPES COLLECTED FROM DIFFERENT ACCESSIONS OF TAMIL NADU STATE, INDIA

Diversity within and among the population of Gloriosa superba collected from five different location of Tamil Nadu State, India, were explored by using Inter Simple Sequence Repeat (ISSR) DNA sequencing method. A total of 86.27% of polymorphic bands were seen in 94 reproducible bands generated from 12 number of ISSR primer ranging between 200bp to1000bp of band width. ISSR primer produces the bands with an average polymorphism of more than ninety nine percent among all the ecotypes. The dendrograms drawn for the analysis of genetic similarity in all the ecotypes. Our studies revealed that, genetic variations among different accessions of Gloriosa superba (L) was very well identified with the help of ISSR finger printing technique.

Conservation, ex vitro direct regeneration, and genetic uniformity assessment of alginate-encapsulated nodal cuttings of Sphagneticola calendulacea (L.) Pruski

A well-organized procedure was established for the conservation and distribution of Sphagneticola calendulacea (L.) Pruski [synonym Wedelia chinensis (Osbeck) Merrill] for the first time, using alginate-encapsulated nodal segments (NSs) as synthetic seeds. The ideal beads were obtained through a combination of 2.5% sodium alginate and 75 mM calcium chloride with 84.40 ± 2.20% rate of shoot emergence. The maximum regeneration (88.84 ± 2.24%) from synthetic seeds was achieved on liquid 1/2Murashige and Skoog (MS) medium in comparison to its other formulations. Furthermore, superior frequency (91.09 ± 2.24%) of complete plantlet (having both shoots and roots) formation was achieved when synthetic seeds were cultured on liquid 1/2MS (1.5% sucrose) fortified with 1.0 mg L−1 N6-benzyladenine plus 0.25 mg L−1 α-naphthalene acetic acid. Synthetic seeds could be effectively stored at low temperature (8 °C) up to 90 days with a survival rate of 52.38 ± 3.06%, whereas higher temperature (25 °C) did not support regeneration after 75 days of storage. The plantlets were successfully acclimatized to natural conditions with ~ 89% survival frequency. To by-pass the time-consuming in vitro culture step after encapsulation, synthetic seeds were directly regrown into complete plantlets ex vitro on sand, soil, and vermicompost (1:1:1; w/w). Regeneration rate of 42.22 ± 2.22% was attained when NSs were pretreated on 1/2MS medium containing 4.0 mg L−1 indole-3-acetic acid for 24 h in dark, prior to encapsulation. The random amplified polymorphic DNA and intersimple sequence repeat fingerprinting profiles demonstrated genetic uniformity amongst the regenerated plantlets, in vitro mother plant, as well as in vivo wild plant.

Analysis of the molecular diversity of R. solani isolates from five Ugandan agro-ecological zones using inter - simple sequence repeat markers

This study used seven inter-simple sequence repeat (ISSR) markers to characterize 55 R. solani isolates in order to establish their genetic diversity. The isolates were from five common bean growing agro-ecological zones of Uganda; the Southwest highlands (SW), Lake Victoria crescent and Mbale farmlands (LVC), Teso farming system (TFS), the Northern mixed farmlands (N) and the Western highlands and Semliki flats (W). DNA was extracted from 7-day old R. solani isolates growing on potato dextrose agar and amplified using PCR. Molecular analysis based on the ISSR fingerprints established moderate genetic diversity (mean = 0.389 ± 0.022). In addition, a high degree of intraspecific variation was observed by cluster analysis which generated a dendrogram with 5 highly reliable clusters (p ≥ 0.95) whose composition was independent of agro-ecological zones. Further evidence of intraspecific variation was provided by analysis of molecular variance which ascribed all the observed variation to genetic differences within the isolates. Isolates from SW, W, TFS and N had significant standardized index of association values indicative of clonal reproduction while isolates from LVC did not have significant values whence were sexual. The genetic diversity revealed by our study means that screening common bean germplasm for sources of resistance to R. solani should be done using diverse pathotypes and secondly, the breeders should pyramid many disease resistance genes in elite cultivars to provide durable resistance against R. solani.

Evaluation and comparison of the genetic structure of Bunias orientalis populations in their native range and two non-native ranges

We studied the invasive warty cabbage Bunias orientalis (Brassicaceae) in three geographically distinct areas. Using inter-simple sequence repeat fingerprinting, we analyzed warty cabbages, including non-native populations, from the eastern Baltic and western Siberian regions and native populations from southwestern Russia. The eastern Baltic region and western Siberia represent the two opposite directions of B. orientalis spread in climatically different zones. The genetic structures of the native and non-native B. orientalis populations were assessed through analysis of molecular variance (AMOVA) and the Bayesian clustering method and by determining the main measures of genetic diversity. AMOVA revealed considerable population differentiation in both the native and invasive ranges. Our results did not indicate a decrease in genetic diversity in the non-native populations of B. orientalis. Similar measures of genetic diversity and genetic structure were determined in the invasive populations in two geographically and ecologically distinct, non-native regions located in Europe and Asia. In both of these regions, higher genetic diversity was detected in the non-native populations than in the native region populations, which may be due to multiple introductions. However, Bayesian clustering analysis revealed slightly different sources of invasive populations in the two non-native regions. Genetic diversity patterns revealed the lack of isolation by distance between populations and confirmed the influence of anthropogenic factors on the spread of B. orientalis. The significance of native populations as germplasm resources for breeding is discussed.

Genetic divergence and allelic-specificity in relation to expression of voltinism in silkworm using ISSR and RAPD fingerprinting

The silkworm B. mori is a multicellular organism revealing genetic resources which makes an ideal model for lepidoptera for the present investigation. With the objective of targeting distinctive markers for utilization in future breeding programmes, Bivoltine and Polyvoltine silkworm strains were used by inter-simple sequence repeats (ISSR) and random amplified polymorphic-DNA (RAPD) fingerprinting to detect their genetic versatility and volatility. Six ISSR primers generated 99 markers, of which 76.76% were found to be polymorphic with an average number of observed alleles (Na) (1.86 ± 0.40), an effective number of alleles (Ne) (1.43 ± 0.30) as well as six RAPD primers that produced a total of 95 bands, developing 61.05% polymorphism with Na (1.93 ± 0.51) and Ne (1.18 ± 0.30). The dendrogram produced by UPGMA analysis, based on Dice’s coefficient, clustered four races into two major groups which accurately segregated them according to their inheritance of voltinism. In this research, the ISSR markers were more accurate than the RAPD markers and ISSR also displayed better polymorphism. The outcome showed that the bivoltine strains exhibited higher allelic expressions with ISSR primers when compared to the polyvoltine strains. Despite exhibiting their unique race by certain DNA markers, most of the primers represented voltinism-specificity. Hence molecular marker amplification is a beneficial approach to reveal genetic divergence among closely related strains, and molecular characterization of phylogenetic relationships in addressing evolutionary evidences of individuals.

Analysis of molecular variance and population structure in southern Indian finger millet genotypes using three different molecular markers

The genetic relationship among 42 genotypes of finger millet collected from different geographical regions of southern India was investigated using random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR), and simple sequence repeats (SSR) markers. Ten RAPD primers produced 111 polymorphic bands. Five ISSR primers produced a total of 61 bands. Of these, 23 bands were polymorphic. The RAPD and ISSR fingerprints revealed 71.3 and 37.4% polymorphic banding patterns, respectively. Thirty-six SSR primers yielded 83 scorable alleles in which 62 were found to be polymorphic. Out of 36 SSR primers used, 14 primers (46.6%) produced polymorphic bands. The SSR primer UGEP7 produced a maximum number of six alleles. Mean polymorphic information content (PIC) of RAPD, ISSR and SSR were 0.44, 0.28, and 0.14, respectively. Molecular variances among the population were 2, 11, and 1% for RAPD, ISSR, and SSR markers, respectively. SSR produced 99% molecular variance within individuals. RAPD and ISSR markers produced a low level of molecular variance within individuals. The STRUCTURE (model-based program) analysis revealed that the 42 finger millet genotypes could be divided into a maximum of four subpopulations. Based on the Bayesian statistics, each RAPD and SSR marker produced three subpopulations (K=3), while ISSR marker showed four subpopulations (K=4). This study revealed that RAPD and SSR markers could narrow down the analysis of population structure and it may form the basis for finger millet breeding and improvement programs in the future.

Genetic and Chemical Profiling of Gymnema sylvestre Accessions from Central India: Its Implication for Quality Control and Therapeutic Potential of Plant.

Background:Gymnema sylvestre, a vulnerable plant species, is mentioned in Indian Pharmacopeia as an antidiabetic drugObjective:Study of genetic and chemical diversity and its implications in accessions of G. sylvestreMaterials and Methods:Fourteen accessions of G. sylvestre collected from Central India and assessment of their genetic and chemical diversity were carried out using ISSR (inter simple sequence repeat) and HPLC (high performance liquid chromatography) fingerprinting methodsResults:Among the screened 40 ISSR primers, 15 were found polymorphic and collectively produced nine unique accession-specific bands. The maximum and minimum numbers of amplicones were noted for ISSR-15 and ISSR-11, respectively. The ISSR -11 and ISSR-13 revealed 100% polymorphism. HPLC chromatograms showed that accessions possess the secondary metabolites of mid-polarity with considerable variability. Unknown peaks with retention time 2.63, 3.41, 23.83, 24.50, and 44.67 were found universal type. Comparative hierarchical clustering analysis based on foresaid fingerprints indicates that both techniques have equal potential to discriminate accessions according to percentage gymnemic acid in their leaf tissue. Second approach was noted more efficiently for separation of accessions according to their agro-climatic/collection siteConclusion:Highly polymorphic ISSRs could be utilized as molecular probes for further selection of high gymnemic acid yielding accessions. Observed accession specific bands may be used as a descriptor for plant accessions protection and converted into sequence tagged sites markers. Identified five universal type peaks could be helpful in identification of G. sylvestre-based various herbal preparations.SUMMARY Nine accession specific unique bandsFive marker peaks for G. sylvestre.Suitability of genetic and chemical fingerprinting Abbreviations used: HPLC: High Performance Liquid Chromatography, ISSR: Inter Simple Sequence Repeats, CTAB: Cetyl Trimethylammonium Bromide, DNTP: Deoxynucleotide Triphosphates

Assessment of ISSR based molecular genetic diversity of Hassawi rice in Saudi Arabia

Inter simple sequence repeat (ISSR) analysis, using 14 primers was performed to estimate genetic diversity among 27 landraces of Hassawi rice growing in Al-Ahsa region of Saudi Arabia and deposited at King Abdulaziz City for Science and Technology with KACST IDs. The average polymorphism produced by 11 selected primers was more than 75%. The analysis of ISSR polymorphism divided the examined rice landraces into two groups; In one group (A), one accession (KACST 191) was clearly delimited as a distant landrace from other 12 landraces grouped in two clusters; cluster I of seven landraces of close geographic distributions; four of them grow at close geographic locations (KACST IDs 32, 183, 184, 185, 186, 187 and 188) and cluster II is comprised of five landraces KACST IDs (190, 308, 352, 353 and 355). In group B, the landraces were more closely related to each other as compared to the landraces of group A. In this group a small cluster of two landraces (KACST 305 & KACST 333) was clearly distant from a large group of three clusters comprised of landraces having KACST IDs 189 & 192, landraces 302, 306, 307, 308 & 310 and landraces with KACST IDs 334, 351, 354, 356 & 357 respectively. These results indicate that ISSR fingerprints are efficient in the identification and resolution of genetic diversity between the landraces of the Hassawi rice and will be an efficient method in the authentication of the rice germplasm in the gene bank of Saudi Arabia.

Molecular variation of improved durum wheat genotypes based on inter-simple sequence repeats fingerprinting

Durum wheat (Triticum turgidum L. var. durum) is an important crop with high protein content and superior cooking quality which used for Pasta production. In present study, the molecular diversity of eighteen durum wheat breeding lines along with one durum wheat check cultivar were evaluated based on inter simple sequence markers. Eight used primers amplified a total of 93 bands, among which 77 bands (about 83%) were polymorphic. A total of 77 polymorphic fragments were scored with average 9.6 polymorphic bands per primer. The polymorphism information content value ranged between 0.27 and 0.36 for ISSR primers. Cluster analysis using UPGMA method and Dice similarity coefficient grouped the 19 genotypes into four separated clusters. The Dice similarity coefficients revealed maximum similarity (0.91) between 20A-URDYT-10 and 20A-URDYT-11 genotypes. PCA based on molecular data distinguished genotypes similar to the cluster analysis results. The results revealed that ISSR technique is a simple, informative and suitable approach for assessment of molecular diversity in durum wheat.

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).

Comparative analysis of ISSR marker polymorphism in populations of yak (Bos mutus) and in F1 hybrids between yak and cattle in the Sayan-Altai region

The genetic variability in seven yak populations from the Sayan-Altai region and in F1 hybrids between yak and cattle (khainags) was investigated with the help of a technique that involves the use of inter simple sequence repeat (ISSR) markers generated with PCR primers (AG)9C and (GA)9C. Samples for the analysis were collected in Mongolia, Tuva, and Altai from 2008 through 2012. The examined yak populations differed in in the presence/absence of ISSR fragments, as well as in their frequency. In total, 46 ISSR fragments were identified using two marker systems; the proportion of polymorphic loci constituted 76% and 90% for the AG-ISSR and GA-ISSR markers, respectively. For the total sample of yaks, total genetic diversity (Ht), within-population diversity (Hs), and interpopulation diversity (Gst) constituted 0.081, 0.044, and 0.459 for the AG-ISSR and 0.137, 0.057, and 0.582 for the GA-ISSR markers, respectively. Based on ISSR finger printing, species- and breed-specific DNA patterns were described for the three groups of animals (yaks, cattle, khainags). For the domestic yak, the species-specific profile was represented by eight ISSR fragments. Genetic relationships between the yak populations, cattle breeds, and khainags were examined with the help of four different approaches used in the analysis of population structure: estimation of phylogenetic similarity, multidimensional scaling, principal component analysis, and cluster analysis. Clear evidence on the differentiation of the populations examined at the interspecific, as well as at intraspecific, level were obtained. Similar (relative); as well as remote (isolated), yak populations were identified. Khainags occupy an intermediate position between yak and cattle. However, the data on the ISSR-PCR marker polymorphism (genome polymorphism, population structure).indicate that part of the analyzed khainag genome was more similar to the yak genome than to the cattle genome.

Comparative efficiency of functional gene-based markers, start codon targeted polymorphism (SCoT) and conserved DNA-derived polymorphism (CDDP) with ISSR markers for diagnostic fingerprinting in wheat (Triticum aestivumL.)

Three molecular markering techniques: inter-simple sequence repeat (ISSR); start codon targeted (SCoT), conserved DNA-derived polymorphism (CDDP) markers were compared for fingerprinting of 40 varieties of bread wheat. The number of scoreable and polymorphic bands produced using the ISSR, SCoT and CDDP primers for varieties was more than that of genotypes. Average polymorphism information content (PIC) for ISSR, SCoT and CDDP markers was 0.39, 0.41 and 0.34, respectively, and this revealed that three different marker types were equal for the assessment of diversity amongst genotypes. Cluster analysis for three different molecular types revealed that genotypes taken for the analysis can be divided in three and four distinct clusters. There were no significant differences among these markers in terms of the evaluation of genotypes. These results suggest that efficiency of SCoT, CDDP and ISSR markers was relatively the same in fingerprinting of genotypes but SCoT and CDDP analysis are more effective in fingerprinting of wheat genotypes. To our knowledge, this was the first detailed report of a comparison of performance among two targeted DNA region molecular markers (SCoT and CDDP) in comparision with ISSR technique on a set of samples of wheat cultivars. Overall, our results indicate that SCoT, ISSR and CDDP fingerprinting could be used to detect polymorphism for genotypes of wheat.