[Show abstract][Hide abstract] ABSTRACT: Sweet cherries can be grafted on a wide range of rootstocks belonging to Prunus avium, Prunus cerasus, Prunus mahaleb, Prunus angustifolia or hybrids of different Prunus species. Identification of Prunus rootstocks using morphological traits is almost impossible particularly during the dormant season. However, molecular analysis carried out on actively growing shoot tips, leaves or dormant buds provides good opportunity to reliably distinguish rootstocks. In this study, DNA was extracted from the leaves of a total of 184 sweet cherry rootstock candidates belonging to P. avium L., P. cerasus L., P. mahaleb L. and P. angustifolia L. previously selected from the north-western part of Turkey. The rootstock candidates were tested with ten simple sequence repeat (SSR) primers, developed for the Prunus genus. The primers successfully identified all rootstock candidates. The results showed that the number of alleles per locus ranged from 10 (UDAp-401, UCD-CH21 and CPSCT010) to 20 (UCD-CH31) with an average of 13.3 alleles per locus, indicating that the SSRs were highly informative. Unweighted Pair-Group Method with Arithmetic mean analysis demonstrated that P. avium accessions are closely related to P. cerasus. The reference rootstocks were clustered with their associated botanical species.
[Show abstract][Hide abstract] ABSTRACT: In this research, the methanolic extracts of Convolvulus arvensis were tested for genotoxic and inhibitor activity on the total soluble protein content and the genomic template stability against corn Zea mays L. seed. The methanol extracts of leaf, stem and root of C. arvensis were diluted to 50, 75 and 100 μl concentrations and applied to corn seed. The total soluble protein and genomic template stability results were compared with the control. The results showed that especially 100 μl extracts of diluted leaf, stem and root had a strong inhibitory activity on the genomic template stability. The changes occurred in random amplification of polymorphic DNA (RAPD) profiles of C. arvensis extract treatment included variation in band intensity, loss of bands and appearance of new bands compared with control. Also, the results obtained from this study revealed that the increase in the concentrations of C. arvensis extract increased the total soluble protein content in maize. The results suggested that RAPD analysis and total protein analysis could be applied as a suitable biomarker assay for the detection of genotoxic effects of plant allelochemicals.
Toxicology and Industrial Health 02/2012; · 1.71 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Selenium is an essential mineral for a healthy life. Appropriate doses of it may undertake a protective role in the organism. In this study, the protective role of selenium (Se(4+)) against aflatoxin B(1) (AFB(1))-induced DNA damage was determined using random amplified polymorphic DNA on two plants including Vicia faba and Zea mays. It was observed that the concentrations of 0.1, 0.2 and 0.4 ppm of AFB(1) have increased polymorphism value, total chlorophyll inhibition rate (IR(c), %) and total protein IR (IR(p), %). Unlike protein, chlorophyll contents and genomic template stability were decreased. With the addition of different concentrations (0.8 and 80 ppm) of Se(4+) to the treated samples with AFB(1), the values return to normal. An 800-ppm concentration of Se(4+), on the contrary, could not inhibit the toxicity of AFB(1) but caused an increase in toxicity level of AFB(1)/enhanced the toxicity level of AFB(1). Results suggested that Se(4+) has an antagonistic effect against AFB(1) toxicity and that the degree of antagonistic effect of Se(4+) against AFB(1) was related to its concentration.
Toxicology and Industrial Health 02/2012; · 1.71 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Northeastern Turkey is recognized as one of the most important germplasm centers for the grape in the world. In the present study, simple sequence repeat markers were used to investigate the genetic diversity between four Vitis vinifera cv. Kabarcik populations sampled from the Coruh Valley in Turkey, at altitudes of 800-1,150 m. The mean observed number of alleles per locus varied from 2 (loci VVMD7 and VVMD24) to 6 (VVS2) among populations. The population from the highest altitude showed the greatest average number of alleles, 4.5. With regard to the six loci examined in all populations, the mean observed heterozygosity was higher than the expected heterozygosity. Among the loci, VVS2 (probability of identity = 0.137) was found to be the most informative among populations. Genetic distances between populations ranged from 0.072 to 0.216. Genetic differentiation among populations was strongly related to geographic distances in all populations.
[Show abstract][Hide abstract] ABSTRACT: We examined genetic differences of four Vitis vinifera populations (A, B, C, D) including local Kabarcik cultivar grown along an altitude gradient of 800, 900, 1000, and 1150 m above sea level in the Coruh Valley (800 m: A population; 900 m: B population; 1000 m: C population; 1150 m: D population). Leaf samples were used for both RAPD and fatty acid analysis. A total of 60 individuals with 15 individuals per population were included in this study. RAPD analyses showed various band sizes, which ranged from 250 to 3000 bp. Mean polymorphic locus ratios were determined as 96.29% considering four populations. The highest percentage of polymorphic loci (97.8%) was produced by the highest altitude. Thirty-two different fatty acids were found; linoleic acid was the most common in all four populations. According to the dendograms obtained from statistical analyses of RAPD and fatty acid profiles the populations that were close to each other in terms of geographical distance also were similar genetically.
[Show abstract][Hide abstract] ABSTRACT: Wild sweet cherry (Prunus avium) trees are abundant in the northern part of Turkey, including the Coruh Valley. We analyzed 18 wild sweet cherry genotypes collected from diverse environments in the upper Coruh Valley in Turkey to determine genetic variation, using 10 SSR primers. These SSR primers generated 46 alleles; the number of alleles per primer ranged from 3 to 7, with a mean of 4.6. The primer PS12A02 gave the highest number of polymorphic bands (N = 7), while CPSCT010, UDAp-401 and UDAp-404 gave the lowest number (N = 3). Seven groups were separated in the dendrogram, although most of the genotypes did not cluster according to phenological and morphological traits. This level of genetic diversity in these wild sweet cherry genotypes is very high and therefore these trees would be useful as breeders for crosses between cultivated sweet cherry and wild genotypes.
[Show abstract][Hide abstract] ABSTRACT: The pomegranate has been used traditionally in Coruh Valley in Turkey for a long time; fruits are harvested from wild, semi-domesticated and cultivated trees. In the valley, it occurs in general along with olive trees. We sampled 23 wild-grown pomegranate genotypes sampled from different parts of Coruh Valley and compared them using RAPD primers to determine genetic variability. Eighty-six RAPD primers were used for molecular characterizations, among which 12 gave reliable polymorphic patterns. These primers generated 145 RAPD bands of which 91% were polymorphic. The highest polymorphism ratio was observed with primers OPY06, OPY13, OPBA03, OPBB03, OPBB07, and OPBB09 (100%), while the lowest was with OPBB09 and OPBB10 (75%). The band size was between 250 and 2400 bp. There were five main clusters in the dendrogram; the highest genetic similarity was 0.24 and the lowest was 0.08.
[Show abstract][Hide abstract] ABSTRACT: The aim of the present study was to evidence the possible antagonistic effect of Zinc (Zn(2+)) and Calcium (Ca(2+)) against cadmium (Cd(2+))-induced DNA damage by using random amplification of polymorphic DNA (RAPD) and metabolic activities in Vicia faba. The results showed that all doses of Cd(2+) (10( -3) M, 10(-5) M) caused an increase in polymorphism value and a decrease in genomic template stability (GTS %). In addition, when 10( -4)-10(-6) M Ca(2+), 10(-6) M Zn(2+) were added together with 10(-3) M, 10(-4) M, 10(-5) M of Cd(2+), polymorphism value decreased besides GTS, total protein and chlorophyll content increased. Results suggested that Zn(2+) and Ca(2+) have an antagonistic effect against Cd(2+). The order of the antagonisms of Ca(2+), Zn(2+) against Cd(2+) toxicity was Ca(2+) > Zn(2+). Especially, the degree of antagonistic effect of Zn(2+) against Cd(2+) is probably related to its concentration ratio.
Toxicology and Industrial Health 10/2010; 27(1):73-80. · 1.71 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Turkey is one of the most important genetic resources of the date plum, Diospyros lotus, especially in the northeastern part of the country. Authenticating the identity of germplasm resources of D. lotus would be of great value for breeding. We examined the genetic variability of 11 D. lotus genotypes sampled from Coruh Valley in Turkey. One hundred and twenty-eight DNA markers were generated by 12 random primers. The highest polymorphism ratio was observed with the primer OPA-01 (71%) while the lowest was with OPY-01 (36%). The band size was between 350 and 2500 bp for these primers. The percentage of polymorphic bands was 58%, which demonstrated the efficiency of these primers. The similarity between genotypes ranged from 0.48 to 0.76. The RAPD markers permitted us to distinguish all the genotypes.
[Show abstract][Hide abstract] ABSTRACT: Turnip (Brassica rapa var. rapa) is one of the main vegetables consumed by people living in Eastern Anatolia in Turkey. In this region, farmers obtain their own seeds for production, which results in considerable morphological variability. We examined the genetic variation and relationships among 11 turnip genotypes sampled from diverse environments of the Erzurum region located in Eastern Anatolia in Turkey. Thirty-two Operon RAPD primers were screened; among them, 20 gave reproducible and clear DNA fragments after amplification. The average polymorphism ratio was 90.4%. The genetic distance between turnip genotypes were found to range from 0.302 to 0.733, indicating high genetic variability. Eleven genotypes were divided into three main clusters in a dendrogram; ETS2 and ETS8 genotypes were the most distant. We conclude that RAPD analysis would be useful for genotyping turnip genotypes.
[Show abstract][Hide abstract] ABSTRACT: Random amplified polymorphic DNA (RAPD) and fatty acid (FAME) profiles were used to examine phenotypic and genetic relationships among 16 Centaurea species growing wild in the eastern Anatolia region of Turkey. Thirteen decamer primers were used to examine polymorphism. According to the RAPD results, 99 amplicons in the size range of 50-1000 bp were produced from 13 primers in 16 Centaurea species. Genetically four distinct groups were determined among the species of Centaurea, which represents high genetic variation. In the 16 species, 14 fatty acids were determined according to FAME results. Both FAME and RAPD results showed that C. virgata is genetically different from other species. The differences in the composition of fatty acids among Centaurea species suggest that fatty acid profiles could be used to differentiate among some of these species. Results of this study show that RAPD and FAME analyses are consistent.
[Show abstract][Hide abstract] ABSTRACT: In this study, the protective role of selenium (Se 4+ ) against cadmium (Cd 2+ ) toxicity induced DNA damage was determined by using RAPD. The results showed that all doses of Cd 2+ caused an increase in polymorphism value and a decrease in genomic template stability (GTS %). In addition, when 0.08, 8 and 800 ppm concentrations of Se 4+ were added, cadmium polymorphism value decreased and GTS increased. Results suggested that Se 4+ has an antagonistic effect against Cd 2+ and the degree of antagonistic effect of selenium against Cd 2+ is probably related to its concentration ratio.
[Show abstract][Hide abstract] ABSTRACT: This study was carried out to determine genetic relationships among 23 apricot cultivars from Turkey by using randomly amplified polymorphic DNA (RAPD) technology. Among the 40 decamer random primers were used for PCR reactions, 12 primers showed reproducible polymorphic patterns. These primers produced 121 bands, out of which 118 were polymorphic. UPGMA (Unweighted Pair Group Method using Arithmetic average) derived dendrogram, grouped the cultivars into one cluster and one outlier. The main cluster further divided into three subclusters. The highest dissimilarities found between Hacihaliloglu and Kabaasi cultivars (0.108). The variation detected among the closely related genotypes indicates the efficiency of RAPD markers over the morphological and isozyme markers for the identification and construction of genetic linkage maps.
Romanian Biotechnological Letters. 01/2009; 14:4582-4588.
[Show abstract][Hide abstract] ABSTRACT: Random amplified polymorphic DNA analysis was carried out in 35 autochthonous table grapevine cultivars grown in Coruh valley. Fifty-five oligonucleotide primers were screened on cultivars, and among them, 12 primers showed clear polymorphic patterns. PCR amplification with 12 primers generated a total of 157 polymorphic bands. There was genetic variation among the cultivars with values of genetic diversity ranging from 0.19 to 0.72 using the Jaccard coefficient. UPGMA analysis of the distance matrix resulted in a dendrogram with two main clusters. The first cluster included 28 cultivars and the second 7 cultivars. The greatest genetic similarity was observed between cultivars Gah and Kolik, while the greatest dissimilarity was observed between cultivars Gah and Siyah Kus Uzumu. The dendrogram revealed that the cultivars present in Coruh valley can be distinguished to a relatively high degree.
[Show abstract][Hide abstract] ABSTRACT: Turkey is an important producer of cornelian cherries (Cornus mas L.), especially in northern Anatolia. Seed propagation and long-term human selection has given rise to a great diversity
of trees. Twenty-six cornelian cherry genotypes (CC1–CC26) from the Coruh Valley in northern Anatolia were evaluated for genetic
relationships by using Randomly Amplified Polymorphic DNA (RAPD) markers, based on 56 decamer random primers, seven of which
showed reliable polymorphisms. These seven primers generated 80 markers, with 77 (96.25%) displaying polymorphisms. Cluster
analysis of the cornelian cherry genotypes was performed based on data from polymorphic RAPD bands, by using Jaccard’s similarity
coefficient and the Unweighted pair-group method with arithmetic average (UPGMA) clustering method. A similarity matrix showed
that the highest genetic similarity (0.913) was between CC15 and CC16 and the least (0.129) was between CC4 and CC16. The
cophenetic correlation coefficient between the similarity matrix and the cophenetic matrix of the dendrogram was relatively
high (r=0.87), supporting the validity of the dendrogram. Based on these results, RAPD analysis can be used for the characterization
and grouping of cornelian cherry genotypes. Genetically divergent genotypes identified in this study may be useful for future
breeding programs. This is the first study demonstrating that RAPD analyses can be used to differentiate and classify cornelian
[Show abstract][Hide abstract] ABSTRACT: The interspecific variability of fatty acid (FA) composition and RAPD profiles was used to examine biochemical and genetic relationships among six pomegranate cultivars, which dominate pomegranate production in Southern Anatolia Region of Turkey. Fatty acid composition of pomegranate leaves was determined by using gas chromatography. Differences in the FA composition were found among cultivars. In particular, cv. kirli hanim had a distinct fatty acid profile that differs from the other cultivars. Linoleic acid was not detected in this cultivar, whereas the other cultivars had various levels of linoleic acid. RAPD data also showed that this cultivar formed a unique pattern. The differences in the composition of fatty acids among pomegranate cultivars suggested that fatty acid profiles could be used to differentiate among some of the pomegranate cultivars. RAPD analysis was also useful for grouping the pomegranate cultivars.
Biochemical Systematics and Ecology 11/2007; · 1.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Turkey is one of the most important mulberry fruit producers in the world. In particular, in Eastern and Inner part of Turkey,
mulberry fruits are processed into several products such as `Mulberry Pekmez', `Mulberry Pestil', `Mulberry Kome' etc. Therefore,
mulberry fruits give higher economic returns thus have greater employment potentials in Turkey. In order to improve the yield
and fruit quality through breeding, the genetic variations and relationships among 15 selected white mulberry genotypes (Morus alba L.) were evaluated using Random Amplified Polymorphic DNA (RAPD). A total of 101 DNA markers were generated by 16 random
primers, with an average of 6.3 easily detectable markers per primer. Several RAPD markers showed unique patterns of mean
frequency that differed among the white mulberry genotypes. The distance matrix showed that the highest genetic distance (0.902)
was between EMS13 and EMS8 and the least (0.413) was between EMS12 and EMS15. According to the results, RAPD analysis can
be used for the characterization and grouping of mulberry genotypes. The genetically divergent genotypes identified from this
study would be of much use in the future breeding program.
Plant Systematics and Evolution 05/2007; 265(3):251-258. · 1.15 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In this study, we examined phenotypic and genetic relationships between 15 Thymus species including T wildly growing in Eastern Anatolia region of Turkey by using Fatty acid (FAMEs) and RAPD profiles. According to the gas chromatography results, 16:0, 19:1:ω9t fatty acids were found in almost all analyzed thymus species. Also, C9 Dicarboxylic acid was observed in all species except for T. transcaucasicus, T. pubescens T. haussknechtii, T. convolutus, T. fallax. Moreover some fatty acids like 15:0 iso, C20 N alcohol, and C25 N alcohol were only observed in T. leucotrichus, T. haussknechtii, T. haussknechtii respectively (38, 28; 37, 40; 14, 78). On the other hand, RAPD analysis was carried out in 15 Thymus species. Twenty oligonucleotide primers were screened on Thymus, and among them, 7 primers showed clear polymorphic patterns. Cluster analysis of Thymus species was performed based on data from polymorphic RAPD bands, by using Jaccard's similarity coefficient. A similarity matrix showed that the highest genetic similarity (0.077) was between T. canoviridis and T. haussknechtii and the least (0.867) was between T. convolutus and T. transcaucasicus. In addition to this, three genetically distinct groups were determined between Thymus species.
[Show abstract][Hide abstract] ABSTRACT: The present study employed FAMEs and RAPD to investigate the patterns of biochemical and genetic variation among and within three different populations of Vicia canescens L. Fourteen primers were used for the RAPD and polymorphic bands were obtained with eight primers. Biochemical and genetic distances were calculated and dendrograms were obtained for all studied populations using both RAPD and FAMEs methods. The results of our RAPD analysis suggest that the highest percentage of polymorphic loci (63.7%) was recorded in pine population, which was followed by the campus (60.8%) and colonizing (43.1%) populations. A UPGMA analysis was carried out using Jaccard's index of similarity for 45 individuals in the three populations, which produced a dendrogram. The index revealed that the campus and colonizing populations are the closest ones, while pine and campus populations are the farthest.