Analysis of Genetic Relationships Between Wild Roses (<Emphasis Type="Italic">Rosa</Emphasis> L. Spp.) Growing in Turkey

Rosa L. taxa are dominantly used for horticulture, food, medicinal, ornamental and aesthetic purposes. Rosa is represented with approximately 200 wild species in the world. The number of natural Rosa species in Turkey is reported as about 31. Rosa species are widely distributed in all regions in Turkey. In this study, RAPD and ISSR markers were applied to assess genetic diversity and genetic relationships among 27 species of Rosa. The UPGMA cluster was constructed using a combination of data from RAPD and ISSR markers. The dendrogram revealed two main clusters. Each cluster was divided into subgroups. This investigation showed that genetic distance was relatively significant among the species. As the results of the study close genetic relationships were found between evolutionary relations, morphplogical properties, and phytogeographical distributions of the Rosa species, The results also propose that RAPD and ISSR markers are useful tools for indicating genetic relationships among Rosa genotypes.     

Utility of RAPD,ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp.

The application and informativeness of RAPD, ISSR, IRAP and REMAP markers to study the genetic diversity and relationship among the Citrus and its relative genotypes were investigated. High levels of polymorphism were observed for all four marker systems. The RAPD technique generated the highest number of polymorphic bands and average number of polymorphic band per assay unit. Average limit of the discriminating power was very close to its actual discriminating power of each marker. The highest and the lowest values of effective number of patterns were obtained from the marker REMAP (5.94) and RAPD (4.48), respectively. Correlation between the genetic similarities matrices were estimated from all four markers using the Mantel matrix correspondence test, and results showed significant correlations among the RAPD, ISSR, IRAP and REMAP similarity matrices. The highest correlations were found comparing RAPD and ISSR markers, whereas RAPD and REMAP (r = 0.143) markers were poorly correlated. To assess the usefulness of the overall information provided by these marker data for establishing phylogenetic relationships and Citrus germplasm classification, cluster analysis was performed. All four techniques, solely or in combination, discriminated the genotypes very efficiently and generated a high similarity in dendrogram topologies, although some differences were observed. The linkage analysis was conducted based on the segregation of 38 RAPD, 13 ISSR, 19 IRAP and 9 REMAP loci in 96 progeny of an intergeneric cross Citrus sinensis and Poncirus trifoliata. Among the 81 studied loci 65 loci distributed on five linkage groups. Comparing the result obtained with RAPD, ISSR, IRAP and REMAP markers in this study, IRAP and REMAP proved to be as a reliable molecular marker for fingerprinting, mapping and diversity study of Citrus and its relatives.     

Use of ISSR,SRAP, and RAPD markers to assess genetic diversity in Turkish melons

The genetic relationships among 63 melon (Cucumis melo L.) genotypes collected from various regions of Turkey were determined by comparing their molecular ISSR, SRAP, and RAPD markers with those of 19 foreign melon genotypes to investigate the taxonomic relationships and genetic variation of Turkish melon germplasm. Total 162 polymorphic markers (69, 18, and 75 obtained from ISSR, SRAP, and RAPD primers, respectively) were used to define the genetic similarity among the melon genotypes by dendrogram or two and three dimensional scalings. The average similarity (SM coefficient) between any two pairs of accessions examined as estimated by molecular variation was 0.73 ± 0.48. Within-group genetic similarities ranged between 0.46 and 0.96. Related genotypes or genotypes collected from similar regions were partitioned to similar clusters. Southeastern Anatolian genotypes were distinctly apart from group inodorus and group cantalupensis (sweet) genotypes. This reinforced the position of Turkey in the secondary genetic diversity center of melon. The genetic diversity among Turkish genotypes (H = 0.28 and I = 0.42) was only a little less than that of the world accessions (H = 0.30 and I = 0.45). On the other hand, the percentage of polymorphic loci among Turkish melon genotypes (90.7%) was even higher than that of the world accessions (87.6%).     

A comparative analysis of the genetic diversity between inbred lines of Zinnia elegans using morphological traits and RAPD and ISSR markers

Genetic diversity within Zinnia elegans is key to the genetic improvement of this important ornamental species. Here, morphological traits and RAPD and ISSR molecular markers were used to assess levels of polymorphism across 20 inbred lines. Thirty-four morphological traits were scored and also 147 RAPD marker-fragments, as amplified by 12 arbitrary primers, and 128 ISSR marker-fragments as generated by 9 primers. The number of polymorphic loci, the percentage of polymorphic loci, Shannon's Information index (I) and the effective number of alleles (Ne) were calculated from the RAPD data as 100, 68.03%, 0.3559 and 1.4169, respectively. From the ISSR data, these respective statistics were calculated as 97, 76.38%, 0.4013 and 1.4728. Thus, ISSR markers were considered slightly superior to RAPD markers for assessing genetic diversity between the accessions; however, Mantel's test indicated significant correlation (R = 0.733) of the RAPD and ISSR results. By contrast, the morphological matrix showed low correlation with both RAPD and ISSR data matrices (R = 0.3814 and 0.3765, respectively). Cluster analysis showed that groupings of the accessions according to all three methods correlated well with their geographic region of origin, but flower color was not strongly associated with the genetic classification of these inbred lines of Z. elegans.     

Genetic relationships of gladiolus cultivars inferred from fluorescence based AFLP markers

Gladiolus is one of the important commercial flowers with a large number of cultivars. However, genetic relationships among its genotypes have not been reported. This study analyzed genetic relatedness of 54 gladiolus cultivars using amplified fragment length polymorphism (AFLP) markers. A total of 24 AFLP primer pairs with three samples were initially screened, from which 9 primer sets that showed clear scorable and highly polymorphic bands were selected for AFLP reactions. Fluorescence-labeled amplification products were subjected to electrophoresis and then analyzed using an automated sequencer. A dendrogram was constructed by the unweighted pair group method using the arithmetic average (UPGMA). The number of AFLP fragments generated per primer set ranged from 10 to 151 with fragment sizes varying from 50 to 450 bp. A total of 660 AFLP fragments were detected, of which 658 (99.70%) were polymorphic. All the primers except E-AGG/M-CTA displayed 100% polymorphism. All cultivars were clearly differentiated by their AFLP profiles. The AFLP data were compared with previously obtained RAPD data and combined to generate a common dendrogram. The first cluster was dominated with indigenously bred cultivars while the second was dominated with exotic cultivars. This shows that most of the exotic cultivars as well as indigenous cultivars are closely related with each other. However, two indigenous cultivars viz., Pusa Suhagin and Pusa Archana share genetic similarity with exotic cultivars. Among the genotypes selected for the investigation, Pusa Gunjan was identified as the most distinct genotype. The AFLP markers developed will help future Gladiolus cultivar identification, germplasm conservation and new cultivar development. The assessed genetic relationships among gladiolus cultivars may enhance the efficiency of breeding program by selecting desirable parents with reduced breeding cycle.     

Genetic diversity and relationships of lotus (Nelumbo) cultivars based on allozyme and ISSR markers

Genetic diversity and genetic relationships of lotus (Nelumbo Adanson) cultivars were evaluated using allozyme and ISSR markers. The samples used covered 11 accessions of possible hybrids between Nelumbo nucifera and Nelumbo lutea and 92 accessions of N. nucifera including 69 flower lotus, 13 rhizome lotus, 5 seed lotus and 5 wild lotus. For allozyme studies, a total of 31 alleles at 23 loci of 18 enzyme systems were detected of which 5 (21.7%) loci Aat, Idh, Mdh-2, Pgd, Sod were polymorphic. The loci of Aat and Idh included two alleles, Mdh-2, Pgd and Sod included three alleles. Eighteen genotypes were detected with the 13 alleles of the 5 polymorphic loci. The parameters of average allele number, observed heterozygosity, expected heterozygosity and Shannon information index of 92 N. nucifera samples were 1.35 ± 0.71, 0.06 ± 0.21, 0.05 ± 0.14, 0.10 ± 023, respectively. Thirteen ISSR primers generated 93 loci, of which 37.63% were polymorphic across all samples. The percentage of polymorphic loci, average allele number, expected heterozygosity and Shannon information index of 92 N. nucifera samples were 26.67%, 1.30 ± 0.46, 0.10 ± 0.18 and 0.15 ± 0.25, respectively for the ISSR data. The ‘Bottleneck effect’ and rapid propagation of clones after the ice ages may explain the low genetic diversity of lotus. The dendrograms based on ISSR and allozymes were not congruent. Based on the ISSR data, the 103 samples were divided into the N. nucifera group (Group I), and the group containing inter-specific hybrids between N. nucifera and N. lutea (Group II). The flower lotus, rhizome lotus, and seed lotus each has multiple sources of origin. Plant size, a criterion commonly used in the classification of cultivars of lotus, is not correlated with genetic variation. Flower color is correlated with the cultivar classification to some degree, but its variation is complex in the hybrids.     

Genetic diversity of Indonesian cauliflower cultivars and their relationships with hybrid cultivars grown in Australia

The objectives of this study were to investigate genetic variation and relationships between Indonesia-, Australian- and European-based cultivars and to evaluate variation within Indonesia cultivars as all cultivars are open-pollinated. Eight cauliflower cultivars collected from three production regions in Indonesia and four F₁ hybrids cultivars grown in Australia were evaluated using RAPD and ISSR markers. DNA polymorphisms generated from 10 polymorphic RAPD primers were used to construct a dendogram using the unweighted pair-group method with arithmetic averages (UPGMA) and to generate a fingerprinting key. ISSR marker analysis using 14 primers were attempted but DNA polymorphisms could not be clearly identified. The RAPD technique indicated that variation occurred both within and between Indonesian cultivars. Comparison between Indonesian-, Australian- and European-based cultivars showed that Indonesian cultivars have unique genotypes and would be good sources of genes for future crop improvement.     

Cultivar identification and genetic diversity analysis of broccoli and its related species with RAPD and ISSR markers

A total of 18 genotypes of broccoli were subjected to random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) marker analysis. Seventy-four RAPD and eight ISSR primers generated 344 and 67 polymorphic bands, respectively. All broccoli genotypes could be distinguished with two-primer combinations, indicating that RAPD and ISSR markers can be used to efficiently identify broccoli cultivars. These 18 broccoli genotypes could be separated into two major sub-groups. The first major sub-group (A) included 13 genotypes and the second major sub-group (B) was comprised of five genotypes belonging to early-maturating cultivars. Genetic diversity analysis was performed on the 18 broccoli genotypes, one radish genotype, and six related Brassica accessions. All accessions could be clustered into two groups (radish and Brassica) based on the unweighted pair group of arithmetic average (UPGMA) cluster analysis. The UPGMA analysis indicated that broccoli is most closely related to cauliflower, than to cabbage and Chinese cabbage.     

30份莲种质资源的RAPD遗传多样性分析

采用RAPD分子标记技术对30份莲(Nelumbo nueifera Gaertn.)种质资源的遗传多样性进行鉴定.筛选出14对有效引物进行PCR扩增,共产生2 146条带,其中有1 516条为多态性条带,各对引物的平均多态性条带为108.29条,扩增条带的多态率达70.64％.对所得到的30份莲种质资源的RAPD图谱...     

Molecular characterization and genetic relationship among almond cultivars assessed by RAPD and SSR markers

RAPDs and SSRs were used to study the genetic diversity of Iranian almond cultivars and their relationship to important foreign cultivars and three related species. Eight unidentified almond Shahrodi cultivars and three wild almonds (Prunus communis, Prunus orientalis and Prunus scoparia) were also included. Of the primers tested, 42 (out of 80) RAPD and 18 (out of 26) SSR primers were selected for their reproducibility and high polymorphism. A total of 664 polymorphic RAPD bands were detected out of 729 bands. The number of presumed alleles revealed by the SSR analysis ranged from 3 to 10 alleles per locus with a mean value of 6.64 alleles per locus. Both techniques discriminated the genotypes very effectively, but only RAPDs were able to discriminate the cultivars Monagha and Sefied. Results demonstrated an extensive genetic variability within the tested cultivars as well as the value of SSR markers developed in peach for characterization of almond and related species of Prunus. Dice similarity coefficient was calculated for all pair wise comparisons and was used to construct a UPGMA dendrogram. For both markers a high similarity in dendrogram topologies was obtained although some differences were observed. All dendrograms, including that obtained by the combined use of both the marker data, depicted the phenetic relationships among the cultivars and species, depending upon their geographic region and/or pedigree information. Almond cultivars clustered with accession of P. communis showing their close relationship. P. orientalis and P. scoparia were clustered out of the rest of P. dulcis.     

Germplasm diversity and genetic relationships among walnut (Juglans regia L.) cultivars and Greek local selections revealed by Inter-Simple Sequence Repeat (ISSR) markers

Inter-Simple Sequence Repeat (ISSR) markers were used for the assessment of genetic diversity among walnut (Juglans regia L.) selections from Greek native populations in comparison to internationally cultivated walnut genotypes. Similarity coefficient values from 0.13 to 0.93 (with an average of 0.48) were found among the 56 accessions examined, which indicated the presence of a high degree of genetic variability. Most international cultivars were grouped together while most Greek native populations could not be placed into a distinct group. The Greek native population genotypes were found more diverse than the international cultivars. The mean similarity coefficient values for the former and latter were 0.44 and 0.56, respectively. In the cultivar group, two subgroups were distinguished; one consisted of genotypes involving ‘Payne’ and the other ‘Franquette’ in their pedigrees. Some cultivars and populations could not be grouped according to their pedigrees or collection area. Analysis of molecular variance (AMOVA) revealed that a larger part of the genetic variation exists among Greek walnut populations within a collection region (89%) than among the regions (11%). The pairwise regional PhiPT values indicated that the most geographically distant regions are the most genetically differentiated. The high variability existing in the Greek germplasm in combination with their valuable agro-morphological traits suggested that it would be beneficial to utilize this native germplasm pool in walnut breeding programs and germplasm management activities to maximize genetic diversity in cultivated walnut.     

DNA fingerprinting and genetic diversity analysis of late-bolting radish cultivars with RAPD,ISSR and SRAP markers

Three molecular marker systems, RAPD (random amplified polymorphic DNA), ISSR (inter-simple sequence repeat) and SRAP (sequence-related amplified polymorphism), were employed for identification and genetic diversity analysis of 35 elite late-bolting radish cultivars. Detected by 35 RAPD primers, 22 ISSR primers and 17 SRAP primer combinations, the proportions of polymorphic bands were 85.44%, 85.2% and 85.41%, respectively, and the mean genetic similarity coefficients between pairs of genotypes were 0.781, 0.787 and 0.764, respectively. Each of the three molecular marker systems can identify all the cultivars. Five sets of three-RAPD primers, 3 sets of three-ISSR primers and 16 sets of three-SRAP primer combinations were able to distinguish all the cultivars. A linear relationship was observed between Resolving power (Rp) of a primer and its ability to distinguish genotypes. The 35 cultivars were clustered into three major groups based on the RAPD, ISSR and marker combination data with UPGMA, which are in high accordance with their own origins and main characteristics. The results demonstrated that these three marker systems could be useful for identification and genetic diversity analysis of radish cultivars.     

Development of ISSR- and RAPD-derived SCAR markers for identification of Gladiolus germplasm

Gladiolus is an economically important ornamental crop, cultivated for its beautiful flowers throughout the world. The correct genotype identification of plant material is very significant for the floriculture industry. The aim of this study was to develop sequence-characterised amplified region (SCAR) markers from RAPD and ISSR fragments for identification and authentication of Gladiolus germplasm. The SCAR markers developed could be easily employed as valuable tools to identify newly developed Gladiolus cultivars. The SCAR markers, viz. ScG12, ScG34, and ScG36, are specific to the DNA from all 62 Gladiolus cultivars, as they did not amplify the DNA of other taxa of the family Iridaceae, including Iris, Amaryllis, and Narcissus. All three SCAR markers distinguished Gladiolus from other taxa of the family Iridaceae, whereas marker ScAm was specific to the ‘Amethyst’ cultivar. Our results confirmed that this particular SCAR marker distinguished the ‘Amethyst’ cultivar from the other 62 Gladiolus cultivars investigated in the present study. This development of SCAR markers based on RAPD and ISSR markers seems to be the maiden attempt for Gladiolus cultivars.     

豆瓣菜种质资源遗传多样性的RAPD和ISSR分析

以8个豆瓣菜的品种为试材，用筛选出的79个RAPD引物和34个ISSR引物对这8个品种的基因组DNA进行扩增，分别扩增出361条和179条谱带，每个引物扩增出的带在3～10条之间，平均每个引物扩增出约5条带。根据所得的条带进行聚类分析，两种标记产生的聚类图存在一些差异，但它们都可以较好地将8个品种按亲缘关系的远近划分为3个不同的类群。Mantel测试得出相关系数r=0．58155，表明RAPD和ISSR两种分子标记技术的相关度很低。     

Analysis of genetic diversity among Indian short-day onion (Allium cepa L.) cultivars using RAPD markers.

Summary

Randomly amplified polymorphic DNA (RAPD) markers were used to estimate genetic diversity among 24 cultivars of short-day onions. Total genomic DNA was extracted and subjected to RAPD analysis using 90 arbitrary 10-mer primers. Of these, 15 primers were selected which yielded 137 bands, 91.24% of which were polymorphic. None of the primers produced a unique banding pattern for each cultivar. RAPD data were used to calculate a Squared-Euclidian Distance matrix which revealed a minimum genetic distance between cultivars ‘AFLR-722’ and ‘PBR-140’, and a maximum genetic distance between cultivars ‘PBR-139’ and ‘A.Kalyan’, and ‘MS-48’ and ‘A.Kalyan’. Based on the distance matrix, cluster analysis was done using a minimum variance algorithm.The dendrogram thus generated, based on Ward’s method, grouped the 24 onion cultivars into two major clusters. The first cluster consisted of cultivars from the northern region, and the second of cultivars from the southern region of India. The present study shows that there is high diversity among the onion cultivars selected and indicates the potential of RAPD markers for identification and maintenance of onion germplasm for crop improvement purposes.     

RAPD markers reveal polymorphism among some Iranian pomegranate (Punica granatum L.) genotypes

In this study RAPD markers were used to determine the diversity level among 24 Iranian pomegranate genotypes. One hundred decamer random primers were used for PCR reactions, among which 16 showed reliable polymorphic patterns. These primers produced 178 bands, of which 102 were polymorphic. Cluster analysis of the genotypes was performed based on data from polymorphic RAPD bands, using Jaccard's similarity coefficient and UPGMA clustering method. The highest and lowest similarities detected between genotypes were 0.89 and 0.29, respectively. At a similarity of 60%, the genotypes were divided into four sub-clusters. Cophenetic correlation coefficient between similarity matrix and cophenetic matrix of dendrogram was relatively high (r = 0.9) showing the goodness of fit of the dendrogram. RAPD markers showed to be a useful tool for studying the genetic diversity of pomegranate.     

山楂（Crataegus pinnatifida Bge.)遗传多样性的RAPD和ISSR标记分析

 利用RAPD和ISSR标记对35份山楂（Crataegus pinnatifida Bge.）资源进行了DNA多态性分析。12个RAPD引物共扩增出110条清晰的谱带,其中89条显示多态性,平均每个引物扩增出7.4条多态性谱带。13个ISSR引物共扩增出110条清晰的谱带,其中94条显示多态性,平均每个引物扩增出7.2条多态性谱带。基于RAPD和ISSR标记,利用UPGMA分别构建了35份山楂资源的聚类树状图。距离系数分别为0～0.62（RAPD）和0～0.64（ISSR）,表明山楂具有较高的遗传多样性。     

Genetic diversity and phylogenic relationships in date-palms (Phoenix dactylifera L.) as assessed by random amplified microsatellite polymorphism markers (RAMPOs)

Random amplified microsatellite polymorphisms (RAMPOs) were used to assess genetic diversity among 30 date-palm cultivars and 10 male trees. Using 18 primers combinations, 197 bands were scored and 186 were polymorphic suggesting the high level of polymorphism among studied cultivars. Moreover, taking into account the high percentage of polymorphic bands (ppb), the resolving power (R_p) together with the polymorphism information content (PIC) scored values, all the tested primer sets contribute strongly in the discrimination of date-palm genotypes. In addition, the topology of the derived UPGMA dendrogram exhibited cultivars’ clustering made independently both from the geographical origin and/or from the sex of trees. The present data support the Mesopotamian origin of the date-palm domestication. Thus we assume that the used method is efficient to assess genetic diversity within date-palm cultivars. Data are discussed in relation with the opportunity of the RAMPO method to provide additional molecular markers suitable in the improvement of the date-palms germplasm characterisation.     

Assessment of genetic diversity among mango (Mangifera indica L.) genotypes using RAPD markers

Knowledge about the extent of genetic diversity/relatedness in mango germplasm is vital for developing coherent strategies for future gains in productivity. The genetic diversity/relatedness among mango cultivars/genotypes developed in Pakistan has not been investigated previously. We have assessed the genetic diversity among 25 mango genotypes/cultivars using randomly amplified polymorphic DNA (RAPD). Sixty random ten-mer primers were surveyed, out of which 45 yielded amplicons in all the genotypes. Genetic similarity between genotypes/cultivars was in the range of 64–89% with an average of 74%. Similarly, the genetic relatedness among all variants derived from a mango cultivar Chaunsa was in the range of 81.18–88.63%. These coefficients were utilized to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA). The genotypes were grouped into three (A, B, C) clusters. Generally, genotypes originating from Pakistan were grouped in cluster ‘A’ while cluster ‘B’ primarily composed of southern India as well as Florida cultivars. Kensington Pride was the most distantly related genotype which grouped with Maya and Yakta, forming a distinct cluster ‘C’.     

EST-PCR markers developed for highbush blueberry are also useful for genetic fingerprinting and relationship studies in rabbiteye blueberry

The pedigrees of most rabbiteye blueberry (Vaccinium virgatum) cultivars can be traced back to four wild selections, ‘Ethel’, ‘Clara’, ‘Myers’, and ‘Black Giant’; thus, they result from a very narrow germplasm base and are highly related. Until now randomly amplified polymorphic DNA (RAPD) has been the only type of molecular marker used in rabbiteye blueberry. Here we have tested whether a type of sequence-tagged site (STS) marker which utilizes specific ∼20-mer primers from expressed sequence tags (ESTs) of highbush blueberry (V. corymbosum), called EST-PCR markers, are useful for genetic fingerprinting and relationship studies in rabbiteye blueberry. Of 44 EST-PCR primer pairs, from an assortment of genes expressed in flower buds of cold acclimated and non-acclimated plants, and shown to amplify polymorphic fragments among a collection of highbush genotypes, 40 (91%) resulted in successful amplification, and 33 of those (83%) amplified polymorphic fragments among the rabbiteye genotypes. The average number of scorable bands per primer pair was two. A dendrogram constructed from genetic similarity values, based on the EST-PCR marker data, tended to group siblings and parent/progeny together, generally agreeing with pedigree information. A group of 20 markers from five EST-PCR primer pairs distinguished all the genotypes in this study. These markers are as easy to generate and as affordable as RAPDs, but are based on actual gene sequences, and should have general utility for DNA fingerprinting, genetic diversity, and mapping studies.