Genetic Diversity Among Brazilian Cultivars and Landraces of Tomato Lycopersicon Esculentum Mill. Revealed by RAPD Markers

Random amplified polymorphic DNA markers (RAPD) were used to estimate the variability of 35 tomato accessions (Lycopersicon esculentum Mill.). A total of 257 reproducibly scorable bands were obtained from 20 primers, 78.6% of which were polymorphic. The percentage distribution of RAPD markers shows a bimodal distribution, and the frequency of rare alleles is similar in commercial and landrace accessions. Genetic distances among accessions were calculated and a dendrogram showing the genetic relationships among them was constructed allowing for the separation of four groups. Twenty out of 23 Brazilian landraces fell within one group, whereas commercial cultivars were distributed in the four groups. AMOVA analysis of RAPD data showed that, despite the high within Brazilian landraces and commercial cultivars variation, these two groups are significantly different, indicating that landraces can be a source of variation for breeding programs.     

Genetic Diversity in Accessions of Wild Rice Oryza granulata from South and Southeast Asia

Oryza granulata, an upland wild rice species, represents an unique germplasm for possessing abilities of tolerance to shade and drought, immune to bacterial blight and resistance to brown planthopper. Although low degree of genetic variability has been revealed within its populations, little genetic information at the species level is available in determining rational conservation strategies. Here we used dominant DNA marker random amplified polymorphism DNA (RAPD) to assess the genetic variability among 23 accessions of O. granulata that collected from main distribution areas worldwide. Twenty decamer primers generated a total of 243 bands, with 83.5% of them (203 bands) being polymorphic. Calculation of Shannon index of diversity revealed an average value of 0.42 ± 0.25, indicating that O. granulata maintains a relatively high degree of genetic diversity on the species level. Analysis of genetic dissimilarity (GD) showed that genetic differentiation occurred among studied accessions, which supports the feasibility of current ex situ conservation strategies. We also suggested that information based on population studies, which could be achieved by international co-operation, is needed to conserve this widespread germplasm more effectively.     

AFLP Fingerprinting in Pigeonpea (Cajanus cajan (L.) Millsp.) and its Wild Relatives

Detection of DNA polymorphism in cultivated pigeonpea (Cajanus cajan) and two of its wild relatives Cajanus volubilis and Rhynchosia bracteata is reported here for the first time using amplified fragment length polymorphism (AFLP) fingerprinting. For this purpose, two EcoRI (three selective nucleotides) and 14 MseI (three selective nucleotides) primers were used. The two wild species shared only 7.15% bands with the pigeonpea cultivars, whereas 86.71% common bands were seen among cultivars. Similarly, 62.08% bands were polymorphic between C. volubilis and pigeonpea cultivars in comparison to 63.33% polymorphic bands between R. bracteata and pigeonpea cultivars, and 13.28% polymorphic bands among pigeonpea cultivars. The cluster analysis revealed low polymorphism among pigeonpea cultivars and very high polymorphism between cultivated pigeonpea and its wild relatives. The AFLP analysis also indicated that only one primer combination (EcoRI + ACT and MseI + CTG), at the most any four primer pair combinations, are sufficient for obtaining reliable estimation of genetic diversity in closely related cultivars like pigeonpea material analyzed herein. AFLP analysis may prove to be a useful tool for molecular characterization of pigeonpea cultivars and its wild relatives and for possible use in genome mapping.     

Genetic Diversity and Relationships of Wheat Landraces from Oman Investigated with SSR Markers

Little is known about genetic diversity and geographic origin of wheat landraces from Oman, an ancient area of wheat cultivation. The objectives of this study were to investigate the genetic relationships and levels of diversity of six wheat landraces collected in Oman with a set of 30 evenly distributed SSR markers. The total gene diversity, (H_T), conserved in the three durum wheat (Triticum durum desf.) landraces (H_T = 0.46) was higher than in the three bread wheat (Triticum aestivum L.) landraces (H_T = 0.37), which were similar to Turkish and Mexican bread wheat landraces calculated in previous studies. Genetic variation partitioning (G_ST) showed that variation was mainly distributed within rather than among the durum (G_ST = 0.30) and bread wheat (G_ST = 0.19) landraces. Based on modified Rogers’ distance (MRD), the durum and bread wheat landraces were distinct from each other except for a few individuals according to principal coordinate analysis (PCoA). One bread wheat landrace (Greda) was separated into two distinct sub-populations. A joint cluster analysis with other landraces of worldwide origin revealed that Omani bread wheat landraces were different from other landraces. However, two landraces from Pakistan were grouped somewhat closer to Omani landraces indicating a possible, previously unknown relationship. Implications of these results for future wheat landrace collection, evaluation and conservation are discussed.     

新疆灰霉病菌多态性及其致病力分化分析

灰霉病菌(Botrytis cinerea)是引起植物病害的重要病原。本研究将来自新疆3个主要生态区域的12个灰霉病菌菌株, 经人工接种于7个寄主的离体叶片上测定病原菌的致病性, 并采用RAPD技术分析了12个菌株的遗传多态性。研究结果表明, 12个灰霉菌株的致病力存在明显差异, 可分为强、中、弱3种致病型, 其中来自和田的黄瓜灰霉菌和伊犁特克斯的番茄灰霉菌致病力最强; 阿克苏番茄灰霉菌的致病力最弱。根据在不同寄主上的致病反应, 12个菌株被划分为4个菌群。RAPD分析结果表明, 在0.65阈值下, 12个灰霉菌株可分为4个菌群, 说明供试灰霉菌株间有高度的遗传分化。灰霉病菌致病力强弱与菌株寄主、地理位置均无直接相关性, 但灰霉菌株的遗传距离与菌株来源存在明显相关性。     

Inter-simple sequence repeat (ISSR) and RAPD variation among wild barley (Hordeum. vulgare subsp. spontaneum) populations from west Turkey

Inter-Simple Sequence Repeat (ISSR) and Randomly Amplified Polymorphic DNA (RAPD) markers were used to analyze genetic distance among H. vulgare subsp. spontaneum populations from west Turkey. Fifty-five RAPD and 10 ISSR primers were used to detect variation among sample. A total of 55 polymorphic loci were found using 65 primers. Two distinct cluster groups were clearly established among populations. The minimum variation was detected between Pinarbasi and Bornova (GD = 0.192) populations and the maximum was found between Icmeler and Aydin populations (GD = 0.926). As two dominant markers, RAPD and ISSRs are effective and promising marker systems for detecting genetic variation.     

Polymorphism and Genotype-specific Markers for Dichanthium Identified by Random Amplified Polymorphic DNA

One hundred decamer arbitrary primers were tested for PCR based amplification of seven genotypes (IG2208-S-1, IG2177, IG2180, IG2178, IG2165-S-1-1, IG2165-1 and Local-1) of an apomictic grass, Dichanthium annulatum, with the aim of screening polymorphic primers and genotype-specific markers. Out of 100 decamer primers tested, 42 produced no amplification or smeared non scorable bands, 12 amplified only single band and 46 yielded more than one polymorphic bands. Thirty-two primers out of 46 selected showed high level of polymorphism, producing 3–15 reproducible bands each for the seven Dichanthium genotypes examined. Among the total of 307 amplified fragments 222 were polymorphic, 53 bands were unique to the genotypes and 32 were monomorphic. Thus, with selected primers sufficient polymorphism could be detected to allow identification of individual genotypes. Genetic similarities of RAPD profiles generated were estimated via a coefficient of DICE and then the data were processed by cluster analysis (UPGMA). The maximum similarities between two genotypes (IG2180 and IG2178) was 58% and these two made a cluster with genotype IG2177 having similarity of only 54%. It clearly corroborated existence of high levels of polymorphism in this grass though being apomictic in nature. Primers like OPE-16, OPG-02, OPG-18, OPH-05, OPH-09, OPH-16, OPI-07 and OPF-06 found most informative as they produced specific bands pertaining to five out of seven genotypes. Polymerase chain reaction (PCR) offers a substantially simple, rapid and reliable method for identification of large number of Dichanthium genotypes once enough number of reproducible and suitable primers is screened.     

Characterization of genetic variation and relationships among Choix germplasm accessions using RAPD markers

Choix, a plant in the tribe Maydeae of the grass family, has been cultivated in Asia for several thousand years. It is a potential gene resource for improvement of other cereal crops because of its nutritional value and tolerance to stress. Genetic variation and relationships among 21 Choix lachryma-jobi L. accessions were characterized by random amplified polymorphic DNA (RAPD) markers. A total of 205 DNA fragments across all materials were amplified with 31 random primers, averaging 6.61 per primer. Among amplified fragments, 115 showed polymorphism averaging 3.71 per primer. Of amplified markers, 56.1% were polymorphic, indicating considerable variation at the DNA level among these accessions. Some fragments were accession-specific. Pair-wise genetic similarity (GS) among 21 accessions ranged from 0.809 to 0.301. The 21 accessions clustered into two major groups. Three exotic Choix accessions clustered together. Three other Choix accessions, collected from Guangxi, China, clustered into a cohesive subgroup. Four wild types of Choix clustered into the same subgroup. These results indicated that the classification by RAPD data reflected the differences in geographic origins and evolution in Choix.     

Genetic diversity in the Olive tree (Olea europaea L. subsp. europaea) cultivated in Portugal revealed by RAPD and ISSR markers

To assess the genetic diversity of the most important olive cultivars used in Portugal, a base collection was established with two hundred and one accessions of eleven cultivars from the different agro-ecological-regions (AER) of olive oil production. Inter-cultivar diversity was evaluated using seven RAPD primers producing fifty-nine polymorphic markers that enable cultivar distinction. Discriminant analysis according to fruit use and AER revealed a genetic structure associated with local selection both for fruit exploitation and agro-ecological adaptation. Intra-cultivar diversity of the ancient cultivar Galega was also investigated. Three RAPD and five ISSR primers produced ninety-three polymorphic markers upon seventy-seven accessions from five AERs. Total accession discrimination was achieved. UPGMA clustering and discriminant analysis revealed that the genetic diversity was predominantly structured according to accessions origin. The within and among AER variation revealed by AMOVA supported this genetic structure and showed a high proportion of intra-AER variability. These evidences suggest that Galega is composed by a mixture of different genotypes adapted to local conditions, indicating that this cultivar is in an early stage of domestication and should be treated as a landrace instead of a uniform cultivar. The assessment of Galega genetic diversity within each of the five AERs indicated the highest significant level (H_g = 6.23 at p< 0.001) in Ribatejo-Santarém. This finding associated with the distinctiveness of Galega in relation to other Portuguese cultivars and with the recent insights of olive tree domestication allowed us to hypothesize that Ribatejo-Santarém was the ecological region of origin and dispersion of this ancient cultivar.     

Assessing the Genetic Diversity in the International Cocoa Genebank,Trinidad (ICG,T) using Isozyme Electrophoresis and RAPD

Random amplified polymorphic DNA (RAPD) and isozyme electrophoresis (IE) techniques were used to estimate the level of genetic diversity in a sample of cacao germplasm existing at the International Cocoa Genebank, Trinidad. Twenty-six cocoa populations represented by 459 cocoa genotypes were analysed using IE and 22 populations represented by 353 cocoa genotypes were analysed using RAPD. Despite few differences in the classification of the populations, both techniques revealed three major groups: the indigenous trees, the cultivated Trinitario and the cultivated trees from Ecuador. Two-thirds of the partitioned diversity were found within populations and one-third between the populations, with both techniques.     

Evaluation of the discriminance capacity of RAPD, isoenzymes and morphologic markers in apple (Malus x domestica Borkh.) and the congruence among classifications

Twenty-one apple accessions were characterised and classified taxonomically with randomly amplified polymorphic DNA (RAPD). The results were compared with morphological and isoenzymatic classifications of the same material by calculating the congruence between similarity matrices. The results confirmed the greater discrimination capacity of RAPD compared with isoenzymes, although the taxonomic clusters obtained with both types of markers were congruent. The genetic relationships calculated using RAPD and isoenzymes showed little congruence with the morphological relationships among accessions. Isoenzymatic markers are useful in germplasm banks to evaluate the diversity of newly introduced accessions. The use of RAPD markers are especially beneficial to discriminate between material that is genetically similar, to evaluate genetic variability within a collection and to choose the components of the core collection.     

Characterisation of germplasm accessions of Napier grass (pennisetum purpureum and P. purpureum×P. glaucum Hybrids) and comparison with farm clones using RAPD

Fifty six germplasm accessions of the important East African fodder crop Napier grass, Pennisetum purpureum, and its hybrids with P. glaucum, were characterised using 67 random amplified polymorphic DNA (RAPD) fragments. No or very low intra-accession variation was found for 49 of the accessions examined, confirming field observations that this species is predominantly clonally propagated. Comparison of intra and inter-accession variation identified several groups of identical/similar accessions that could be targeted if the collection is to be rationalised, and also highlighted two misplantings of germplasm material during transfer to a field trial site. A neighbour joining dendrogram of Jaccard's similarity estimates, clearly separated 50 accessions of P. purpureum from three P. glaucum individuals, and placed six hybrid accessions in an intermediate position. These groupings were well supported by a nested AMOVA (P<0.001; 29.5% of total variance due to taxonomic delineation). The main group of P. purpureum individuals could be further differentiated into five sub-groups (designated East Africa, Southern Africa, USA1, USA2 and Miscellaneous, to reflect the majority membership of sub-groups) and examination of the within P. purpureum component of the nested AMOVA, found them to be significantly different (P<0.001; 18.8% of variance). Genetic diversity across all accessions was found to be fairly high (Shannon's diversity index 0.306) and thus the collection probably represents a wide genetic base for this species. In addition to germplasm accessions, 25 Kenyan farm clones were also analysed. A principal coordinate analysis found that all but one of the clones clustered with the main P. purpureum group of accessions, indicating that the majority are probably not interspecific hybrids. The origin and pedigree of clones is discussed based on genetic similarity amongst clones and to germplasm accessions.     

Analysis of Microsatellite Diversity in Ethiopian Tetraploid Wheat Landraces

The extent and patterns of microsatellite diversity in 141 Ethiopian tetraploid wheat landraces consisting of three species Triticum durum Desf., T. dicoccon Schrank and T. turgidum L. were analyzed using 29 microsatellite markers. A high level of polymorphism and a large number of alleles unique for each species were detected. Compared to emmer (T. dicoccon) and poulard (T. turgidum) wheats, a higher genetic diversity was observed in T. durum. The A-genome was more polymorphic than the B-genome in all the three species. Microsatellites with (GA) _n -repeats had a higher number of alleles than (GT) _n -repeats. A species pairwise comparison was made to determine the percentage of shared alleles and a large number of common alleles among species were observed. Average gene diversity, across the 29 microsatellite loci, was 0.684 for T. durum, 0.616 for T. dicoccon and 0.688 for T. turgidum. Genetic distances were lower between T. durum and T. turgidum (0.26) than between T. durum and T. dicoccon (0.34) or between T. turgidum and T. dicoccon (0.38). A significant correlation (p < 0.01) was found between the number of alleles per locus and the gene diversity in all the three species. Allelic frequency variation was highest between T. turgidum and T. dicoccon (10.62%) and lowest between T. durum and T. turgidum (4.86%). A genetic similarity coefficient of 0.34, 0.46 and 0.37 was found in T. durum, T. dicoccon, and T. turgidum, respectively. The dendogram, which was constructed on the basis of a similarity matrix using the UPGMA algorithm, distinguished all accessions represented in the study.     

Genetic Diversity among Wild Common Beans from Northwestern Argentina Based on Morpho-agronomic and RAPD Data

The genetic diversity among 10 wild populations of common bean Phaseolus vulgaris var. aborigineus was analyzed by means of RAPD markers and morpho-agronomic data. The study was performed on populations collected from different sites located in the provinces of Jujuy, Salta and Tucumán in northwestern Argentina. Ten quantitative traits and 33 random primers were scored. Clustering based on morpho-agronomic traits and RAPD markers generated similar phenograms that grouped bean populations based on their site of collection. The levels of diversity observed among populations were low suggesting they have a common ancestor. The levels of diversity shown by morpho-agronomic traits were higher compared to those of molecular markers, most probably due to the effect of the environment. Furthermore, a 480-bp DNA band identified a group of wild populations collected from similar sites. Breeding strategies need to exploit this diversity to broaden the genetic base of commercial beans to develop high yield cultivars.     

Analysis of genetic diversity in Turkish sesame (Sesamum indicum L.) populations using RAPD markers⋆

The genetic diversity of 38 cultivated populations of Sesamum indicum L. from four different regions of Turkey was estimated at the DNA level with the random amplified polymorphic DNA (RAPD) technique. Sixty-one bands were obtained for all populations 78% of which were polymorphic. Analysis of molecular variance (AMOVA) was used to investigate the genetic diversity of the populations which yielded highly significant differences among populations within regions (91.9% of the total genetic diversity). According to AMOVA and Shannon's index that were performed separately for each region, the highest value of genetic variation was observed among Northwest region populations (CV = 7.7; H₀ = 0.304) and lowest in the Southeast regions' populations (CV = 2.6; H₀ = 0.068). Nei and Li's similarity index was calculated and phylogenetic tree was established using the neighbor-joining algorithm. This phenetic analysis grouped 35 of 38 accessions in six groups leaving three highly diverse accessions outside. Wagner phylogenetic method was used to assess the phylogenetic relationships among the populations. In the majority-rule consensus tree, only 7 of the 32 forks showed above 60% occurrence. Using Principal Coordinate Analysis (PCO) of the RAPD data set, the groups were clearly separated along the first three axis. These results indicate that RAPD technique is useful for sesame systematics, and should be valuable for the maintenance of germplasm banks and the efficient choice of parents in breeding programs.     

RAPD and AFLP assessment of genetic variation in a landrace of pepper (Capsicum annuum L.), grown in North-West Italy

In several regions of Italy as well as other parts of southern Europe, the heterogeneity of the land, the climate and the soil favour the survival in cultivation of a large number of landraces specifically adapted to local conditions. Knowledge on the level and distribution of their genetic variation can help to develop appropriate strategies, in order to suistainably manage in situ these germplasm resources at risk of genetic erosion. C. annuum is an herbaceous diploid species and is considered to be self-pollinating, although different rates of out-crossing have been recorded. We used random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers to assess genetic diversity within and between five populations of a landrace of Capsicum annuum L., grown in a limited area in north-west Italy and locally known as Cuneo pepper. Partitioning the genetic variation with Shannon's diversity index revealed that 41.6% occurred between and 58.4% within populations. Analogous results were obtained when the analysis was based only on RAPD or AFLP markers. However, AFLP was more reliable, since a lower range of variation was observed among primer combinations in detecting the two components of genetic variation. Notwithstanding the rather high level of within genetic variation detected, the five populations were clearly differentiated and differed in the frequency of alleles exclusive and/or present at very low frequencies. Our results show the need for accurate estimation of allele frequencies, in order to identify populations to which priority should be given for dynamic conservation of landraces.     

Relationships Among <Emphasis Type="Italic">Brassica napus</Emphasis> (L.) Germplasm from Spain and Great Britain as Determined by RAPD Markers

The genetic diversity and the relationships among a collection of Brassica napus L. European populations were evaluated using random amplified polymorphic DNA markers. The study included 33 accessions of B. napus collected from Galicia (northwestern Spain) and 18 British cultivars, 16 accessions of B. napus and two accessions of Brassica oleracea L. used as controls. DNA from 25 individuals per population was analyzed using 18 decamer primers. One hundred thirty-eight amplification products were scored of which 105 were polymorphic. These bands ranged in size from 350 to 2500 base pairs. Similarity coefficients and cluster analysis were computed and six groups were obtained. Cluster I was the largest and included all the landraces from northwestern Spain, except two accessions that grouped separately into Clusters III and IV, respectively. A low level of genetic variability was detected among the B. napus Spanish genotypes, while considerable diversity was present among the British ones, which grouped into three groups, two main clusters and one group formed by one accession. Cluster II included all commercial varieties grown in Great Britain whereas Cluster V grouped local varieties maintained by the growers for many years. Cluster VI was a singularity formed by one entry. British accessions of B. oleracea had the greatest dissimilarity with all the other populations and grouped separately in Clusters VII and VIII. As conclusion, B. napus landraces used in northwestern Spain as leafy-green vegetable probably have an independent origin from B. napus crops grown in other European regions. Besides, separate domestication in northwestern Spain and Great Britain for a different end use might have led to two distinct gene pools.