Genetic diversity in Lima bean (Phaseolus lunatus L.) as revealed by RAPD markers

The genetic variability of 46 accessions of the Lima bean (P. lunatus L.) including 16 wild forms and 30 landraces belonging to the three cultigroups Big lima, Sieva, Potato, and their intermediates, was evaluated using RAPD (Random amplified polymorphic DNA) markers. Twelve oligonucleotide primers produced 172 RAPD markers which allowed the differentiation of two main groups: the mesoamerican and the andean groups. This was confirmed by an AMOVA analysis which indicated that 37.7% of the variation was found between these two groups. For each botanical form (wild and cultivated), the molecular markers showed that small-seeded types (i.e. Sieva and Potato types and their related wild forms) had a wide distribution (from Mexico to Argentina) while the large-seeded types (Big lima type and its related wild forms) were circumscribed to the narrow west-coastal region from Ecuador to Bolivia. The results are in favour of an independent domestication process within the two groups, as the differentiation between mesoamerican and andean accessions was found to occur in both wild forms and landraces. Within each of the two main groups, wild forms and landraces were also found to be genetically differentiated and higher genetic diversity was observed among landraces than among wild forms. Within the mesoamerican landraces, low but significant differentiation between the Sieva and Potato cultigroups was observed. Some suggestions and hypotheses are discussed about evolution of the two small-seeded types. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity of Cannabis sativa germplasm based on RAPD markers

Random amplified polymorphic DN A (RAPD) markers were generated from 13 cultivars and accessions of Cannabis sativa L. Approximately 200 fragments generated by 10 primers of arbitrary sequence were used to assess the level of DNA variation. Statistical analysis was performed using the Dice coefficient of similarity and principal coordinate analysis. The grouping of the accessions according to the cluster analysis was in good agreement with their origin and lines with common ancestors were grouped together. Principal coordinates 1 and 2 revealed a clear separation of Italian and Hungarian germplasm and a third group, including a mixture of genotypes coming from different places; the third coordinate separated the Korean group which is probably the most divergent germplasm. Variability within the two cultivars ‘Carmagnola’ and ‘Fibranova1’ was also shown, suggesting good possibilities for long–term selection work. RAPD markers provide a powerful tool for the investigation of genetic variation in cultivars/accessions of hemp.     

Genetic diversity in camelina germplasm as revealed by seed quality characteristics and RAPD polymorphism

Camelina is an alternative oilseed crop species with limited information about the origin and diversity of available germplasm. Therefore, a set of 130 camelina accessions from a world collection was evaluated for oil content, protein content and 1000‐seed weight in field experiments grown in three macro‐environments in Austria. Based on phenotypic data, accessions were categorized into four groups with different seed characteristics using k‐means cluster analysis or principal component extraction. Subsequently, a representative set of 41 accessions was subjected to random amplified polymorphic DNA (RAPD) analysis. Of 24 primers, 15 were polymorphic producing a total of 30 marker loci. Genetic distance estimates between the 41 accessions were calculated, based both on RAPD polymorphism and on seed quality characteristics, and dendrograms were generated for comparison. Similarities were found between the two different clustering approaches, and grouping was partly in agreement with pedigree information or geographic origin. However, as the two estimates of diversity sampled different segments of the genome, i.e. regions coding for seed characteristics or phenotypically neutral genomic regions highlighted by discrete markers, the correlation between the two distance matrices was low.     

Genetic diversity of late blight resistant and susceptible Indian potato cultivars revealed by RAPD markers

Twenty-four tetraploid Indian potato cultivars were characterized by using RAPD markers to assess diversity within and between late blight resistant and susceptible cultivars. Sixty-four random decamer primers generated802 fragments, ranging in size from 60–3200 bp, with 96.4% fragment polymorphism. Shannon's index of diversity was used to quantify the degree of variability present within and between the variety types. Most of the diversity was detected within variety types, with 88% of variation being within and 12% being between the resistant and susceptible cultivars. No clear groupings based on late blight resistance and susceptibility or kinship was reflected on the dendogram. The late blight resistant cultivars exhibited higher variability compared to susceptible cultivars and they were more dispersed on the PCO plot. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic diversity and identification of cymbidium cultivars as measured by random amplified polymorphic DNA (RAPD) markers

DNA from thirty-six cymbidium cultivars was examined using polymerase chain reaction (PCR) to determine the efficiency of randomly amplified polymorphic DNA (RAPD) markers in identifying cultivars and determining levels of genetic variability. A total of 132 RAPD markers, 78% of which were polymorphic, were produced from 15 10mer arbitrary primers. All the cultivars were distinguishable when a number of primers was considered. One cultivar, Blue Smoke ‘Green Meadow’ could be distinguished from all the rest based only on lack of the OPA5-370 fragment. Genetic distances among the cultivars were estimated based on the amount of band sharing and ranged from 0.08–0.50 with an average of 0.29. Cluster analysis of genetic distance estimates grouped siblings together with each other and parents with offsprings, thereby agreeing with known parentage information and corroborating isozyme data obtained from a separate study. The possible application of the observed polymorphism and variation to cymbidium breeding is discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic Relationships in Malus Evaluated by RAPD 'Fingerprinting' of Cultivars and Wild Species

The potential use of RAPD markers for taxonomic studies in Malus was investigated using 18 accessions of wild species and 27 apple cultivars. 29 preselected random decamer primers were applied to three sets of Malus genotypes. Random amplified polymorphic DNA (RAPD) ‘fingerprints’ were analysed for polymorphic amplification fragments, and coefficients estimating genetic similarity were calculated on the basis of about 50 polymorphic RAPD loci in each set of genotypes. Cluster analysis by an unweighted pair-group method with arithmetic averages (UPGMA) revealed that, in the cultivars, the molecular classification was in good agreement with the known lineage. A dendrogram generated for the wild species gave relationships that were, in principle, in accordance with the known phylogenetic information. Closely related species from section I were clearly distinguishable from those of sections III and IV. On the molecular level, a high degree of genetic diversity was found among both different apple cultivars and wild species of the genus Malus. The results gave additional evidence for the hypothesis that M. pumila and M. sylvestris were involved in the origin of the cultivated apples.     

Genetic diversity and relationships among Lablab purpureus genotypes evaluated using RAPD as markers

Summary Genetic variation in 40 accessions of Lablab purpureus was evaluated using random amplified polymorphic DNA as markers. A high level of genetic variation in this species was detected but this was mainly restricted to the difference between cultivated and wild forms. Of the cultivated genotypes, genetic variation among Asian collections was significantly higher than that among African collections. The three most divergent cultivated genotypes were all from Asia. Four of the five wild accessions, two from Zimbabwe and the other two from Zambia, were closely related. The other one, CPI 31113 collected from Uganda, was highly divergent. The two commercial forage varieties used in Australia, Rongai from Kenya and Highworth from India, were not very different.     

Study of genetic diversity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers

Fifty-eight accessions of sesame (Sesamum indicum L.), an important oil seed crop of the tropics and subtropics were analysed using random amplified polymorphic DNA (RAPD) technique. The material analysed comprised 36 collections from 18 different states of India and four adjoining countries of the Indian subcontinent, and 22 exotic accessions from 21 sesame growing countries around the world. The results from PCR amplifications with the selected 24 random 10-mer primers were statistically analysed. The value of Jaccard’s similarity coefficients ranged from 0.19 to 0.89. The results indicated the presence of high level of genetic diversity. However, the extent of genetic diversity was greater in the collections from Indian subcontinent as compared to the exotics. Among the Indian accessions, the collections from Rajasthan and North-eastern states were highly diverse. The phenetic analysis grouped 48 out of 58 accessions in six clusters and the remaining highly diverse accessions were placed outside these close-knit clusters. The Bootstrap estimates obtained by Wagner parsimony analysis were significant for seven out of 49 nodes in the majority-rule consensus tree (<95% occurrence). The results of both the analyses were, however, broadly comparable when the constitution of the individual clusters were considered. The principal components analysis indicated that the first two components accounted for only 21% of the total variations and in order to explain <75% of variations 18 components were required. The high level of genetic diversity prevalent among the Indian collections is probably indicative of the nativity of this crop species. Similarly, the relatively lower level of polymorphism in exotic germplasm could be ascribed to the comparatively recent introductions of limited germplasm of this crop into some of the non-traditional sesame growing countries. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic relationships and diversity among Tibetan wheat, common wheat and European spelt wheat revealed by RAPD markers

An endemic hexaploid wheat found in Tibet, China was taxonomically classified as a subspecies in common wheat, i.e. Triticum aestivum ssp. tibetanum. Seven accessions of the Tibetan wheat, 22 cultivars of common wheat and 17 lines of spelt wheat were used for RAPD analysis to study the genetic relationships of the Tibetan wheat with common wheat and spelt wheat, and to assess the genetic diversity (GD) among and within the taxa. RAPD polymorphism was found to be much higher within spelt wheat and the Tibetan wheat than within common wheat. The GD value between the Tibetan wheat and common wheat is lower than that between the Tibetan wheat and spelt wheat. The result of cluster analysis showed that the 46 genotypes were distinctly classified into two groups. Group 1 included all European spelt wheat lines, while group 2 includes all Chinese common wheat and the Tibetan wheat accessions. However, the Tibetan wheat was substantially differentiated from Chinese common wheat at a lower hierarchy. Our results support an earlier classification of the Tibetan wheat as a subspecies in common wheat. European spelt wheat and the Tibetan wheat showed much higher genetic diversity than Chinese common wheat, which could be used to diversify the genetic basis for common wheat breeding. This revised version was published online in July 2006 with corrections to the Cover Date.     

Variation in Capsicum annuum revealed by RAPD and AFLP markers

Genetic relationships were examined among thirty-four pepper (Capsicum annuum) cultivars of different types. Two types of PCR-based markers were used, RAPD and AFLP, and their relative effectiveness was compared. A dendrogram based on RAPD markers separated the large-fruited sweet cultivars from the small-fruited pungent peppers, and the former group showed less divergence than the latter. The percentage of polymorphic markers was lower for AFLP than for RAPD markers (13 and 22% respectively). However, AFLP primers amplified on average six times more products than RAPD markers. The average numbers of polymorphic products per primer were 1.6 and 6.5 for RAPD and AFLP primers, respectively, i.e., AFLP primers were four times more efficient than RAPD primers in their ability to detect polymorphism in pepper. While four blocky type cultivars were indistinguishable by RAPD, two AFLP primer pairs were sufficient to distinguish the four cultivars from each other. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity among wild sugarcane germplasm from Laos revealed with markers

A group of 35 wild Saccharum complex clones, collected in Laos(ECL), was studied for its nuclear genetic diversity by RFLP revealed by 10dispersed low copy probes. Representatives of the main germplasmdiversity, regularly used in introgression, were also included. A preliminarycharacterisation of the new clones was performed by Erianthus specificprimers. A set of the 11 ECL clones most outstanding for their diseaseresistance and vigor and basic germplasm members were also characterisedby 9 cytoplasmic probes. Nuclear diversity evidenced that ECL clonesrepresented an independent genetic pool consisting at least of 3 differentgroups. A group of bands was exclusively exhibited by ECL clones. Theoccurrence of genetic recombination among them was suggested by thepresence of the new bands in 2 or 3 clonal groups. Erianthus specificamplification was positive for 7 ECL clones from different nuclear groups.Dendrogram analysis based on cytoplasmic diversity divided genotypes into2 major cytoplasmic types comprising 5 groups. The ECL clones separatedin 2 distinct groups: one located in the same cytoplasmic type as Erianthus clones; the other one, in an intermediate position, closer to Saccharum species. Basic clones groups were consistent with theirtaxonomic classification. The diversity revealed by nuclear singlecopy/nuclear repetitive/cytoplasmic patterns of the ECL germplasmcontrasts with what is usually observed and points to an active populationevolution. Further studies needed to confirmed this hypothesis arediscussed.     

Genetic relationships between Sicilian wild populations of Brassica analysed with RAPD markers

Brassica comprises very variable species, both morphologically and genetically. Among these species, the Sicilian populations of Brassica sect. Brassica, species related to kale crops form a complex group. The genetic relationships among 15 populations occurring in Sicily and one from Calabria, representing the existing diversity, have been investigated using random amplified polymorphic DNA (RAPD) markers. This assay, carried out with 22 arbitrary primers, generated 236 polymorphic fragments, 21 of which were specific for single populations (mainly Brassica insularis, Brassica incana and Brassica macro‐carpa). Jaccard's genetic distances were computed and the phylogenic tree was established using the UPGMA algorithm. The dendrogram obtained showed four branches grouping: (1) B. incana populations; (2) B. insularis and B. macrocarpa, occurring in small islands around Sicily; (3) B. rupestris populations; and (4) B. villosa populations. Within B. rupestris, only B. rupestris subsp. brevisiliqua was clustered in the B. villosa group. The classification obtained is discussed with regard to the morphological, ecological and geographical data.     

绿豆SSR标记的开发及遗传多样性分析

SSR标记以其数量丰富、多态性好、共显性遗传等优点在基础研究和育种工作中发挥了重要作用,但目前绿豆基因组中的SSR标记依然较少。本研究将磁珠富集法和测序技术相结合高通量检测绿豆基因组SSR位点,鉴定出3,275,355个SSR位点,开发了2742个SSR标记。选取其中157个SSR进行PCR验证,发现有90个(57.33%)标记在10份材料中表现出多态性。挑选40个条带清晰、多态性高、染色体上均匀分布的标记对90份绿豆资源进行遗传多样性分析,单个位点检测到的等位变异数为2~8个,平均为3.0个,有效等位基因数为1.31~4.21个,平均为2.16。Nei’s基因多样性指数在0.23~0.76之间,平均为0.51。多态性信息含量为0.22~0.72,平均为0.43。聚类分析将90份材料分为2个类群,包含4个组。第I组主要由北方资源组成,第Ⅱ组种质来源较为分散,第Ⅲ组主要由山东的资源构成,第Ⅳ组包含多数河北的种质资源。本研究开发的多态性SSR标记不仅可以用于绿豆种质资源的遗传多样性分析,也将在高密度遗传图谱构建、基因定位和分子标记辅助育种中发挥重要作用。     

Genetic diversity among elite Bulgarian barley varieties evaluated by RFLP and RAPD markers

Genetic variation among five elite winter barley cultivars (H. vulgare L.) currently grown in Bulgaria was assessed at the molecular level using restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) markers. The present study sampled RFLPs in four well characterized multigene families in barley: the seed storage protein loci; the 18S, 5.8S and 26S ribosomal DNA loci; the loci coding for 5S ribosomal RNA and the loci coding subunit α of ATP-A complex in the mitochondrial genome. RFLPs were detected in three out of five investigated chromosomal loci in the barley cultivars studied. RAPD assay using arbitrary 10-base primers was applied to generate amplified length polymorphic markers in barley. Overall a total of 15 polymorphic phenotypes were found among the studied barley cultivars by using 11 out of 25 tested primers. All RAPDs were considered as dominant genetic markers except for two, where PCR and Southern blot analysis indicated the presence of codominant amplification products. Five RAPD polymorphisms in F₁ and F₂ progenies of the cross between Alpha and Obzor were inherited in Mendelian fashion. The determined values for the genetic variation proved a high genetic similarity among the tested cultivars. Genetic similarity (GS) calculated from RFLP and RAPD data ranged from 0.888 to 0.997 with a mean GS – 0.933. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic organization of aromatic rice as revealed by RAPD markers: A case study in conserving crop genetic resources on farm

Summary On-farm conservation of landraces is one strategy to maintain the diversity of crop germplasm in local agro-ecosystems. The genetic structures of landraces are a key biological factor in on-farm conservation strategies. To accumulate a genetic understanding that will help establish a methodology for on-farm conservation, the genetic organization of landraces of aromatic rice in Namdinh province, Vietnam was analyzed using RAPD markers. Eighteen RAPD markers detected 38 genotypes among 320 aromatic rice samples growing at 23 sites of farmers' fields and in the experimental field that derived from 13 sites. Geographical variation was observed in the frequency of genotypes, whereas individual landraces could not be distinguished by RAPD markers. Genetic variation within a site was generally smaller than that among sites. The degree of genetic similarity of the plants in a site varied among sites, as did the number of genotypes. Changes in genetic structure over time were investigated using experimental populations each derived from approximately 30 plants from 13 farmers' fields. The differences detected by DNA markers between the genetic structural in the farmers' fields and those in experimental fields suggested that genetic drift is a major cause of these differences. The present study suggests that DNA markers are an essential means to monitor the genetic structures of heterogeneous landraces of rice, and are useful for selecting study sites for the on-farm conservation of genetic diversity as well as for successive monitoring.     

Genetic diversity of wild and cultivated soybeans growing in China revealed by RAPD analysis

To evaluate the genetic diversity and to clarify the genetic relationships of wild and cultivated soybeans growing in China, 21 wild soybean accessions and 27 cultivated soybean landraces were analysed by using the random amplified polymorphic DNA method. The data show that wild soybean has a higher genetic variation than cultivated soybean, indicating that genetic variation has been reduced by domestication of wild soybean. Based on Nei's genetic similarity coefficient, all the accessions were classified into two major clusters, corresponding to wild and cultivated varieties of soybean. Furthermore, within each species, the accessions tend to form sub‐clusters that are in agreement with their geographical origins, demonstrating that an extensive geographical genetic differentiation exists in both species. For cultivated soybean, the varieties from the same geographical region but with different seasonal types were found to have closer genetic relationships than varieties from different geographical regions but with the same seasonal type. This result indicates that geographical differentiation plays a key role in the genetic differentiation of both wild and cultivated soybeans. Cultivated soybean varieties with different seasonal types in a region might have been established mainly from the local genotypes.     

Identification and genetic diversity analysis of date palm (Phoenix dactylifera L.) varieties from Morocco using RAPD markers

Genetic variation among 43 date palm (Phoenix dactylifera L.) accessions, including 37 accessions from Morocco and 6 cultivars from Iraq and Tunisia, was studied using Random Amplified Polymorphic DNA (RAPD) markers. The pre-screening of 123 primers on four genotypes allowed selection of 19 primers which revealed polymorphism and gave reproducible results. All 43 analysed genotypes were distinguishable by their band patterns. RAPD technology therefore appears very effective for identifying accessions of date palm. RAPD-based genetic distance was used to determine the relationships between the accessions. The grouping-association identified by cluster analysis was rather weak. However, morphologically similar varieties clustered together. A relatively low polymorphism and a lack of evident organisation are observed among the date palm varieties grown in Morocco. This could be related to the mode of introduction and maintenance of the Moroccan date palm germplasm involving limited foundation germplasm, exchange of cultivars between plantations, and periodic development of new recombinant cultivars following sexual reproduction. This revised version was published online in August 2006 with corrections to the Cover Date.