Polymorphic Random Amplified Polymorphic DNA Research Articles

Unveiling Genetic Variation in Garlic Genotypes in Response to Rust Disease Using RAPD Markers

Garlic (<em>Allium sativum</em>), cultivated worldwide for its medicinal and nutritional value, faces challenges due to diseases caused by various pathogens. In this study, eleven garlic genotypes from Iran and one from China were selected and sown under natural infection rendered by the rust fungus (<em>Puccinia alli</em>) over two consecutive years. Subsequently, disease distribution and severity, percentage of infection and susceptibility of different garlic genotypes to rust disease were investigated. The results showed that genotype Solan was the most susceptible, with disease severity of 30.81%. In comparison, genotypes Aliabad and Bahar were resistant against rust disease with the lowest infection percentages of 13% and 16.37%, respectively. Further, genetic diversity was assessed using random-amplified polymorphic DNA (RAPD) markers. Out of 10 primers used, 95 scorable bands were generated, of which 66 (69.48%) were found to be polymorphic. A dendrogram was constructed based on RAPD polymorphism using the UPGMA method, and the genotypes were separated into six distinct clusters based on Jaccard's coefficient of similarity. Additionally, it was observed that there is no genetic differentiation among the genotypes based on their geographical origin. This study highlights the significant diversity in resistance and susceptibility among garlic genotypes, which can be harnessed in plant breeding programs.

Analysis of Genetic Diversity of Mobula sp. in Cilacap Using RAPD (Random Amplified Polymorphic DNA) Markers

Devil rays (Mobula sp.) are in an endangered status, so conservation measures are needed. One of the first steps is to identify the level of genetic diversity. This study aims to determine the genetic diversity of mobula in Cilacap based on DNA bands of RAPD (Random Amplified Polymorphic DNA) polymorphism genetic markers. This research was conducted in September 2021 – June 2022. Sampling was carried out at PPS Cilacap and molecular analysis was carried out at the Biotechnology Laboratory building 3, Faculty of Fisheries and Marine Sciences, Padjadjaran University. The research procedure began with preservation of the devil rays (Mobula sp.) sample, isolation of sample DNA, electrophoresis of isolated DNA results, calculating DNA purity, DNA amplification, electrophoresis of DNA amplification results, and data processing and analysis. DNA isolation was carried out using the Promega Kit method. The electrophoretic results of DNA isolation from the three mobula rays samples showed quite good results. Band samples CIL 10 and CIL 9 looked thick and did not smear, while C13 produced bands and there was a visible smear. The results of calculating the purity of DNA isolated from mobula rays CIL 9, CIL 10, CIL 13 have a purity value of 1.94, 1.96, 1.80. Results The highest concentration of DNA was CIL-13 sample with a value of 452.90 ng/μL while the lowest concentration was CIL-10 which was 419.90 OPE-01 resulting in 10 out of 20 visualized polymorphic bands. The similarity index of CIL-9 to CIL-10 in the OPE-01 primer was 40% while the similarity index of CIL-9 and CIL 10 to CIL-13 was 35%. The average similarity index shows that the genetic diversity of the Mobula species is moderate. Morphologically, CIL-09 is a species of Mobula thrustoni, CIL 10 is a species of Mobula mobular, and CIL-13 is a species of Mobula tarapacana. CIL-9 (M. thrustoni) has a closer similarity index to CIL-10 (M. mobular) than CIL-13 (M. tarapacana). OPE-01 primer is good for analyzing diversity in mobula rays (Mobula sp.). OPE-01 has 10 out of 20 visualized polymorphic bands.

The Efficiency of Long Primers Compared to The Short Primer for RAPD Technique in Date Palm

Random Amplified Polymorphic DNA (RAPD) applies single arbitrary short primers (8-12nucleotides) to produce many amplified discrete DNA. Limited reports and studies were done onthe use of long primers (over 12 bases). This study was performed to investigate the potential valueof long primers (15-21 bases) for generating RAPD polymorphisms. We compared both short andlong primers in RAPD assays of two date palm cultivars grown in Malaysia: Ajwa and Barhi. Thenumber of produced polymorphic fragments ranged in order from 2 and 38 bands for short andlong primers in Ajwa. Meanwhile, more polymorphic fragments were generated by long primersin Barhi, which were 50 and only five bands for short primers. 18-mer GY107 and 20-mer CO4primers yielded 100% polymorphism in Ajwa and Barhi, respectively. Moreover, long primersproduced more DNA fragments and a wider range of DNA fragment sizes (from 140-1600 bp,with respect to 300-1000 bp obtained with 10-mer primers). Hence, a significant correlation wasobserved between primer length and the number of polymorphic fragments within the long primergroup, suggesting that increasing primer length above 15 bases may demonstrate enhancedproduction of more polymorphism.

Molecular diversity analysis of rice (Oryza sativa L.) genotypes using RAPD and SSR marker

Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) molecular markers were used for detecting the genetic variability of 20 rice genotypes using 79 SSRs and 30 RAPD primers. Among primers used, a set of 16 SSR and 14 RAPD markers showed polymorphism, and banding patterns were scored as 1 (present) or 0 (absent) in the datasheet which was further analyzed by using Jaccard’s similarity coefficient and SAHN clustering. The number of alleles, PIC value, and heterozygosity for individual 16 SSR and 14 RAPD markers were used to assess the degree of polymorphism among the rice genotypes. A total of 36 polymorphic loci were found in 16 polymorphic SSR markers and 77 polymorphic loci were observed in 14 polymorphic RAPD markers. The number of alleles produced per locus ranged from 2 (RM447, RM21, RM171, RM237, RM25, RM283, RM510, RM259, RM334, RM433, RM489, and RM212) to 3 (RM263, RM152, RM413, and RM3331) in 16 SSRs markers and 3 (OPR-05) to 9 (OPR-02 and OPC-06) in 14 RAPD. In SSRs, the PIC value diverse from 0.30 (RM447) to 0.58 (RM152) with an average of 0.38 per locus and an average value of heterozygosity (0.49). RAPD analysis showed an average PIC value of 0.78. Based on the information generated, the 20 rice genotypes were grouped into two main clusters in both the analysis of the marker. In SSR markers analysis, cluster I comprised 4 genotypes and cluster II comprised 16 genotypes and in RAPD cluster I was shown 2 genotypes and cluster II show 18 genotypes.

Molecular characterization of traditional mango germplasm of coastal Andhra Pradesh using RAPD markers

A study was conducted at Horticultural research station, Venkataramannagudem for evaluating the variability of mango germplasm to conserve the elite ones and to identify the superior genotypes using molecular markers for future crop improvement. Genetic variation and relationship among 34 traditional mango germplasm were analyzed using Random Amplified Polymorphic DNA (RAPD) markers. Fifteen out of the twenty primers screened were informative and 177 amplified DNA bands with sizes ranging from 100 - 5000 bp were selected as RAPD markers. The number of amplified fragments varied from 3 (OPG 13) to 20 (OPX 04) with an average of 11.8 polymorphic fragments per marker. Specific RAPD markers for some mango germplasm were identified. Unweighted Pair Group Method using Arithmetic means (UPGMA) cluster analysis grouped all the germplasm into two clusters with a genetic similarity coefficient range of 0.67 to 0.88. The accessions within the germplasm i.e., Banganapalli -1, Banganapalli -2 and Banginapalli-3 showed genetic similarity which is in good agreement from a single ancestor with their putative pedigrees. The genotypes Panukula Mamidi and Rajamamidi were closely clustered since these two genotypes are native to the Vizianagaram district. Similarly, the genotypes Nuzividu Tiyya Mamidi and Nuzividu Rasalu occurred in the same cluster indicated that these genotypes also originated from the same geographical area, it can be concluded that they were separated into the cluster based on geographic origin. This study showed clearly that germplasm from coastal Andhra Pradesh unveiled maximum diversity and indicated the potential of RAPD markers for the identification of mango germplasm for breeding purposes. Keywords: Cluster analysis, Dendrogram, Mango, Polymorphic information content and RAPD markers

Genetic diversity and population structure analysis of rice false smut pathogen in North India using molecular markers

AbstractFalse smut, caused by Ustilaginoidea virens, is one of the emerging diseases of rice in the world. The fungi show a high degree of morphological and cultural variability and produce diverse symptoms. India is a vast country with 44‐million‐ha rice production area and has only one report on genetic diversity and population analysis of U. virens from the eastern and north‐eastern region. Ten polymorphic RAPD and 21 SSR markers were used to analyse the genetic diversity and population structure of 81 isolates of U. virens from northern India, the second largest rice‐growing region. In this study, higher Polymorphic Information Content (PIC) and Quality Nature of Data (QND) data in simple‐sequence repeats (SSR) markers over random amplified polymorphic DNA (RAPD) revealed its higher efficacy; thus, SSR markers are highly informative and can help to dissect the genetic structures of U. virens. All markers yielded a total of 180 alleles with 1.0 effective alleles per loci. Genetic diversity ranged from 0.1 to 0.39. The principal coordinate analysis (PCoA), and structure analysis identified two genetic clusters of U. virens isolates with some degree of distinctness according to locations. But clusters, PCoA and structure analysis did not group the isolates according to their geographical origin and this may be due to high gene flow (Nm = 1.14).

Development of Molecular Markers Associated with Resistance to Gray Mold Disease in Onion (Allium cepa L.) through RAPD-PCR and Transcriptome Analysis

Onions (Allium cepa L.) are one of the most consumed vegetable crops worldwide and are damaged by several fungal diseases in the field or during storage. Gray mold disease caused by the necrotrophic pathogens Botrytis cinerea and Botrytis squamosa is a disease that reduces the productivity and storage life in onions. However, it is difficult to control gray mold disease in onions by using physical and chemical methods. Breeding resistant onions against gray mold disease can reduce the damage caused by pathogens, reduce the labor required for control, and reduce environmental pollution caused by fungicides. However, onions have a large genome size (16Gb), making them difficult to analyze, and have a biennial cycle, resulting in a very long breeding period. Therefore, in this study, markers were developed to shorten the onion breeding period. First, random amplified polymorphic DNA (RAPD) was performed to confirm the genetic relationship between the gray mold disease-resistant and -susceptible lines through a dendrogram. In addition, the sequence characterized amplified region (SCAR)-OPAN1 marker to select resistant lines was developed using a polymorphic RAPD fragment. Second, the RNA-seq of the gray mold-resistant and -susceptible onion lines were analyzed using NGS technology. Using the RNA-seq results and DEG and GO analyses were performed, and the variants, such as SNPs and indels, were analyzed to develop a selectable marker for the resistant line. This study developed the SNP-3 HRM marker for selecting gray mold disease-resistant lines by using the SNPs present in the aldo-keto reductase (AKR) gene with high expression levels in these lines. The SCAR-OPAN1 and SNP-3 HRM markers developed in this study could be used to select gray mold disease-resistant onions in breeding programs to reduce the damage caused by gray mold disease.

Characterization of Eggplant Genotypes for Different Resistance Mechanisms Against Leucinodes orbonalis.

Host plant resistance mechanisms play an important role in developing cultivars with resistance to the target pests; information regarding morphological and biochemical factors contributing to the resistance is essential for developing pest-resistant cultivars. As a result, we investigated the contribution of various morphological and biochemical characters in forty-two eggplant genotypes against Leucinodes orbonalisGuenée, in Himachal Pradesh, India. Out of all the phenotypic parameters evaluated, pericarp thickness (r = 0.89) has significantly positive correlation with fruit infestation, whereas trichome density had significantly negative correlation (r = - 0.89). Analysis of the biochemical compounds in the eggplant genotypes revealed that total phenols (r = - 0.71), polyphenol oxidase (r = - 0.63), peroxidases (r = - 0.35), phenylalanine ammonium lyase (r = - 0.71) and solasodine (r = - 0.81) had significantly negative correlation with the per cent fruit infestation by L. orbonalis while the reducing sugars (r = 0.66) and non-reducing sugars (r = 0.62) showed a significantly positive correlation. Molecular characterization by random amplified polymorphic DNA (RAPD) primers also revealed the presence of high genetic diversity among different eggplant genotypes, where 17 polymorphic RAPD primers produced a total of 167 amplicons, among which 144 amplicons were polymorphic and 23 monomorphic bands. PCR-amplified DNA fragment size ranged from 100 to 2500 bp, mean polymorphism was 86.42% and the average PIC value was 0.444. Jaccards coefficient-based dendrogram grouped 40 eggplant genotypes into two major clusters. Results also revealed that the resistant genotypes accumulated higher levels of defensive biochemical enzymes such as phenols, PO, PPO, PAL and solasodine to confer insect resistance. Molecular characterization also revealed that genotypes in the present study were genetically diverse and could be used in future breeding and improvement programmes in this crop. Genotypes, IC411485 and IC090951, in particular, can be used as varied parents in breeding programmes to generate improved lines in terms of resistance to L. orbonalis.

Assessment of Somaclonal Variations in Embryo-derived Axillary Shoots of Chickpea using Molecular Markers

Background: Somaclonal variation is considered as a source of genetic variation for crop improvement. It has been investigated using cytological, biochemical and molecular techniques.Methods: Genetic stability in the embryo-derived axillary shoots of 4 chickpea genotypes was assessed using eight inter-simple sequence repeat (ISSR) and 19 random amplified polymorphic DNA (RAPD) primers. Result: RAPD primers produced 94 and ISSR primers produced 38 distinct and scorable alleles, with an average of 4.9 alleles for RAPD and 4.75 for ISSR primers. The polymorphic information content (PIC) ranged from 0.36 to 0.90 for RAPD and from 0.50 to 0.87 for ISSR. ISSR recognized a 90%, but RAPD recognized 82% similarity value. No absolute similarity value was between the mother plant and the regenerated shoots for the overall genotypes. At a 90% similarity value, 15 out of the 20 regenerated shoots from ‘Giza 88’ group with their mother plant using ISSR markers; however, 11 regenerated shoots grouped with their mother plant in one central cluster for ‘Giza 4’ using RAPD markers. The observed variations in the total number of polymorphic RAPD and ISSR bands and the number of bands specific to the mother and regenerated shoots, detected intra-clonal variation and genetic instability seem to be genotype-dependent.

Molecular identification and analysis of Psidium guajava L. from indigenous tribes of Taiwan

Psidium guajava L. is a perennial fruit tree in subtropical and tropical areas. In Taiwan, P. guajava has been used as anthro-pharmacological plants by aboriginal people to treat acute diarrhea, cough and intestinal spasmodic diseases. The classification and functional identification of P. guajava remains unsolved these days. In this study, molecular markers 18S rRNA, internal transcribe spacer (ITS) region of ribosomal DNA, trnL intron and trnL-trnF intergenic spacer (IGS) of chloroplast DNA (cpDNA), and random amplified polymorphic DNA (RAPD) were used for the molecular identification of 18 P. guajava samples from different indigenous tribes, 2 from non-indigenous tribe, and 12 commercial cultivars from markets in Taiwan. Molecular methods restricted fragment length polymorphism (RFLP) and denatured gradient gel electrophoresis (DGGE) are found time-consuming and less efficient as compared to RAPD, thus are not suitable for samples of high homology. In this study, 18S rDNA, ITS and cpDNA trnL intron and trnL-trnK intergenic spacer were also tested molecular marker; however, results analyzed by molecular algorithm UPGMA, Neighbor-Joining, Parsimony or Maximum likelihood showed no discriminations (data not shown). On the other side, ten 10-mer oligonucleotide primers were used in RAPD to amplify the specific genes from 32 guava samples. Four primers, OPB 17, OPG 6, OPY 15 and OPY 18, were able to direct the amplification and yielded a total of 82 polymorphic RAPD patterns. Thirty-two genotypes on the dendrogram were identified and were divided into two major groups, the uncultivated and commercial cultivars. Based on the cluster analysis, the red-flesh Psidium samples that were believed to have high medical function were grouped independently. The results suggest that RAPD is useful for the discrimination of uncultivated, cultivars and potential Psidium of high economy.

Genetic identification of Chinese drug materials in yams (Dioscorea spp.) by RAPD analysis

The botanical origins of Chinese drug materials in yams were examined among eighteen cultivarities/ species of Dioscorea by randomly amplified polymorphic DNA (RAPD). DNA isolated from fresh leaves were used as a template in polymerase chain reactions (PCR) using thirty random decamer primers. Eighteen primers produced 237 polymorphic RAPD markers, which were scored for all the lines studied. Four primers including OPP-04, OPP-15, OPAP-04 and OPAP-10, could distinguish all tested samples. Genetic distances and similarities among eighteen cultivarities/species were calculated, and a cluster analysis was used to generate a dendrogram showing a phylogenetic relationship. The studied Dioscorea species could be divided into five subgroups by phylogenetic analysis. Genetic distance and similarity analysis showed that line 70W37 was distantly related to 70W47, and line 70W41 was closely related to 70W59. RAPD technique could be successfully applied for the rapid identification and differentiation of Dioscorea species.

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.

Genetic variation of maiden lily (Lilium rubellum Baker) within and among three natural populations in Fukushima Prefecture in Japan

Lily ( genus Lilium ) is one of the most important flowers for bulb and cut flower production in the world. Lilium rubellum Baker is a native species of Japan that exhibits early flowering, is pink coloured, and possesses a pleasant fragrance, which makes it an important genetic resource for breeding lilies. In this work, the genetic diversity of L. rubellum was studied among three natural populations located in Fukushima Prefecture, Japan, which have been designated as the Mt. Azuma, Nango and Atsushio-kano populations. A total of 31 accessions collected in 1997 were analysed using Random Amplified Polymorphic DNA (RAPD) markers. Eighteen decamer primers produced 98% polymorphic RAPD bands; furthermore, 11 of the 18 primers produced 10 or more polymorphic bands with a mean per primer Polymorphic Information Content of 0.382. Among the three populations, the mean Shannon index, Nei´s gene diversity and percentage of polymorphic loci were 0.2749, 0.4099 and 76.7%, respectively. These data revealed that there is a high genetic diversity within all the populations. Analysis of the three genetic diversity indices within populations showed that the Nango population had the highest genetic diversity, whereas the Atsushio-kano population had the lowest. An unweighted pair group method with arithmetic mean dendrogram based on Jaccard´s similarity coefficient was constructed, and the three populations of L. rubellum collected in the Fukushima prefecture were clearly differentiated at 0.61 similarity index. The Nango and Mt. Azuma populations were genetically closer than the Atsushio-kano population. The analysis of molecular variance showed a 29.53% variance among the populations. This study revealed that there is high genetic diversity within populations and moderate genetic diversity among the three natural populations of L. rubellum Baker in the Fukushima Prefecture of Japan.

Utilizing RAPD Analysis as Molecular Markers for comparison between Various Callus and Mother Plant of Jatropha curcas L.

Calli were induced from different explants of Jatropha curcas L. seedling on MS basal agar medium in presence of different plant growth regulators. at different levels for 4 weeks Random Amplified Polymorphic DNA (RAPD) markers were used for the assessment of genetic variation of callus grown in different hormonal combinations in comparison with the mother plant. A total of 8 arbitrary sequence primers were evaluated. Of 8 primers used for the RAPD analysis, primers showed consistent band patterns. In total, scorable bands were observed with the primers. The total number of amplicons produced per primer varied from 5 for OPA-07 and OPB-12 to as many as 8 bands for OPB-10, OPC- 09 and OPR-17. The average number of bands per primer was 6.625. Out of 53 bands, 36 were polymorphic (67.92%). The average number of polymorphic RAPD bands was 4.5 per primer. the highest similarity (0.71) with mother plant was recorded in leaf-derived callus (S4) grown on MS solid medium with 2.5 μM NAA plus 2.5 μM IBA, while endosperm callus maintained on MS with hormonal combination 12.5 μM IBA + BAP- 25.0 μM was found to show least similarity (0.54) with mother plant.In this concern, results have been suggested to be useful fast methods for comparing of geneticchanges and variation in plants.

RAPD markers reveal genetic variation between Cichorium spinosum L. and Taraxacum sp.; a substantial medicinal plants of Greece

Fifteen Random Amplified Polymorphic DNA (RAPD) markers were used to measure genetic diversity and genetic relationships between five endemic genera of Mediterranean basin (Greece). Three species of Cichorium spinosum were collected; two from island Crete (Greece) and one from island Kythnos, and other two species of Taraxacom sp. (Asteraceae); are from Orhomenos and Athens. Two hundred-forty amplified products and 163 RAPD bands were scored with an average of 67.91% of them revealing polymorphism across accessions. In this research OPD-05 primer with 24 bands showed the highest number of bands, while the OPM-18 and OPB-16, both of them with 8 bands showed the least number of bands. Also OPV-06 primer with 18 polimorphic bands showed the highest number of bands. The least number of polymorphic bandswere found in OPX-18. UBC-292, OPAN-01, OPB-16, OPM-18, OPD-05 primers. Subsequently, OPD-05 primer with 29.16% showed the least percentage of polymorphism degree, whereas OPM-18 and OPB-16 primers with 87.50% showed the highest percentage of polymorphism. UPGMA clustering based on data from polymorphic RAPD bands revealed two distinct group which joined to form one major cluster at 32% level of similarity. Also Cichorium spinosum, Crete and Cichorium spinosum, Kythnos, varieties with 100% similarity are synonyms. The similarity indices of the RAPD dendrogram ranged between 30% and 100% averagely high enough to suggest useful variability for genetic diversity and plant breeding.

Comparative analysis of diversity based on morpho-metric and molecular markers in chickpea over different environments

Ten morpho-agronomic traits and 80 random amplified polymorphic DNA (RAPD) molecular markers were used to survey genetic diversity in 25 chickpea genotypes. Analysis of variance revealed significant variability among different genotypes for morpho-metric traits. The cluster analysis done using morpho-metric traits grouped 25 genotypes into seven and six clusters in Environment I (Env. I) and Environment II (Env. II), respectively. Three genotypes viz., ICCV-96904, HPG-17, ICCV-95503 and L-HR-1 belonging to diverse clusters were identified divergent and may use in heterosis breeding programme. Of 80 random RAPD markers, 25 were found polymorphic. Three major clusters were identified using 25 polymorphic RAPD markers. The genetic similarity coefficient among genotypes ranged from 0.57 to 0.91. The average polymorphic information content (PIC) for 25 RAPD markers ranges from 0.12 to 0.40. D2-statistic, RAPD analysis and study of genotypes performance revealed sufficient genetic diversity among chickpea genotypes which would be useful in future breeding programme.

Genetic characterization of dahlem red layers by PCR-RAPD

A total of one hundred Randomly Amplified Polymorphic DNA (RAPD) markers were utilized to detect the DNA polymorphisms in a total of 48 full sib mated, half sib mated and non-in bred groups of Dahlem Red birds. Twenty one per cent of the primers tested yielded distinct polymorphic RAPD profiles. Out of 341 amplified bands 204 bands (59.82 %) were found to be polymorphic. The genetic similarity ranged from 83.94 to 87.90 % and, 81.14 to 85.25 % with in group based on band sharing and frequency respectively. Full sib group showed higher genetic similarity then non-in bred group. The genetic similarity based on band frequency ranged from 88.07 to 90.18 %, based on band frequency varied from 72.78 to 79.53 percent. The full sib and half sib groups showed maximum genetic similarity. The genetic distance between full sib and non-inbred groups was found to be the maximum (0.3176), while it was minimum between full sib and half sib groups.

Relationships Among some Pears Genotypes (Pyrus Communis L.) Based on ISSR and RAPD Analysis

Thirty one pears genotypes from east blacksea region were evaluated for genetic relationships by using Randomly Amplified Polymorphic DNA (RAPD) and ISSR (Inter-Simple Sequence Repeats) markers from total 70 RAPD and ISSR primer investigated, 22 could amplify clearly and consistently. Cluster analysis of the pears genotypes was performed based on data from polymorphic bands RAPD and ISSR by using Jaccard’s similarity coefficient and the Unweighted pair-group method with arithmetic average (UPGMA) clustering method. The 31 pear genotypes were classified into two major groups. Cluster A was divided into 2 subclusters: Gumushane pears and Trabzon pears. Cluster B consisted of Artvin pears. The similarity matrix values ranged between 0.105 and 0.968.

English

The effect of drought stress on growth and water relations of four Hibiscus genotypes was investigated. Drought stress significantly retarded vegetative growth as analyzed by plant height, stem diameter, leaf area, fresh and dry weight. The osmotic potential (ys) values decreased with increasing drought time, and the decrease was more pronounced in Fantasia followed by Jay´s orange. Osmotic adjustment (O.A.) increased with drought time, and was greater in Fantasia followed by Jay´s orange and lowest in Annie wood. The genetic diversity among the four hibiscus genotypes was detected by Random Amplified Polymorphic DNA (RAPD) analysis. The data indicate that, thirty-one out of fifty four RAPD markers detected were polymorphic (57.4%). The RAPD specific markers for each genotype were determined. Ten out of the thirty one polymorphic RAPD markers generated were found to be genotype- specific (32.2%). In the meantime, the largest number of RAPD genotype-specific markers was generated for primers OPE-D-07(six markers) while for both of the OPE-B-17 and OP D-05 (two markers each). These markers can be verified as being RAPD markers associated with drought tolerance in the hibiscus genotypes that could help in marker-assisted selection breeding program. Key words: Hibiscus, biomass production, osmotic adjustment, molecular markers, genetic polymorphism.

Cadmium-induced genomic instability in Arabidopsis: Molecular toxicological biomarkers for early diagnosis of cadmium stress

Microsatellite instability (MSI) analysis, random-amplified polymorphic DNA (RAPD), and methylation-sensitive arbitrarily primed PCR (MSAP-PCR) are methods to evaluate the toxicity of environmental pollutants in stress-treated plants and human cancer cells. Here, we evaluate these techniques to screen for genetic and epigenetic alterations of Arabidopsis plantlets exposed to 0–5.0 mg L−1 cadmium (Cd) for 15 d. There was a substantial increase in RAPD polymorphism of 24.5, and in genomic methylation polymorphism of 30.5–34.5 at CpG and of 14.5–20 at CHG sites under Cd stress of 5.0 mg L−1 by RAPD and of 0.25–5.0 mg L−1 by MSAP-PCR, respectively. However, only a tiny increase of 1.5 loci by RAPD occurred under Cd stress of 4.0 mg L−1, and an additional high dose (8.0 mg L−1) resulted in one repeat by MSI analysis. MSAP-PCR detected the most significant epigenetic modifications in plantlets exposed to Cd stress, and the patterns of hypermethylation and polymorphisms were consistent with inverted U-shaped dose responses. The presence of genomic methylation polymorphism in Cd-treated seedlings, prior to the onset of RAPD polymorphism, MSI and obvious growth effects, suggests that these altered DNA methylation loci are the most sensitive biomarkers for early diagnosis and risk assessment of genotoxic effects of Cd pollution in ecotoxicology.