Genetic diversity of different Tunisian fig (Ficuscarica L.) collections revealed by RAPD fingerprints

The genetic diversity in Tunisian fig (Ficus carica L.) was studied using RAPD markers. Thirty-five fig cultivars originating from diverse geographical areas and belonging to three collections were analysed. Random decamer primers were screened to assess their ability to detect polymorphisms in this crop. Forty-four RAPD markers were revealed and used to survey the genetic diversity and to detect cases of mislabelling. As a result, considerable genetic diversity was detected among the studied F. carica accessions. The relationships among the 35 varieties were studied by cluster analysis. The dendrogram showed two main groups composed of cultivars with similar geographic origin. Moreover, the male accessions (caprifigs) were clustered indistinctively within the female ones, suggesting a narrow genetic diversity among these accessions. Our data proved that RAPD markers are useful for germplasm discrimination as well as for investigation of patterns of variation in fig. Since this designed procedure has permitted to establish a molecular database of the reference collections, the opportunity of this study is discussed in relation to the improvement and rational management of fig germplasm.     

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers.

Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut.     

Genetic diversity of worldwide Jerusalem artichoke (Helianthus tuberosus) germplasm as revealed by RAPD markers

Jerusalem artichoke (Helianthus tuberosus) is a wild relative of the cultivated sunflower (H. annuus); it is an old tuber crop that has recently received renewed interest. We used RAPD markers to characterize 147 Jerusalem artichoke accessions from nine countries. Thirty RAPD primers were screened; 13 of them detected 357 reproducible RAPD bands, of which 337 were polymorphic. Various diversity analyses revealed several different patterns of RAPD variation. More than 93% of the RAPD variation was found within accessions of a country. Weak genetic differentiation was observed between wild and cultivated accessions. Six groups were detected in this germplasm set. Four ancestral groups were found for the Canadian germplasm. The most genetically distinct accessions were identified. These findings provide useful diversity information for understanding the Jerusalem artichoke gene pool, for conserving Jerusalem artichoke germplasm, and for choosing germplasm for genetic improvement.     

Efficiency of phenotypic and DNA markers for a genetic diversity study of alfalfa

Information on genetic diversity and germplasm characterization is essential for successful crop improvement. Diverse data sets (pedigree, morphological, biochemical, DNA based-markers) are employed in various aspects of plant analysis. The objective of this study was to determine the efficiency of phenotypic and RAPD markers in diversity assessment of ten alfalfa (Medicago spp.) accessions from Europe, North America and Australia. Field experiment was designed as a randomised complete block with three replications over two consecutive years (2004, 2005) at one location. Twelve morpho-agronomic traits were recorded on 50 plants per each accession. Genomic DNA’s from 16–20 randomly selected individual plants per accession were used for RAPD analysis. Six primers selected in this study generated a total of 93 polymorphic RAPD bands. The number of polymorphic bands detected per primer ranged from 11 to 20. Genetic distances (GD) among investigated accessions and two-dimensional principal coordinate analysis (2D PCoA) based on phenotypic and molecular data were obtained. The average GD between (0.283–0.416) and within (0.247–0.332) accessions based on RAPD data was higher than GD values obtained by morpho-agronomic traits (0.171–0.354 and 0.157–0.261, respectively). 2D PCoA based on GD from RAPD data grouped most of the studied individual plants to four clusters according to their geographical or taxonomy origin. 2D PCoA based only on morpho-agronomic data did not group plants congruently to their origin, probably due to a strong environmental influence on studied traits. Our results indicated that the RAPD markers were effective in assessing genetic diversity within and between studied alfalfa accessions. In addition, the obtained results suggested that the RAPD markers might be useful for grouping of germplasm with similar genetic background and for pre-screening of potential heterotic groups in our breeding programme.     

The Use of Morphological and AFLP Markers in Diversity Analysis of Linseed

Different methods of genetic diversity measures could give better judgment of differentiating important accessions for growers, germplasm curators and plant breeders. Data of 60 accessions of linseed, mainly from Ethiopia, were used to assess their genetic diversity, employing morphological and amplified fragment length polymorphism (AFLP) methods. Analyses of genetic distance, principal components and clusters showed the presence of a wide range of diversity among the studied accessions. The mean for genetic distance estimates of the entire 1770 pairwise accessions was 0.6684 for morphology, while that of AFLP was 0.5734. These genetic distances varied from zero to one for morphology in contrast to 0.29 to 0.71 of the AFLP. Morphological and AFLP based clusters and their accompanying analyses showed different hierarchical patterns of genetic diversity among the accessions. Despite their disparity, the two diversity measures were found independently useful for assessing the degree of relatedness and the overall patterns of genetic variation among the analysed linseed accessions.     

Comparative assessment of variation in the USA Arachis pintoi (Krap. and Greg.) germplasm collection using RAPD profiling and tissue culture regeneration ability

Arachis pintoi accessions were used to study genetic diversity using RAPD markers. Concurrently, two tissue culture protocols were evaluated for organogenesis and the capacity to generate somaclonal variation. Data were collected on callus growth, callus weight gain, and number of regenerated plants. Robust RAPD profiles were obtained and eight primers amplified 100 different bands with 98% polymorphisms. The proportion of polymorphic RAPD loci was 89%. Average genetic distance was 0.36 and indicated that a large amount of genetic diversity exists within the germplasm evaluated. Genetic distances were used to prepare a dendogram for the A. pintoi accessions that separated them into four groups. A large degree of variability for callus induction and callus weight gain was observed among the accessions. Shoot regeneration was achieved for several accessions on both media with no structures indicative of somatic embryogenesis detected. Root induction was difficult to obtain, and many shoots died during this process. RAPD band profiles of regenerated tissue culture plants were similar to their parent plants, and therefore no somaclonal variation was evident using these methods.     

甘蔗种质间亲缘关系及特异标记的RAPD分析

采用RAPD技术分析甘蔗种质问的亲缘关系及特异标记。筛选出25个扩增多态性较强的随机引物,构建了41份甘蔗种质的RAPD指纹图谱,并对RAPD数据进行UPGMA聚类分析。甘蔗栽培品种之间、栽培品种与近缘种之间以及近缘种相互间的遗传相似系数变异范围为0．56～0．92,表明所研究的甘蔗种质之间的亲缘关系较近。此外,发现某些甘蔗亲本种质具有特异RAPD标记带。     

Genetic analysis of Spanish melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) germplasm using a standardized molecular-marker array and geographically diverse reference accessions

Genetic relationships among 125 Spanish melon (Cucumis melo L.) accessions from a Spanish germplasm collection were assessed using a standard molecular-marker array consisting of 34 random amplified polymorphic DNA (RAPD) markers bands (19 primers) and 72 reference accessions drawn from previous studies. The reference accession array consisted of a broad range [Japanese (19) Crete (17), African (15), and USA and Europe (US/EU, 21)] of horticultural groupings (Group Cantalupensis, Group Conomon, Group Inodorus, Group Flexuosus, and Group Chito), and of melon market classes (e.g., Charentais, U.S. Western and European Shipper types, Ogen, and Galia, Honeydew, and Casaba). Spanish melon accessions (largely Casaba, Group Inodorus) were genetically distinct from the reference accessions and other Group Inodorus melons of different origins. Most African accessions showed common genetic affinities, and grouped with the Group Chito and the Group Conomon accessions examined. Those accession groupings were distinct from all other accessions belonging to Group Cantalupensis, Flexuosus, and Inodorus accessions originating from Crete, Japan, Europe, and the U.S. Genetic diversity was highest in accessions of African origin and lowest in accessions of Spanish origin. Additional RAPD markers (49 primers, 141 bands) and 22 selected agronomic traits (quantitative and qualitative) were then used to assess the genetic diversity among Spanish accessions. While cluster analysis using fruit characteristics grouped accessions into cultivars, RAPD-based genetic-distance estimate did not provide consistent accession groupings either by cultivar or geographic origin. While the highest level of polymorphism was detected among melons originating from the central region of Spain, and in the Rochet cultivar, accessions from the Andalucía region and Green cultivars were comparatively less diverse. These results indicate that the Spanish melon accessions could be used to broaden the genetic base of local and foreign Casaba germplasm, to enhance the genetic diversity of U.S and European commercial melon germplasm, and to delineate collection strategies for acquisition of additional Spanish landraces.Communicated by C. MöllersMention of trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the USDA and does not imply its approval to the exclusion of other products that may be suitable.     

Genetic diversity in selected, historical US sugarbeet germplasm and Beta vulgaris ssp. maritima

 Diversity among sugar beet accessions released over the first 50 years of public breeding in the United States was examined to ascertain a baseline of genetic diversity and to gauge the effect of breeding on the loss or gain of diversity over this time period. Accessions were chosen as released germplasm from the major breeding stations contributing to the US germplasm pool and their presumed ancestors from Europe, including representatives for the wild forms Beta vulgaris ssp. maritima. Sixty nine polymorphic RAPD fragments were used for gene frequency analysis, and heterozygosity was determined within and among groups of accessions related either by breeding station or simply inherited agronomic characters for monogerm seed and restoration of fertility in a cytoplasmic male-sterile background. In general, heterozygosity within releases declined with time, but total genetic diversity in the US germplasm pool remained constant. Breeding for the agronomic characters had a marked influence in reducing diversity. Received: 20 October 1998 / Accepted: 28 October 1998     

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.     

Assessment of genetic variation within Indian mustard (Brassica juncea) germplasm using random amplified polymorphic DNA markers

Genetic diversity among 45 Indian mustard (Brassica Juncea L.) genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 (88%) were polymorphic. Of these, 13 were unique to accession 'Pak85559'. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77-0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop.     

萝卜种质资源亲缘关系的RAPD分析

利用筛选出的12个随机引物,对来源于不同国家和地区的有代表性的56份萝卜种质资源遗传多样性进行了RAPD分析,共扩增出109条带,其中多态性带为72条,多态性带百分率为62.9%,种质平均期望杂合度为0.289.系统聚类分析将供试材料分为2大类、9组,主坐标分析将其分为3大类、7组,两种分类方法结果基本一致,后者能更为直观和清楚地反映群体之间的关系.     

山东省无花果种质资源多样性的RAPD分析

利用随机扩增多态性DNA(RAPD)技术,对58份山东省无花果(Ficus caricaL.)资源的多样性进行了评价,经15个随机引物的初步分析表明,其中至少有23个不同的基因型。继而从36个随机引物中筛选出28个多态性好的引物,进一步对这23个不同基因型材料进行RAPD扩增分析,共得到309个清晰稳定的扩增位点,其中多态性位点236个,占76.4%。利用UPGMA法分析发现,这些基因型间的遗传相似系数在0.592~0.960之间,在此基础上,构建了各基因型间的遗传关系树状图。结果表明,山东省内的无花果资源具有较为丰富的遗传多样性。     

Agricultural diversification: the potential for underutilised crops in Africa's changing climates.

Two of the greatest challenges currently facing humanity are the potential consequences of climate change and the actual consequences of reduced agricultural diversity. This paper considers the consequences of both climate change and reduced agricultural diversity on global food security and nutrition. The inextricable link between climate change and crop diversity is examined, particularly in the context of crop production in Africa where most agricultural diversity exists and where climate change will have most impact. The Green Revolution, often seen as a model for increasing global agricultural productivity, is reconsidered in terms of its failure to make a significant impact in hostile tropical environments such as those of much of Africa. An alternative or, at least, a complementary strategy, is advocated where we might better harness the huge repository of indigenous plant species cultivated and conserved by local communities for many generations across variable climates. An example is given of multidisciplinary research on bambara groundnut (Vigna subterranea), an ancient grain legume grown, cooked, processed and traded mainly by subsistence women farmers in sub-Saharan Africa. The experience gained on bambara groundnut is considered as a basis for similar efforts on many other potentially useful underutilised food crops in the climates of the future.     

Genetic diversity of the Bambara groundnut (Vigna subterranea (L.) Verdc.) as assessed by SSR markers

Bambara groundnut ( Vigna subterranea (L.) Verdc.) is an important African legume crop. In this study, a collection consisting of 240 accessions was analyzed using 22 simple sequence repeat (SSR) markers. In total, 166 alleles were detected, with a mean of 7.59 alleles per locus. Allelic and gene diversities were higher in the west African and Cameroon/Nigeria regions with 6.68 and 6.18 alleles per locus, and 0.601 and 0.571, respectively. The genetic distance showed high similarity between west African and Cameroon/Nigeria accessions. Principal coordinate analyses and neighbor-joining analysis consistently revealed that the majority of west African accessions were grouped with Cameroon/Nigeria accessions, but they were differentiated from east African, central African, and southeast Asian accessions. Population structure analysis showed that two subpopulations existed, and most of the east African accessions were restricted to one subpopulation with some Cameroon/Nigeria accessions, whereas most of the west African accessions were associated with most of the Cameroon/Nigeria accessions in the other subpopulation. Comparison with SSR analysis of other Vigna cultigens, i.e., cultivated azuki bean ( Vigna angularis ) and mungbean ( Vigna radiata ), reveals that the mean gene diversity of Bambara groundnut was lower than azuki bean but higher than mungbean.     

The genetic diversity of the Vigna angularis complex in Asia.

A selected set of accessions of components of the azuki bean (Vigna angularis) complex comprising 123 cultivated accessions and 23 wild or weedy accessions from Bhutan, China (including Taiwan), India, Japan, Korea, and Nepal was analyzed using amplified fragment length polymorphism (AFLP) methodology. Using 12 AFLP primer pairs, 580 unambiguous bands were generated, 313 (53.9%) of which were polymorphic among azuki bean accessions. All 580 bands were used to assess phenotypic (band) and genetic (nucleotide) diversity among the 146 azuki bean accessions. The results indicate five major groups of azuki bean germplasm primarily associated with geographic origin of accessions and their status: wild, weedy, or cultivated. These five groups are (i) Himalayan wild, (ii) Nepal-Bhutan cultivated, (iii) Chinese wild, (iv) Taiwan wild - Bhutan cultivated, and (v) northeast Asian accessions. Within the northeast Asian accessions, three subgroups are present. These consist of (v1) Japanese complex - Korean cultivated, (v2) Japanese cultivated, and (v3) Chinese cultivated accessions. The results suggest domestication of azuki bean occurred at least twice, once in the Himalayan region of southern Asia and once in northeast Asia. The remarkable diversity of azuki bean germplasm in the Himalayan region compared with other regions suggests this is a rich source of germplasm for plant breeding. The results suggest there are important gaps in the germplasm collections of azuki bean and its close relatives from various parts of Asia and that specific collecting missions for Vigna germplasm related to azuki bean in the highlands of subtropical Asia are needed.     

Genetic and geographic polymorphism of cultivated tobaccos (Nicotiana tabacum) in Turkey

Nicotiana tabacum (2n = 48) is a natural amphidiploid and shows a distribution over a geographical area in eastern Anatolia. Random amplified polymorphic DNA (RAPD) technique was used to evaluate both genetic diversity among 21 primitive tobacco accessions comparing flue cure virginia genotype (FCV) and their geographical polymorphism as a source of genetic variations for breeding programs. Only 13 of all the 60 random primers used in RAPD showed polymorphism acceptable for characterization of these accessions. Totally 118 RAPD fragments were generated from 13 decamer primer and 64 of them were found polymorphic (54.2%). Mus and FCV showed the smallest genetic distance among accessions cultivated in the eastern Anatolia. These results shows that the RAPD assay is a powerful approach for identifying genetic and geographic polymorphism. This article was submitted by the authors in English.     

The use of RAPD analysis to classify Triticum accessions

 Crop germplasm collections contain a considerable percentage of misclassified accessions which may affect the use of germplasm for agricultural crop improvement. The objective of this study was to determine if random amplified polymorphic DNA (RAPD) analysis could be used to reclassify misclassified Triticum accessions. Twelve accessions suspected to be misclassified, based on morphological characters, as either macha or vavilovii wheat were studied using RAPD and cytological analyses. In the RAPD analysis, a dendrogram, based on Jaccard genetic similarity coefficients, grouped 5 dicoccum-like, 1 timopheevii-like, and 6 monococcum-like accessions with Triticum dicoccum, T. timopheevii, and T. monococcum accessions, respectively. These results were confirmed by the cytological analysis. A RAPD marker specific to the D genome was also detected. This study suggests that RAPD analysis can be used to classify germplasm and to distinguish some species in Triticum. Received: 12 June 1998 / Accepted: 18 August 1998     

Molecular assessment of genetic diversity in mung bean germplasm

RAPD profiles were used to identify the extent of diversity among 54 accessions of mung bean that included both improved and local land races. Out of the 40 primers screened, seven primers generated 174 amplification products with an average of 24.85 bands per primer. The RAPD profiles were analysed for Jaccard's similarity coefficients that was found to be in the range from 0 to 0.48, indicating the presence of wide range of genetic diversity at molecular level. Cluster analysis was carried out based on distances (1-similarity coefficient) using neighbour-joining method in Free Tree package. The dendrogram resolved all the accessions into two major clusters, I (with 11 accessions) and II (with 43 accessions). However, the cluster was further divided into four subclusters (II A with six, II B with nine, II C with 15 and II D with 13 accessions). The distribution of the accessions in different clusters and subclusters appears to be related to their performance in field conditions for 10 morphological traits that were scored. This study indicated that the RAPD profiles provide an easy and simple technique for preliminary genetic diversity assessment of mung bean accessions that may reflect morphological trait differences among them.