Random Amplified Polymorphic DNA Data Research Articles

Effects of Selenium on DNA Methylation and Genomic Instability Induced by Drought Stress in Wheat (Triticum aestivum L.)

The main purpose of the study was to clarify the effect of selenium (Se) on DNA damage and DNA methylation in wheat (Triticum aestivum L.) plants exposed to polyethylene glycol (PEG)-induced drought stress under in vitro tissue culture. Random amplified polymorphic DNA (RAPD) and coupled restriction enzyme digestion-random amplification (CRED-RA) were utilized to explain the DNA damage grade and variations in DNA methylation patterns, respectively. The outcomes indicate that drought stress gives rise to a rise in RAPD profile variations (as DNA damage) and a decrease in genomic template stability (GTS) rate and DNA methylation changes. According to the RAPD data, the greatest GTS value was computed at 56.9% (5% PEG 6000), and the lowest GTS value was 41.2% (15% PEG 6000), demonstrating the adverse effects of PEG 6000. However, DNA damage can be reduced by treatment with sodium selenate (2, 4, and 6 µM of Na2SeO4) together with PEG (5%, 10%, and 15% PEG 6000)-induced water deficits. Moreover, according to CRED-RA analysis, PEG-induced DNA methylation rates were changed after treating different doses of Se. These data demonstrate that Se dose-dependently modulates both DNA damage and methylation alterations induced by drought in wheat.

Assessment of Genetic Diversity among the Elite Rose (Rosa spp.) Accessions Using Rapd Markers

Aims: Owing to its export value in flower trade elsewhere in the world, Rose is the key commercial flower crop and the area under rose cultivation is ever increasing and the end-users always prefer new color variations. Hence, evolving new cultivars with novel color characteristics is the need of the hour, for which understanding genetic variation in the available cultivars is very much needed. 
 Study Design: This investigation was conducted to analyze the genetic diversity of 11 elite and commonly cultivated rose accessions in South India by using randomly amplified polymorphic DNA (RAPD) markers.
 Place and Duration of Study: Department of Floriculture and Landscape Architecture, Horticultural College and Research Institute, TNAU, Coimbatore.
 Methodology: A total of 10 RAPD primers were employed, which was sufficient to distinguish the investigated rose cultivars.
 Results: Among the 44 PCR products produced by these markers, 39 (88.64%) were found to be polymorphic bands. The number of amplified products per RAPD primer varied from 3 to 8 with a mean of 4.4 bands per primer. The Un weighted paired group of arithmetic means (UPGMA) dendrogram distinguished the rose accessions into two major clusters suggesting that the accessions were different from each other. The genetic similarity coefficients were determined with this RAPD data, and they were ranged from 0.59 to 0.89.
 Conclusion: Molecular profiling data of this study have contributed to characterize and catalogue the rose germplasm data, which will be useful to identify the diverse rose lines for further breeding program that have the potential to improve the color variations.

Evaluation in Genetic Variation of Krachai by Sequence Related Amplified Polymorphism (SRAP) and Random Amplified Polymorphic DNA (RAPD) Techniques

Krachais are local name of Thai herb which are identified within 2 genera, namely Bosenbergia (white or red krachai) and Kaempferia (black krachai). The rhizome of Bosenbergia rotunda (L.) Mansf. contains major aromatic compounds against COVID19 but its many morphological characteristics such as leaves, stems and rhizome are like other species in same genus or family. In this study, a total of 13 accessions containing 5 samples of B. rotunda, 2 samples of Boesenbergia spp. and 3 samples of Kaempferia parviflora including 3 samples of other species in same family as outgroups were analyzed and clustered using sequence-related amplified polymorphism (SRAP) and random amplified polymorphism DNA (RAPD) markers. The results showed that 8 SRAP primers (M1E1, M1E2, M1E7, M2E10, M3E9, M5E1, M5E2 and M6E10) could generate 79 polymorphism bands with an average of 92.15% whereas a total of 5 RAPD primers (OPY04, OPY02, OPY04, JAT11 and JAT12) could give 64 polymorphisms with 100% as a percentage of the polymorphism band. The PIC of the SRAP marker (0.470) has a higher value than the RAPD marker (0.264). The highest similarity coefficients within genus Boesenbergia of 1.000 and 0.952 were obtained from SRAP and RAPD markers, respectively. The UPGMA dendrogram of SRAP and RAPD information among krachai presented 2 and 4 groups, respectively. The cluster of Boesenbergia was separated from K. parviflora and other species in same family. Furthermore, the results also pointed that Boesenbergia sp. from Phayao is in correct genus and is B. pandurata (Roxb.) Schltr. because of having red leaf while Boesenbergia sp. from Chiang Rai showed confusion between SRAP and RAPD data. It was concluded that SRAP and RAPD have great potential for the study of genetic diversity of Boesenbergia and other species in family Zingiberaceae.

Genetic relationships and genome verification of Thai banana cultivars using Random Amplification of Polymorphic DNA (RAPD) markers

Abstract. Boonsrangsom T, Fuenghoi C, Premjet D, Suvittawat K, Ratanasut K, Sujipuli K. 2023. Genetic relationships and genome verification of Thai banana cultivars using Random Amplification of Polymorphic DNA (RAPD) markers. Biodiversitas 24: 3758-3765. Edible bananas and plantains, belonging to the family Musaceae, genus Musa, represent one of the most important fruit crops, with an annual production of more than 65 million tons worldwide. Bananas have several hybrid variations since they are descended from the two species Musa acuminata Colla (AA genome) and Musa balbisiana Colla (BB genome). Different morphological traits divide almost hybrid bananas into various genomic groupings. Banana genome categorization and identification, however, have always been challenging issues. This study aimed to assess the genetic relationships and verify the genomes of Thai banana cultivars using random amplification of polymorphic DNA (RAPD) markers. Using the 15 selected RAPD markers, 149 RAPD bands were found, with sizes ranging from 0.2 to 3.2 kb, and 88.6% were polymorphic. Polymorphic information content (PIC) values ranged from 0.18 to 0.42, averaging 0.30. Based on the Jaccard coefficient, the unweighted pair-group method arithmetic average (UPGMA) analysis showed that the banana samples had a similarity range of 0.27 to 1.00 with a mean of 0.56, demonstrating an abundance of viability across six banana genomes. The dendrogram generated from RAPD data revealed that all 18 Musa samples could be divided into two main groups (Group I and II). Three additional subgroups were created for each primary group (A, B, and C). The accurate identification and genetic data on the available genetic resources for bananas will be beneficial for breeding and conservation programs.

Genetic Diversity in Some Sesame (Sesamum indicum L.) Accessions Detected by Agro-morphological Characters and RAPD Markers*

Agro-morphological and Randomly Amplified PolymorphicDNA (RAPD) markers were used to determine the diversity andrelationships among 25 accessions of sesame from Sudan. Data on 16agro-morphological characters were collected from a field experiment,carried out at Shambat for three consecutive seasons (2006-2008) andsubjected to the procedure of cluster analysis. The results showed thatcluster analysis, based on Euclidean distance, of the agro-morphologicalcharacters grouped the 25 sesame accessions into seven clusters.Application of RAPD markers generated 48 bands with a 97.9%polymorphism. A dendrogram constructed from the RAPD data classifiedthe 25 sesame accessions into eight major clusters. It was concluded thatfor efficient estimation of genetic diversity and interrelationships amongsesame accessions, information obtained from both agro-morphologicalcharacters and RAPD should be combined.

Genetic Characterization of Salicornia persica Akhani (Chenopodiaceae) Assessed Using Random Amplified Polymorphic DNA

Salicornia is a wild and annual (biennial, in some species) halophytic plant from Chenopodiaceae family that grows near salt marshes and salted wetlands or the vicinity of coastal areas in Asia, North America, and the Middle East. It is also grown in semi-arid areas of Iran such as Isfahan, Fars, and Yazd provinces. Genetic variability and populations, structure were studied in 10 geographical populations of Salicornia persica. Genetic diversity parameters were determined in these populations. 10 of 20 random amplified polymorphic DNA (RAPD) primers produced 146 reproducible bands with average of 14.6 bands per primer and 88.67% of polymorphism. OPA10 primer showed the highest number of effective allele (Ne), Shannon index (I) and genetic diversity (H). The highest values of genetic diversity in RAPD markers were obtained in Esfahan, Nain, it is 70km to Varzaneh populations. WARD trees of RAPD data grouped the populations in two different clusters/groups, indicating their genetic difference which is discussed in details. The results of this study showed that the level of genetic variation in Salicornia persica is relatively low. WARD-based dendrogram showed a close relationship between members of Esfahan, Varzaneh and Esfahan, the river of Zayanderud at Varzaneh while the Yazd, Meybud and Yazd, Nádüshan protected population differ the most from the other populations. Principal component analysis, however, showed some minor differences with WARD-based dendrograms.

Genetic Relationship and Diversity Analysis in Arecanut (Areca catechu L.) Genotypes using Molecular Markers

Background: Arecanut (Areca catechu L.) is an important plantation crop of India belongs to the family Arecaceae. As it is a highly cross-pollinated crop there is a significant difference among the genotypes. Morphological traits used for determining diversity and relationships among genotypes or variety are prone to environmental influences. Thus, the usefulness of molecular markers has been investigated as a means of characterizing and discriminating difference more precisely. Therefore, the present study was carried out to assess the genetic relationship and diversity among the arecanut genotypes by employing RAPD, ISSR and SSR markers. Methods: A total of 11 genotypes are being grown in University of Agricultural and Horticultural Sciences (UAHS), Shivamogga, Karnataka, India, which includes both local and exotic collections. These 11 genotypes were evaluated for genetic variations using molecular markers viz., random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR) and simple sequence repeats (SSR). Result: All the markers studied showed significant polymorphism among the genotypes. Jaccard’s genetic similarity coefficient values of RAPD, ISSR and SSR markers were found in the range of 0.56-0.76, 0.55-0.74 and 0.52-0.91. The higher similarity was observed between the genotypes Mohitnagar and Mangala, as well as Theerthahalli Local and Hirehalli Dwarf. The genotypes Maidan Local and Cameroon were placed in very distinct clusters, showing that they are having very distinct traits. The dendrogram prepared using SSR data separately and combining data of RAPD, ISSR, SSR markers showed similar results. Therefore, employing SSR markers for further studies will be more useful for identifying germplasm for varietal improvement programmes.

Genetic diversity of avocado (Persea americana Mill.) germplasm in Vietnam using RAPD and ISSR molecular markers

Avocado is a significant cash crop in Vietnam, while little is known about its genetic diversification. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were performed to investigate the genetic diversity of twenty-eight imported and domestic avocado cultivars being maintained at Western Highlands Agriculture and Forestry Science Institute, Dak Lak, Vietnam. 18 RAPD and 15 ISSR primers produced 3183 and 2807 scorable bands, of which 83.92% and 71.72% were polymorphic, respectively. The RAPD markers exhibited an average PIC of 0.27 and Rp index of 12.63 whereas the mean PIC and Rp values of ISSR primers were 0.21 and 13.37, respectively. The correlation between RAPD and ISSR markers was low (r = 0.338), suggesting that the ability to resolve genetic variation among varieties may relate to the number of detected polymorphisms rather than the marker employed. Nevertheless, the correlation between ISSR and combined data was high (r = 0.791) and the correlation between RAPD and combined matrices was even higher (r = 0.897). This indicates that RAPD markers have slightly higher efficiency over ISSR to resolve genetic variation among 28 avocado cultivars. High genetic diversity among 28 avocado cultivars was revealed with the Jaccard’s similarity coefficient ranging from 0.623 to 0.913 based on combined data analysis. The UPGMA dendrogram generated from combined RAPD and ISSR data grouped Vietnamese domestic and imported avocado cultivars into three different groups at 72% similarity. These results could be applied to the avocado conservation and breeding programs

Assessment of sugar beet genetic diversity in the Republic of Kazakhstan by using RAPDmarkers and agromorphological traits

Sugar beet is a highly valuable and profitable crop in the Republic of Kazakhstan. It is the only source of raw materials for the production of crystalline sugar and incidentals (tops, bagasse, and molasses). This study aimed to determine the genetic diversity of 53 sugar beet samples, 19 parental lines, and 34 hybrids from Kazakhstan by using random amplified polymorphic DNA (RAPD) markers, agromorphological traits, root mass weight, and sugar content at the Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Republic of Kazakhstan. The experimental conditions were optimized for the 14 RAPD primers used in this study. The polymorphism index contents varied from 0.24 to 0.46, and all 14 primers were classified as moderately informative. The cluster analysis of RAPD data divided the sugar beet samples into seven groups. The greatest distance (D = 1.4) was noted among the male sterile lines „MS-1611‟, „MS-1631‟, „MS-97‟, and „MS-2113‟ and the pollinator lines „VP-44‟ and „VP-23‟. The samples were divided into six groups on the basis of root mass weight and sugar content via cluster analysis. The hybrids „RMS-90‟, „RMS-134‟, „RMS-133‟, „RMS-136‟, and „Ramnes‟ were grouped in a cluster that showed the highest values of root mass weight, which ranged from 610 g to 680 g. However, the samples with high sugar content (18.2–18.5), i.e., „Shecker‟, „2198‟, „H-22‟, and „1005‟, were grouped into a cluster with a distance of D = 0.8. Lines located at a large genetic distance from each other were recommended for hybridization when creating highly productive hybrids. These findings can be applied in the development of new productive and stable sugar beet hybrids in Kazakhstan.

Morphological and molecular markers based assessment of genetic diversity of a valuable endemic plant Lasiurus sindicus Henr. in the arid region of Rajasthan, India

Morphological and molecular markers are useful in genetic diversity assessment and improvement of plants. In the present study, five morphological traits, random amplified polymorphic DNA (RAPD) and Start codon targeted (SCoT) markers were used for genetic diversity evaluation of Sewan grass (Lasiurus sindicus Henr.), a valuable endemic plant of Indian Thar desert. Accessions collected from 14 different sites were used for measuring morphological traits, namely plant height (PH), number of tillers (NT), number of nodes (NN), leaf length (LL) and spike length (SL) which showed large variations among populations; particularly PH, NT and LL. Ward’s linkage hierarchical cluster analysis exhibited two major clusters and Cluster I contained two minor clusters. The percentage polymorphic bands (PPB) produced were 89.64% and 64.51% for RAPD and SCoT respectively. RAPD markers based dendrogram revealed three clades while there was no clear clade formation with SCoT markers. Single primer amplification reaction (SPAR) analysis with combined data of RAPD + SCoT showed more similarity with SCoT than with RAPD clusters. AMOVA revealed higher variation within population (90%) than among populations (10%) of L. sindicus. The Principal coordinate analysis (PCoA) also supported this result. There was no correlation between morphological and molecular data confirming environmental impact on morphological variation. SCoT and SPAR markers have clearly identified a novel genotype (LS JS 3) which has high values of PH, NN and LL. This study suggests that morphological data combined with molecular data can alone help in the identification of novel genotypes of L. sindicus among its populations.

Analysis of Genetic Diversity Between Eriobotrya japonica (Thunb.) Lindl. (Rosaceae) Populations Growing in the Aegean Region of Turkey

In this study, we performed a genetic diversity using RAPD (Random amplified polymorphic DNA) and ISSR (Inter-simple sequence repeats) markers for some Eriobotrya japonica populations grown in the Aegean region of Turkey. PCR was performed with all DNA samples and primers with ability of scoring band. Phylogenetic analysis and pairwise genetic distance between the populations were calculated by using the PAUP analysis program. According to the RAPD data, a total of 33 bands were obtained and 21 of them were polymorphic. The closest genetic distance (0.09677) was found between Aydın and Nazilli populations, while the most distant value was found 0.44000 between Salihli and Nazilli populations. According to the ISSR data, a total of 43 bands were obtained and 18 of them were polymorphic. The closest genetic distance (0.09302) was found between İzmir and Aydın populations, while the most distant values (0.48276) were found between Denizli and Nazilli populations. As a result of this study, the rate of polymorphism obtained in ISSR technique was found to be lower than the RAPD technique.

Molecular diversity of the Fusarium fujikuroi species complex from maize

Random amplified polymorphic DNA (RAPD) markers were used to estimate genetic relationship and diversity of Fusarium species associated with pink ear rot of maize. Three Fusarium species – F. verticillioides, F. temperatum and F. subglutinans sensu stricto were collected from contaminated corn kernels. A collection of 41 randomly selected Fusarium isolates (16 F. verticillioides, 16 F. temperatum and nine F. subglutinans sensu stricto) was screened for polymorphism with thirty decamer primers. Seventeen primers that had generated a high number of polymorphic loci were used for the analysis of genetic diversity. The primers yielded a total of 146 polymorphic loci, an average of 8.59 polymorphic bands per primer. The percentage of polymorphic bands (%P) was 46.1%. The RAPD-based UPGMA analysis demonstrated that although F. temperatum and F. subglutinans s.s. form two distinct groups they are more similar to each other than to F. verticillioides. Fusarium verticillioides was the most heterogenous species (Nei’s genetic diversity 0.180), while the least heterogenous one was F. subglutinans s.s. whose genetic diversity was 0.098. The analysis of the translation elongation factor 1-α and β-tubulin gene sequences as well as the mating type ratio were employed to support the RAPD data.

Determination of the Genetic Relationships Among Salvia Species by RAPD and ISSR Analyses.

Salvia L. is the largest genus of the family Lamiaceae, which includes approximately 1000 species. According to recent studies, 100 Salvia species in total grow in Turkey. At the same time, 53% of them are endemic. The purpose of this study was to investigate the genetic relationships among 15 Salvia species that grow in wild conditions in Turkey's Eastern Anatolia region. The genetic relationships among 15 Salvia species were investigated using inter-simple sequence repeat (ISSR) and random amplified polymorphic-DNA (RAPD) profiles in the present study. Thirteen ISSR primers and 11 RAPD primers were utilized. The ISSR and RAPD data were combined to construct the unweighted pair group method using arithmetic average cluster. Based on the RAPD and ISSR data, the Salvia species were classified into six groups. As a result of the combined analysis, it was shown that similarities between the species varied between 0.54 (S. rosifolia-S. sclarea, S. rosifolia-S. limbata, and S. staminea-S. verticillata) and 0.93 (S. sclera-S. divaricata). The findings show that the two markers represent powerful instruments for assessing the genetic diversity and relationships among Salvia species.

Characterisation of Thai strawberry (Fragaria × ananassa Duch.) cultivars with RAPD markers and metabolite profiling techniques

Strawberries (Fragaria × ananassa Duch.) are one of the most economically important fruit crops worldwide, several commercially viable cultivars are cultivated in the northern region of Thailand. The morphological characters at the young vegetative seedling stage can be very similar, which has hindered breeding efforts. The present study assesses the ability of random amplification of polymorphic DNA (RAPD) markers and metabolomics techniques to distinguish six strawberry cultivars. Both techniques showed congruent results for the leaf tissue and classified the cultivars into three major clusters. For the most different cultivars, Akihime and Praratchatan No.80, fruits were analysed at eight fruit ripening stages. The data highlighted a broad biological variation at the early ripening stages and less biological variation at the mature stages. Key metabolic differences included the polyphenol profile in Praratchatan No.80 and fatty acid synthesis/oxidation in Akihime. In summary, the RAPD and metabolite data can be used to distinguish strawberry cultivars and elucidate the metabolite composition of each phenotype. This approach to the characterisation of genotypes will benefit future breeding programmes.

Morphological and molecular studies of three species of Boerhavia L. from Ile-Ife, Nigeria

A wide range of plasticity and polymorphism have been documented in the genus Boerhavia. More so, the possible presence of natural hybrids among the species of the genus has made species identification more difficult. This study employed morphological characters, pollen parameters as well as Random Amplified Polymorphic DNA (RAPD) to identify and elucidate the phylogenetic relationship that exists among the three species of Boerhavia distributed in Ile-Ife, Nigeria. Qualitative and quantitative morphological characters were observed and measured respectively. The acetolysis of the pollen grains was carried out according to Erdtman method. Fresh and young leaves of the Boerhavia species studied were collected for genomic DNA extraction using modified Dellarpota procedure. The quality and concentration of DNA was assessed by gel electrophoresis on 2% agarose with known concentrations of undigested lambda DNA. Subsequently, the DNA quantification was done according to standard measurement. The Principal Components Analysis of the morphological traits and the pollen grain studies indicated that the three Boerhavia species studied have a very high level of relationship. However, the Single Linkage Cluster Analysis of the morphological data and the unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of RAPD data revealed that B. erecta is distantly related to B. coccinea and B. diffusa. Despite the fact that the three Boerhavia species studied possess high level of similarity, they can still be distinguished from each other. In conclusion, B. coccinea and B. diffusa are more closely related to each other than B. erecta.
 Key words: RAPD marker, Pollen grains, Phylogenetic relationship, Polymorphism

Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers

Random Amplified Polymorphic DNA (RAPD) analysis was performed to assess the genetic variability in sixteen selected germplasms of rice, Oryza sativa L. using eight decamer RAPD primers. The data obtained from this investigation reveals a high level of polymorphism between cultivars. The primers produced a total of 255 bands of which all 255 bands were polymorphic indicating 100% polymorphism. The size of the amplified bands ranged from 220 bp to 2290 bp. The number of polymorphic fragments ranged from 24 to 49 with an average of 32 polymorphic fragments for each primer. The primer OPX04 produced the maximum number (49) of polymorphic bands while the OPB04 and OPB17 produced the minimum number (24) of polymorphic bands. The polymorphic information content (PIC) values ranged from 0.6616 to 0.8845 with an average of 0.832. The highest PIC value (0.8845) was obtained for primer OPL03. The RAPD data was analyzed to determine the pair-wise genetic similarity coefficients which ranged from 0.00 to 0.83. The BRRIdhan 23 and the BRRIdhan 41 varieties were the closest genotypes with the highest similarity index of 83%. This was followed by 77% similarity between a pair of cultivars Kalamona and Horkuch. On the other hand, 100% dissimilarity was seen between BRRIdhan 53, BRRIdhan 50, BRRIdhan 10, BRRIdhan 70, BRRIdhan 54, BRRIdhan 40, BRRIdhan 23, BRRIdhan 47, BRRIdhan 41 and Dadsail respectively and between BRRIdhan 53 and Horkuch; indicating a high level of variability between paired genotypes. Cluster analysis was performed using Unweighted Paired Group of Arithmetic Means (UPGMA). The UPGMA dendrogram resolved the selected rice cultivars into four clusters.

Diversity analysis of Sweet Potato (Ipomoea batatas[L.] Lam) genotypes using morphological, biochemical and molecular markers

Sweet potato [Ipomeabatatas(L.) Lam.]is a nutritious food crop primarily grown by small and marginal farmers. successful breeding and germplasm conservation programs demands characterization of its germplasm. Here, we tried to determine genetic diversity among 21 sweet potato genotypes using morphological, biochemical and molecular markers. Ten morphological traits were studied and subjected to analysis of variance (ANOVA). Mean square due to germplasm were highly significant as well as wide mean range performance was observed for tuber number per plant, individual tuber weight, tuber fresh yield per plant, tuber dry yield per plant, tuber yield per plot and tuber length. UPGMA (Unweighted Pair Group Method Arithmetic Average) cluster analysis based on morphological traits separated the germplasm into three groups. The genotypes Gautam, Shree Arun, RS-92 and CO-3-4 appeared promising with regard to yield characters. Total phenol was maximum in in V-12 genotype (1.39 mg), while minimum was recorded in Samrat genotype (0.95 mg). The highest total antioxidant was observed in the genotype Samrat (0.30 mg), while minimum was recorded in the genotype Navsari Local (0.16 mg). Molecular diversity analysis was carried out using 25 RAPD (Random Amplified Polymorphic DNA) primers, out of which 13 primers produced 117 reproducible amplicons (106 polymorphic, 7 monomorphic and 4 unique amplicons). UPGMA dendogram based on RAPD data separated the genotypes into two major clusters having the similarity coefficient ranged from 0.56 to 0.76. The results can be used for sweet potato crop improvement through molecular breeding and marker assisted selection of for desired traits in future.

Sequence-characterized amplified region markers and multiplex-polymerase chain reaction assays for kiwifruit cultivar identification

A simple and reliable multiplex polymerase chain reaction (PCR) method was developed using sequence-characterized amplified region (SCAR) markers to identify kiwifruit (Actinidia spp.) cultivars. We observed 183 different polymorphic random amplified polymorphic DNA (RAPD) markers using 23 arbitrary primers in 30 kiwifruit cultivars. The number of polymorphic bands per primer varied from five (OPM-15, OPN-05, and OPN-19) to 12 (OPG-01), with an average of eight. Fifty-eight cultivar-specific polymorphic RAPD fragments were converted into 16 SCAR markers after validating their specificity. Among them, 15 SCAR markers retained the dominant behavior of the original RAPD fragment, whereas the KA11_774 SCAR marker showed a co-dominant polymorphism. Based on RAPD and SCAR data sets, cluster analyses were performed with the unweighted pair-group method of arithmetic averages. The mean genetic similarities were estimated as 0.703 and 0.677 using the RAPD and SCAR markers, respectively. Thirty kiwifruit cultivars were divided into three clusters for RAPD analysis and into two clusters for SCAR analysis, based on a similarity value of 0.67. Overall, the kiwifruit cultivars with a similar breeding background tended to cluster together. Therefore, RAPD and SCAR markers could be successfully applied to assay genetic relationships for kiwifruit cultivar identification. Cluster analysis of combined RAPD and SCAR markers showed very similar results when compared to the RAPD analysis in dendrogram form. The kiwifruit cultivars tested in this study could be identified using only 10 different SCAR markers (KB08_182, KK08_287, KG19_295, KN15_316, KG01_411, KF07_433, KG09_468, KG09_477, KL01_764, and KA11_774). Furthermore, we optimized SCAR markers for simultaneous identification of the 30 kiwifruit cultivars by multiplex PCR, using two sets of five SCAR primer pairs. The developed SCAR markers and multiplex PCR approach facilitate efficient identification of kiwifruit cultivars.

Assessment of Genetic Variation in Soybean (<i>Glycine max</i>) Accessions from International Gene Pools Using RAPD Markers: Comparison with the ISSR System

Soybean (Glycine max) is one of the most important crops in the world in terms of total production and usage. It is also among the least diverse species. The main objectives of the present study were to 1) assess the level of genetic variation among soybean (G. max) accessions from different countries using Random Amplified Polymorphic DNA (RAPD) markers and 2) compare Inter Simple Sequence Repeats (ISSR) and RAPD marker systems in detecting polymorphic loci in soybeans (G. max). Genomic DNAs from 108 soybeans (G. max) accessions from 11 different gene pools were analyzed using several ISSR and RAPD primers. The average level of polymorphic loci detected with the RAPD primers was 35%. The soybean accessions from the China, Netherlands, and Canada gene pools were the least genetically variable with 25%, 26%, and 30% of polymorphic loci, respectively. Accessions from Hungary (43%) and France (48%) showed the highest level of polymorphism based on the RAPD analysis. Overall, RAPD data revealed that the accessions from different countries are closely related with 64% genetic distance values below 0.40. The levels of polymorphic loci detected with the RAPD and ISSR marker systems were in general moderate and similar even if they target different regions of the genome. A combination of different marker systems that include RAPD/ISSR, microsatellites (SSR), and SNPs should provide the most accurate information on genetic variation of soybean (G. max) accessions.

Phylogenetic Analysis of Chrysochamela (Fenzl) Boiss. (Brassicaceae) Taxa Growing in Turkey

In this study, we performed a genetic diversity analysis using RAPD (Random Amplified Polymorphic DNA) and ISSR (Inter simple sequence repeat) markers for some Chrysochamela species growing in Turkey. PCR was performed using RAPD and ISSR primers and genomic DNA samples from each specimen, and the resulting bands were scored. Phylogenetic relationships and genetic distances between the studied taxa were calculated using the PAUP analysis program. According to the RAPD analysis, the closest genetic distance was found to be 0.20000 between C. noeana populations, while the most distant values were found as 0.60000 between C. noeana and C. elliptica. The ISSR analysis also revealed the closest genetic distance as 0.34043 between C. noeana populations, while the most distant values were found to be 0.55319 between C. noeana and C. elliptica. UPGMA (unweighted pair group method with arithmetic mean) dendrogram generated for both RAPD and ISSR analyses consisted of two groups. As a result, it was found that RAPD data were more appropriate for comparison with the previous anatomical and morphological data of the studied taxa.