Analysis of Genetic Diversity in Cultivated and Wild Tomato Varieties in Chinese Market by RAPD and SSR

RAPD and SSR were applied to assess genetic diversity in 61 tomato varieties from different species （Solanum lycopersicum L., hirsutum. Humb L., pimpinellifolium Miller L., chilense Dun. L., chmielenskii L., peruvianum Miller L., parvuflorum Miller L.）. 2 062 and 869 clear fragments were amplified by RAPD and SSR, respectively. On the other hand, more polymorphic products were found by SSR as compared to RAPD, i.e., 100 and 43.84%, respectively. In addition, a higher value of the average similarity coefficient and lower PIC value were reflected in RAPD （0.79, 0.407） compared to SSR （0.56, 0.687）. It can be inferred that SSR was a higher effective marker than RAPD to assess genetic diversity in tomato accessions. Similarly, the genetic base of tomato varieties in Chinese market was narrow. It is suggested that wild tomato varieties should be used to enrich the genetic base of the cultivated tomato varieties.

Study on Classification and Genetic Diversity of Kentucky Bluegrasses by Using RAPD Markers

A total of 69 random primers were screened by using random amplified polymorphic DNA （RAPD） markers to analyze the genetic bands of 32 Kentucky bluegrass cultivars. A total of 197 bands were amplified from 46 primers, among which 195 bands were polymorphic. Each primer could amplify one to nine polymorphic bands with an average of 4.3 per primer. Based on similarity coefficient analysis of RAPD results and by using NTSYS software to cluster analyze with the average UPGMA method, the result showed that 18 cultivars of the 32 were in group 1, three cultivars were in group 2, two cultivars were in group 3, eight cultivars were in group 4, and only one cultivar in group 5.

Classification and Genetic Diversity of Kentucky Bluegrasses by Using RAPD Markers

Total 69 random primers were screened out through RAPD （Random Amplified Polymorphic DNA） markers to analyze the genetic bands of 32 Kentucky bluegrass cultivars. A total of 197 bands were amplified from 46 primers of them, among which 195 bands were polymorphic. Each primer could amplify one to nine polymorphic bands with an average of 4.3 being amplified from an average of primer. Based on the similarity coefficient analysis of RAPD results, NTSYS software and cluster analysis by using average UPGMA method, the result showed that 18 of 32 cultivars were in group 1, three cultivars were in group 2, two cultivars were in group 3, eight cultivars were in group 4, and there was only one cultivar in group 5, which was C2.

The RAPD techniques used to assess the genetic diversity in Draba dorneri,a critically endangered plant species

A successful management and preservation of the natural populations is depending on accurate assessment of genetic diversity. Knowledge of genetic diversity within a population is important for the conservation of the species. Our aim was to assess the genetic diversity in Draba dorneri Heuff. population (Brassicaceae family)—an endemic plant species of conservative interest using Random Amplified Polymorphic DNA (RAPD) technique. The plant species is strictly protected at national level as well as at international level through “Convention on the Conservation of European Wildlife and Natural Habitats”, Bern, 1979 European Council. In this study, a total of 52 primers were scored initially. A total of 77 repro- ducible bands with an average of 6.41 bands per primer were obtained from the 12 primers selected. A cluster analysis (UPGAMA) was used to generate a dendrogram based on Dice coefficient. We found 67% similarity between the samples from the two analyzed slopes. Comparing with other rare plants species, our data revealed a higher level of genetic diversity in D. dorneri population in Retezat Mountains.

Genetic diversity of Ustilago hordei in Tibetan areas as revealed by RAPD and SSR

Covered smut, which is caused by Ustilago hordei（Pers.） Lagerh., is one of the most damaging diseases of highland barley（Hordeum vulgare Linn. var. nudum Hook. f） in Tibetan areas of China. To understand the molecular diversity of U. hordei, a total of 27 isolates, which were collected from highland barley plants from Tibet, Sichuan, Qinghai, and Gansu provinces/autonomous region, were analyzed using random amplified polymorphic DNA（RAPD） and simple sequence repeat（SSR） markers. Among the 100 RAPD primers used, 24 primers exhibited polymorphism. A total of 111 fragments were amplified, of which 103 were polymorphic with a polymorphic rate of 92.79%. The average observed number of alleles（Na）, effective number of alleles（Ne）, Nei＇s genetic diversity（H）, Shannon＇s information index（I） and polymorphism information content（PIC） value in the RAPD markers were 1.9279, 1.5016, 0.2974, 0.4503 and 0.6428, respectively. For the SSR markers, 40 of the 111 primer pairs exhibited polymorphism and provided a total of 119 bands, of which 109 were polymorphic and accounted for 91.60% of the total bands. The Na, Ne, H, I and PIC values of the SSR markers were 1.9160, 1.4639, 0.2757, 0.4211 and 0.4340, respectively. The similarity coefficients ranged from 0.4957 to 0.9261 with an average of 0.7028 among all the 27 isolates used. The dendrogram, which was developed based on the RAPD and SSR combined marker dataset showed that the 27 U. hordei isolates were divided into 3 clusters at similarity coefficient of 0.7314. We determined that RAPD and SSR markers can be successfully used to assess the genetic variation among U. hordei isolates. The RAPD markers revealed higher levels of genetic polymorphism than did the SSR markers in this study. There existed a moderate genetic difference among isolates. The molecular variation and differentiation was somewhat associated with geographical origin but not for all of the isolates.

Genetic Diversity and Species Identification of Cultivar Species in Subtribe Cucumerinae (Cucurbitaceae) Using RAPD and SCAR Markers

DNA polymorphism in the cultivar species;Cucumis sativus L., C. melo L. and Benincasa hispida Cogn. of subtribe Cucumerinae (Cucurbitaceae) in the four northeastern provinces of Thailand was examined by using RAPD technique. Twenty 10-mer primers were produced 212 RAPD fragments, ranging from approximately 120 to 2531 bp. The genetic similarities were estimated from banding profiles using a NTSYS* version 2.1 as a basis for dendrogram construction via the UPGMA method. Cluster analysis divided the taxa under study into 2 clades. Moreover, a RAPD marker: Cm (OPJ11700) was specified to C. melo, and this marker was converted into sequence characterized amplified region (SCAR) marker: Cm (SCJ11516). A pair of sequence-specific primer of clones Cm (OPJ11700) amplified a distinct single band of the same size as the RAPD clones. The SCAR marker was developed successfully to identify C. melo genotype.

Genetic Diversity Caused by Environmental Stress in Natural Populations of Niupidujuan as Revealed by RAPD Technique

Multiplex environmental factors are generally expected to have significant effects on genetic diversity of plant populations.In this study,randomly amplified polymorphic DNA（RAPD） technique was used to reveal the genetic diversity in the same species of four populations collected from Niupidujuan（Rhododendron chrysanthum） at different altitudes,an endangered species,endemic to Northeast China.Initially,twenty informative and reproducible primers were chosen for final RAPD analysis.A total of 152 clear bands were obtained,including 143 polymorphic ones.With the help of POPGENE software,the poly rate was calculated to be 94.07% and the evenness of amplified bands for every primer was 6.8.Additionally,the mean observed number of alleles was 1.7265 with an effective number of 1.3608.An examination of the gene indicated a diversity of 0.2162 with an information diversity index of 0.3313.For these data,the clustering blurred analysis was performed with the aid of NTSYS-pc software to define the Nei＇s gene diversity and the Shannon information diversity index of the four plant populations.The relationships between the genetic diversity indexes on the one hand and the geographic and climatic factors on the other hand were estimated by the Pearson correlation with SPSS 11.0 software.The results of the correlation analysis show that there were significant（P〈0.05） or highly significant（P〈0.01） correlations between each of the genetic diversity indexes and the different temperature which were mainly caused by the altitude different populations located.These data highlight the importance of native populations in shaping the spatial genetic structure in Niupidujuan.

GENETIC DIVERSITY OF FIVE FRESHWATER MUSSELS IN GENUS ANODONTA (MOLLUSCA: BIVALVIA) REVEALED BY RAPD ANALYSIS

Unionidae are an important group of benthic freshwater species. Due to the convergence phenomenon within freshwater mussels, there is still much controversy in the classification of Chinese Unionidae. In China, most studies on freshwater mussels emphasized resource investigation, biology and morphology, while little has been done in genetics, and particularly not in population genetic structure as well as genetic diversity. In order to further understand the status of genetic diversity of different species, random amplified polymorphic DNA (RAPD) markers were used to detect genetic diversity of populations in five species of the genus Anodonta: Anodonta arcaeformis, A. arcaeformis flavotincta, A. fluminea, A. woodiana woodiana and A. w.pacifica. DNA extraction method was based on phenol-chloroform and extracted genomic DNA from the adductor muscle and mantle tissues. Sixteen random primers were used for RAPD amplification and the polymorphism of amplified loci were analyzed. The results demonstrated that the percentage of amplified polymorphic loci for various populations ranged from 34.5% to 62.8%, the mean Shannon’s genetic diversity indices ranged from 0.2021 to 0.3552, and the mean intra-population Nei’s genetic distance ranged from 0.1386 to 0.1713. In all populations of the five species, the genetic diversity for A. arcaeformis was the largest, and that of A. fluminea was the lowest. The inter-population genetic distance between A. w. woodiana and A. w. pacifica was 0.3186, so they can be considered as two sister species at the genetic angle.

Genetic Diversity Analysis of PVY Resistant Potato Varieties (Clones) by RAPD Markers

DNA fingerprints of 37 PVY resistant potato varieties （clones） were generated using PCR-based RAPD analysis. All 37 varieties were differentiated by banding patterns obtained from 17 primers that generated 164 polymorphisms. Similarity matrices were calculated with the simple matching coefficient. The genetic distance value among them was between 0.27 and 0.50, with average value being 0.35. The average link clustering algorithm was used to construct a dendrogram with Statistica. They were classified into three groups according to clustering results, and the results presented some geographic relationship. Dendrogram showed close genetic relationships between a number of varieties （clones） of similar pedigree. This study has shown that RAPD marker is a useful tool for potato variety identification, differentiation, and estimation of genetic relationships.

Genetic Diversity of Testa Pigments and RAPD Marker of Yellow-Seeded Rapeseed (Brassica napus L.)

14 yellow-seeded rapeseed lines (Brassia napus L.) from different genetic sources were used to analyze diversity of testa pigments content, oil and protein content, and RAPD markers. The results showed that the anthocyanin and melanin were the most important pigments in testa and their content were responsible for the variation in seed color ranging from orange to black yellow, 14 yellow-seeded lines could be classified into 3 groups: high anthocyanin content group with anthocyanin content over 2. 54 mg g-1 DW, the seed color was light yellow or orange; low pigments content group with low content of anthocyanin and melanin, the testa was transparent and the seed color was light yellow, greenish yellow or twany; high melanin content group with melanin content over 178. 4U(A290nm) , the testa was black, the seed color was black yellow. Oil content changed from 36.2% to 45. 5%, protein content from 21.1% to 27.7% , and the correlation analysis revealed that the oil content is highly significantly negatively correlated with the protein content. The cluster analysis showed that the extensive genetic variation existed among 14 yellow-seeded lines by using unweighted paired group method with arithmetic average (UPGMA) based on RAPD markers which were amplified with decamer primers, the genetic similarity among them ranged from 0. 25 to 0.909, and 14 yellow-seeded lines could put into 2 clusters corresponding to genome difference.

Genetic Diversity of Peanut (Arachis hypogea L.) Cultivars as Revealed by RAPD Markers

The objectives of this study were to evaluate the genetic diversity of the peanut accessions using Random Amplified Polymorphic DNA (RAPD) molecular marker and to evaluate RAPD markers to be used in peanut as genetic markers and improve such techniques as suitable strategies for peanut germplasm characterization. Twenty peanut accessions were included in this study and were subjected to RAPD molecular markers analysis. Twenty-seven RAPD primers produced 210 amplification products of which 80 (36.4%) were polymorphic. In conclusion, this study reported a successful fingerprinting of peanut accessions using RAPD markers and demonstrated the usefulness of these markers in estimating the extent of genetic variation in peanut germplasm.

Genetic Diversity in Selected Indian Mungbean [<i>Vigna radiata</i>(L.) Wilczek] Cultivars Using RAPD Markers

Random amplified polymorphic DNA (RAPD) markers were used to study the DNA polymorphism in Indian mungbean cultivars. A total of 60 random primers were used in the study and 33 of them generated reproducible RAPD patterns. Amplification of genomic DNA of most popular 24 Indian mungbean cultivars with these RAPD primers yielded 249 fragments that could be scored, of which 224 were polymorphic, with an average of 7.0 polymorphic fragments per primer. Number of amplified fragments with random primers ranged from 2 (OPI 9) to 17 (OPD 7). Percentage polymorphism ranged from 33% (OPX 5) to a maximum of 100% (OPX 4, OPX 6, OPX 13, OPX 15, OPX 19, OPD 5, OPD 7, OPD 20, OPI 4, OPI 6, OPI 13, OPI 14, OPI 18 and OPF 1), with an average of 90%. The Jaccard’s similarity indices based on RAPD profiles were subjected to UPGMA cluster analysis. And genotypes grouped in two major groups. Sixteen out of 24 released cultivars grouped to cluster I. This indicated the narrow genetic base in the Indian mungbean cultivars used in the study. The details of diversity analysis and possible reasons for narrow genetic base in mungbean cultivars are discussed in the present study.

Genetic diversity and relationship between cultivated clones of Dalber- gia sissoo of wide geographical origin using RAPD markers

Random Amplified Polymorphic DNA （RAPD） polymor- phism was employed to assess the genetic diversity in the elite germplasm＇of Dalbergia sissoo. Sixty-seven clones that are under cultivation in northern India, originated frorri six different states of India and Nepal were analyzed with 30 RAPD primers that generated a total of 342 fragments out of which 290 were polymorphic. Total genetic diversity （Ht） varied between 0.01 and 0.37, with an average of 0.19. Shannon＇s Information index （I） varied between 0102 and 0.54, with an average of 0.31. Marker attributes like Polymorphism Information Content （PIC）, Marker Index （MI） and Effective Multiplex Ratio （EMR） values were calculated to assess the discriminatory power of 30 primers used. The PIC values ranged from 0.01 to 0.37 with an average of 0.17 per primer and the EMR ranged from 0.17 to 21.00 with a mean of 8.66 across all genotypes. Closely related clones were C49 and C51 with similarity index of 0.86 while the least similar or most dissimilar clones were C14 and S-DB showing similarity index of 0.58. The UPGMA-phenogram categorized the 67 clones into six clusters based on genetic similarity and dissimilarity. The clustering of clones in relation to their geographical location has been discussed.

Population genetic structure and diversity of high value vulnerable medicinal plant Acorus calamus in India using RAPD and chloroplast microsatellite markers

Acorus calamus is a highly valued medicinal plant with global distribution used in several drugs of health care systems. We evaluated the genetic diversity and population structure of 50 populations of A. calamus from different geographical regions in India through RAPD and chloroplast microsatellite markers. From the total screened 82 RAPD primers and 18 cpSSR primers, 10 RAPD and nine cpSSRs were found polymorphic. The selected 10 RAPD primers produced a total of 96 reproducible bands, out of which 65 were polymorphic （67.70%）. Whereas, the selected nine cpSSR markers produced 26 alleles and all of them were polymorphic. The mean genetic diversity （H T ） among populations using RAPD （H T = 0.263） and cpSSR （H T = 0.530） markers was higher in comparison to the mean genetic diversity within populations. Mean coefficient of gene differentiation （G ST ） between the populations was also high for both RAPD （G ST = 0.830） and cpSSR markers （G ST = 0.735）, whereas the estimated gene flow was very low for RAPD （Nm = 0.102） and for cpSSR （Nm = 0.179）. AMOVA analysis revealed that more genetic variation resided among the populations than within populations. Significant differences （p 0.001） were observed between the populations and individuals within the populations. Cluster analysis of RAPD and cpSSR data using UPGMA algorithm based on Nei’s genetic similarity matrix placed the 50 populations into two main clusters. The implication of the results of this study in devising strategy for conservation of A. calamus is discussed.

Genetic Diversity of the Palestinian Fig (<i>Ficus carica</i>L.) Collection by Pomological Traits and RAPD Markers

Analysis of differentiation (genetic diversity and related relationships) among 22 landrace (Ficus carica L. sativa) and 2 wild form (F. carica L. caprificus) accessions of fig growing under the same environmental conditions in the Palestinian Fig Collection, Til, Nablus, Palestine, using PCR-based Random Amplified Polymorphic DNA (RAPD) and pomological markers, revealed considerable genetic diversity. The phenotypic analysis shows that pomological traits were permitted to evaluate morphological variability of fig landraces. The Jaccard similarity coefficient between landraces was determined by cluster analysis using the UPGMA method. Based on the genetic relationships among genotypes as illustrated by the dendrograms, generated from pomological and RAPD data by UPGMA clustering method, the following 12 genotypes: Qaisi, Mwazi, Barqawi, Inaqi, Swadi, Kharobi, Hmadibiadi, Sfari, Khdari, Biadi, Qrawi, and Slati, may be considered as distinct landraces. The remaining genotypes may be considered as synonymous (4) (Hmadi and Hmari, and Ajloni and Adloni), or closely related (6) landraces (Zraqi and Ghzali, Blati and Neami, and Qraee and Khurtmani). The wild fig forms clustered together and may be considered as distinct genotypes. Clustering patterns obtained from the combined (pomological and RAPD) markers had higher discriminatory power to discriminate fig landraces than using either pomological or RAPD markers alone. These results proved the importance of both pomological and RAPD markers to elucidate in part denomination problems and relationships among cultivars. Wide phenotypic and molecular diversity found in fig germplasm indicates a considerable potential for improving this crop.

Genetic Diversity and Phylogenetic Relationships among Phytophthora capsici Isolates from Guizhou Province by RAPD

Ten random primers with clear amplification profile, significant and stable main band were screened from RAPD （Random Amplified Polymorphie DNAs） primers to analyze the genetic diversity among eight Phytophthora capsici isolates from Huaxi District, Wudang District and Kaiyang County of Guiyang City, and Zunyi County, Suiyang County and Luodian County of Zunyi City in Guizhou Province. A total of 70 DNA fingerprints were obtained, including 57 polymorphic bands, with a polymorphic percentage of 81.43%, suggesting abundant genetic diversity among experimental Phytophthora capsici isolates. According to the ampli- fied DNA fingerprint profiles, using genetic similarity coefficient 0.5 as the threshold, experimental Phytophthora capsici isolates were clustered into three genetic categories by UPGMA cluster analysis. The analysis result indicated that there was no direct correlation between the genetic similarity and cultivation areas of vari- ous Phytophthora caosici isolates.

Genetic Diversity among Geographically Separated <i>Cyperus rotundus</i>Accessions Based on RAPD Markers and Morphological Characteristics

The diversity of globally distributed populations of purple nutsedge was assessed using molecular marker data and morphological traits. Cluster analysis of binary random amplified polymorphic DNA (RAPD) data and morphological traits indicated that the global population of purple nutsedge consisted of two clades. Cluster analysis of the RAPD data supported separation of the purple nutsedge accessions evaluated into two distinct clades of 11 and 33 accessions. Except for accessions identified as California* and Arizona, all USA accessions were clustered with accessions from Taiwan, Western Samoa, New Zealand, Malaysia, Japan, El Salvador, Columbia, Australia, Thailand and West Indies. A second cluster included accessions from Sudan, Greece, Iran, California*, Arizona, Brazil, Argentina, Mauritius, Philippines, Indonesia and Tanzania. The accessions from Sudan, Greece, Iran, Mauritius, and Tanzania were distributed along a similar longitudinal axis. Cluster analysis based on morphological traits though not identical to that based on RAPD data also supported separation into two clades and perhaps a third. The lack of genetic diversity among accessions supported the hypothesis that spread and propagation into new environments were largely by tubers which preserved genetic identity. The lack of diversity particularly among New World and USA accessions may also reflect a relatively recent introduction of the species into the Americas and a low level of outcrossing.

Genetic Diversity and Structure of East African Tall Coconuts in Tanzania Using RAPD Markers

RAPD markers were used to estimate levels of genetic diversity and structure among twelve East African Tall (EAT) coconut (Cocos nucifera L.) accessions that are maintained at Chambezi station. Ten primers were used in the analysis of 120 accessions. Cluster analysis was performed based on Jaccard’s coefficient and Nei genetic distances. Further analyses included principal coordinate analysis (PCA) and finally bootstrap analysis. The cluster analysis revealed two main clusters. One cluster contained provenances from Lindi and Mtwara regions (south) and those from Coast and Dar es Salaam regions (central);the second had provenances from Tanga region, which is the northern part of the coastal belt. A similar distribution of provenances was shown by the results of the principal coordinate analysis, whose first three coordinates explained 56% of the total variation. The results were able to discriminate between the different provenances and provide evidence of the different origins for the coconut palms in the northern and southern parts of coastal coconut-growing belt. The two major clusters concur well with the history and distribution of coconuts in the coastal belt of Tanzania.

RAPD analysis for genetic diversity of germplasm resources of <i>Strobilanthes</i>

The 18 samples representing 18 populations of Strobilanthes cusia (Nees) O. Ktze in Fujian Province of China were analyzed with RAPD markers. Eleven primers were used, a total of 106 bands were scored and 88 of them were polymorphic. The percentage of polymorphic loci was 77.36%, Nei’s gene diversity was 0.2420, and Shannon’s index was 0.3700. The 18 populations were classified into 2 groups based on the RAPD data by the method of hierarchical cluster analysis. Most of the populations from Fujian were clustered into a group, other populations were clustered into the other group. There was a high level of genetic diversity among the populations, and the genetic differentiation was obvious among the populations from Fujian.