Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] as revealed by RAPD markers

The present study, using RAPD analysis, was undertaken to characterize genetic variation in domesticated cowpea and its wild progenitor, as well as their relationships. The materials used consisted of 26 domesticated accessions, including accessions from each of the five cultivar-group, and 30 wild/weedy accessions, including accessions from West, East and southern Africa. A total of 28 primers generated 202 RAPD bands. One hundred and eight bands were polymorphic among the domesticated compared to 181 among wild/weedy cowpea accessions. Wild accessions were more diverse in East Africa, which is the likely area of origin of V. unguiculata var. spontanea. Var. spontanea is supposed to have spread westward and southward, with a loss of variability, loss counterbalanceed in southern Africa by introgressions with local perennial subspecies. Although the variabilty of domesticated cowpea was the highest ever recorded, cultivar-groups were poorly resolved, and several results obtained with isozyme data were not confirmed here. However primitive cultivars were more diverse than evolved cultivars, which still suggests two consecutive bottlenecks within domesticated cowpea evolution. As isozymes and AFLP markers, although with a larger number of markers, RAPD data confirmed the single domestication hypothesis, the gap between wild and domesticated cowpea, and the widespread introgression phenomena between wild and domesticated cowpea.     

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.     

Interrelationships among Coconut (Cocos Nucifera L.) Accessions Using RAPD Technique

The genetic relationships among 33 coconut germplasm accessions were analyzed using RAPD markers. The germplasm accessions were collected from various coconut growing regions viz. South Asia (SA), South East Asia (SEA), South Pacific (SP), Atantic and America, and Africa. Forty-five random primers produced a total of 399 polymorphic markers. The Polymorphism Information Content (PIC) ranged from 0.031 to 0.392 and the Marker Index (MI) ranged from 6.28 to 0.031 among the primers. Based on the MI a set of 5, 10 and 15 informative and reproducible primers were identified. The mantel matrix correlation was calculated to compare the similarity matrices of a set of reproducible informative primers and global primers. There was significant correlation among the similarity matrices (r ≥ 0.50). The similarity matrix based on 399 polymorphic markers was used to construct the dendrogram to show the genetic relationship among the accessions. Similarity values ranged between 0.573 and 0.846. There was less genetic similarity (based on Jaccard's coefficient) among South Pacific and South East Asian accessions. The clustering pattern obtained in the present study was in agreement with the earlier reports based on RFLP, SSRs and AFLPs.     

Genetic diversity of Syrian pistachio (<Emphasis Type="Italic">Pistacia vera</Emphasis> L.) varieties evaluated by AFLP markers

Pistachio (Pistacia vera L.) is a strategic nut tree species in the Middle East which holds comparative advantage over other fruit trees in view of its hardiness, income generation opportunities and benefits for the ecosystem. Yet pistachio cultivation depends on a very narrow genetic base, in spite of the existence of many varieties still marginally exploited. Syria is an important center of diversity for pistachio. A country wide ecogeographic survey in this country was carried out to determine the extent of pistachio genetic diversity and its use. As a whole, 114 accessions were collected from 37 farms to assess diversity at morphological and molecular level. Molecular evaluation was carried out using Amplified Fragment Length Polymorphism (AFLP) technique and performed using seven primer pair combinations. Results from the studies allowed the identification of 25 pistachio female varieties in Syria, some of which unique and described for the first time. Three groups of pistachio diversity were identified by cluster analysis which provides useful information about the distribution of genetic diversity in Syria for enhanced use and sustainable conservation.     

Analysis of genetic diversity among European and Asian fig varieties (<Emphasis Type="Italic">Ficus carica</Emphasis> L.) using ISSR,RAPD, and SSR markers

Nineteen fig varieties and lines from Europe and Asia have been fingerprinted by ISSR, RAPD, and SSR markers, respectively, using 13, 19, and 13 primer combinations. All primers produced 258 loci, with the highest number of loci (119) generated by RAPD (R _p: 48.42). Clustering analysis was applied to the three marker datasets to elucidate the genetic structure and relationships among these varieties. Mean genetic similarities were 0.787, 0.717, and 0.749, respectively, as determined using ISSR, RAPD, and SSR. Each marker system produced incompletely separated clusters, although a weak binding group based on race type appeared in the combined dataset. Comparisons of coefficients revealed no correlation between different similarity matrices; congruence was observed between similarity matrices and co-phenetic matrices in all markers. Analysis of molecular variance (AMOVA) showed that most of the total polymorphism was attributable to within-group variance (ISSRs + RAPDs, 97.41%; SSRs, 90.18%). These results suggest that the genetic diversity of this fig population is low and that multiple marker utilization is critical to estimate the relatedness of figs at the variety level. Additionally, it was presumed that ‘Houraihi’, the oldest variety in Japan, was disseminated independently of other foreign varieties in the 17th century or before then.     

Genetic diversity in grasspea (Lathyrus sativus L.)

Genetic diversity was investigated in 348 accessions and subaccessions of grasspea (Lathyrus sativus L.) from 10 geographical regions. Polymorphism for 20 isozymes of 13 enzyme systems was studied to estimate the genetic diversity. The Near East and North Africa regions included the most variability for these isozyme systems, suggesting that the center of diversity (center of origin) for grasspea is in this general area. The lowest variability was found in accessions and subaccessions from South America, followed by those from Sudan–Ethiopia. Diversity was measured for individual loci over regions and EST-1 and SKDH had the highest genetic diversity. The closest genetic diversity was observed for LAP-2, followed by AAT-1 and PGM. The closest genetic distance existed between populations from the Near East and North Africa. Populations from South Asia and Sudan–Ethiopia, though geographically widely separated, exhibited a closer genetic distance from each other than from other regions.     

Genetic diversity in Tunisian perennial ryegrass revealed by ISSR markers

The genetic diversity in Tunisian perennial ryegrass (Lolium perenne) was examined by the help of inter-simple sequence repeats (ISSR). Starting from eighteen accessions, a large number of polymorphic ISSR markers were currently generated using appropriate primers (a total of 136, which average of 12.6 polymorphic bands/primer). These markers were considered to estimate the genetic distance among accessions and to draw phylogenetic trees. Our data provide evidence of a high degree of genetic diversity in Tunisian ryegrass. In addition, both cultivars and wild types present a high degree of divergence suggesting a complex domestication process in this crop. Moreover, spontaneous populations of Tunisian ryegrass have been identified as important ecotypes that are suitable in selection programs to improve grasslands.     

Genetic relationships and diversity among Brazilian cultivars and landraces of common beans (Phaseolus vulgaris L.) revealed by AFLP markers

The genetic variation and relationships among 31 accessions of Phaseolus vulgaris L., and two representatives of Vigna unguiculata L., were evaluated by AFLP analysis. A total of 263 DNA fragments across all materials were scored using nine primer combinations, averaging 32 per primer. More than 95% of the amplification products showed polymorphism, indicating high variation at the DNA level among these accessions. Pair-wise genetic similarity (Jaccard's coefficient) ranged from 0.553 to 0.840, with a mean of 0.765. Twenty-three accessions (70%) clustered into three groups. A majority of the commercial cultivars (91%) clustered within a single group, whereas the landraces were distributed along all the variation. An apparent correlation with phaseolin types was detected. Results of this study suggest that Brazilian landraces truly represent the overall genetic variability of Phaseolus vulgaris, confirming the multiple origins of these materials, and their potential as a source of variation for breeding programs.     

Genetic diversity of Pakistan wheat germplasm as revealed by RAPD markers

Wheat breeding in Pakistan started in 1930s before partition in the United India and so far has released more than 68 cultivars, but no systematic analyses of the genetic diversity of Pakistan wheat have been made. Twenty Pakistan wheat cultivars released from 1933 to 2002 were examined for genetic diversity and relationships using random amplified polymorphic DNA (RAPD) markers. Forty-two RAPD primers were applied and 184 polymorphic bands were generated for each cultivar. Most of the cultivars were genetically interrelated, although six of them displayed some genetic distinctness. The RAPD variation observed among these cultivars was low. Only 40.7% of the total scorable bands were polymorphic, and 26.1% of the polymorphic bands were observed most frequently (f = 0.95) among the 20 cultivars. The proportions of polymorphic bands for each cultivar ranged from 0.67 in ‘Yecora’ to 0.84 in ‘C-250’ with an average of 0.76. About 1.4% of the RAPD variation might have been fixed over the 69 years of wheat breeding, but such fixation was not statistically significant. These results are significant for future improvement and conservation of Pakistan wheat.     

Genetic diversity in Sorghum bicolor(L.) Moench accessions from different ecogeographical regions in Malawi assessed with RAPDs

Genetic variation within and among several Sorghum populations from different agroecological zones in Malawi were investigated using random amplified polymorphic markers (RAPDs). DNA samples from individual plants were analyzed using 35 oligonucleotides of random sequence. Twenty five of these primers allowed amplifications of random polymorphic (RAPD) loci. Overall, 52% of the scored loci were polymorphic. Every accession was genetically distinct. The analysis of molecular variance revealed that the within-region (among accessions) variations accounted for 96.43% of the total molecular variance. Observed variations in allelic frequency was not related to agroecological differences. The degree of band sharing was used to evaluate genetic distance between accessions and to construct a phylogenetic tree. Further analysis revealed that the sorghum accessions analyzed were genetically close despite considerable phenotypic diversity within and among them. It is suggested that all the sorghum landraces currently available in Malawi should be conserved both ex situ and in situ to maintain the current level of genetic diversity.     

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces assessed by Random Amplified Polymorphic DNA (RAPD) markers

Genetic diversity in 12 landraces of bambara groundnut (Vigna subterranea), an indigenous African legume, was evaluated using Random Amplified Polymorphic DNA (RAPD) markers. DNA from individuals of each landrace was also analysed to determine the level of heterogeneity within landraces. RAPDs revealed high levels of polymorphism among landraces. The percentage polymorphism ranged from 63.2% to 88.2% with an average of 73.1% for the 16 RAPD primers evaluated. The construction of genetic relationships using cluster analysis groups the 12 landraces in two clusters. RAPDs are useful for the genetic diversity studies in V. subterranea and can identify variation within landraces.     

Genetic diversity within a range of cultivars and landraces of flax (Linum usitatissimum L.) as revealed by RAPDs

Analysis of the extent and distribution of genetic diversity incrop plants is essential for optimizing sampling and breedingstrategies. We used random amplified polymorphic DNA (RAPD)markers to assess genetic diversity and relationships in 22 Canadiancultivars, 29 selected world cultivars and 10 landraces of flax(Linum usitatissimum L.). RAPDvariation was generally low and more variation was detected among,than within, the investigated flax accessions. Based on 53 variableRAPD loci observed for the 61 accessions, the landraces had a lowerproportion of fixed recessive RAPD loci (0.427) (i.e.,more genetic variation) than all of the flax cultivars examined(0.492). The linseed cultivars had a lower proportion ofrecessive loci (0.469) than the fiber flax cultivars(0.529). Canadian linseed cultivars had a lower proportionof recessive loci (0.465) than the selected world flaxcultivars (0.512). A trend was also observed that the rateof loss in genetic variation in Canadian flax breeding programs overthe last fifty years was approximately two variable loci per 100 lociper 10 years. Clustering analyses based on similarity estimatesshowed that the fiber cultivars were more related (or similar toeach other) and were classified as a homogeneous group. All ofthe linseed cultivars were clustered in diverse groups with the ninelandrace accessions. Implications of these findings for flax breedingand germplasm management are discussed.     

Genetic diversity analysis in Boerhavia diffusa L. of different geographic locations in India using RAPD markers

Boerhavia diffusa is extensively used in herbal medicines as well as in the Ayurvedic system, because it contains a set of clinically important compounds. In the present study, the genetic variability in Boerhavia diffusa between accessions of different geographical origin within the Indian territory is assessed through random amplified polymorphic DNA (RAPD) markers. Twenty-eight accessions of Boerhavia were screened with eighteen primers of which nine were found to be the most informative. The degree of polymorphism was found to be high in accessions collected from different places of Uttar Pradesh (Set II) in comparison to other states of India (Set I). A relatively lower level of polymorphism was recorded in accessions collected from diverse locations around Lucknow (Set III). Accessions from neighbouring geographical regions exhibited more similarity than those from distant regions (as revealed by the set I analysis). Certain diagnostic markers may be correlated with morphological character(s) such as plant type. BDL appeared most distinct and divergent from the rest of the accessions and the BDJ plant in set II also showed least similarity estimate. Fragments of 5.62 Kb and 4.47 Kb with primer GN59 was found to be unique for BDP and BD2 having ovate leaf character, whereas ovoid leaf genotype exhibited 0.79 Kb (GN34 primer) fragment. Similarly a unique band type (0.35 Kb) with primer GN83 was present in BDL and BD1 that share light pink flower. Jaccard's, and Nei and Li similarity coefficient values amongst the accessions were in the range of 0.22 to 0.89 and 0.33 to 0.93, respectively. Association of RAPD markers with the leaf characteristics, flower colour as well as with geographical locations has been made. This shows that RAPD markers are also useful for the study of genetic structure of Boerhavia populations.     

Genetic diversity among Northwestern Argentinian cultivars of common bean (Phaseolus vulgaris L.) as revealed by RAPD markers

The genetic diversity of 10 commercial cultivars of common beans, developed in Northern Argentina was analyzed based on RAPD markers. Sixteen primers were assayed and among them only 4 showed polymorphisms. A similarity matrix was generated by applying three different association coefficients, Simple Matching, Jaccard and Dice. By the UPGMA method dendrograms were generated and also the principal coordinate analysis was performed. The similarity values found were higher than 40% suggesting that genetic diversity is low. Both cluster analysis and principal coordinates analysis associated commercial cultivars either to the Andean or the Mesoamerican gene pool.     

AFLP-based genetic diversity assessment among Chinese vegetable mustards (<Emphasis Type="Italic">Brassica juncea</Emphasis> (L.) Czern.)

Amplified fragment length polymorphism (AFLP) analysis was used to evaluate the genetic relationships and diversities of Chinese vegetable mustards. Fourteen pairs of primers generated a total of 366 scorable fragments among 16 accessions of Brassica juncea studied, of which 296 bands were polymorphic with an average of 21.1% polymorphic bands per primer combination. Genetic similarities were obtained using Nei and Li similarity coefficients, and a dendrogram of the 16 accessions was made by UPGMA clustering method. The Nei and Li Similarity coefficient value ranged from 0.63 to 0.88. This result indicated that the 16 accessions of B. juncea possessed high level genetic variations. The cluster analysis showed that the vegetable mustards could be grouped into two main groups and some minor rami, which was partially in accordance with the traditional classification that based on different edible organs of vegetable mustards. The incongruity between morphological and molecular classification might be attributed to the high selection pressure during domestication of Chinese vegetable mustards, producing some accessions with similar genetic backgrounds evolving into abundant morphological variations. The great diversification among Chinese vegetable mustards not only provides an excellent object for molecular evolution research of B. juncea but also is of great value for widening the genetic basis of breeding programs and breeding materials selection. Besides, our study also indicates that AFLP are informative and can provide significant insights for genetic diversity research in B. juncea.     

Genetic structure among earthworms (Lumbricus terrestris L.) from different sampling sites in western Germany based on random amplified polymorphic DNA

Earthworms are being used as bio-indicators to assess terrestrial pollution. However, it is often not known whether their populations possess a uniform genetic structure, which would allow comparison of residues or biological properties of earthworms from different sampling locations. In order to investigate this point, random amplified polymorphic DNA (RAPD) variation was surveyed in earthworms (Lumbricus terrestris) from five different sampling sites in Germany. Forty oligonucleotide RAPD primers (10 base pairs in length) were screened, three of which produced high polymorphic band patterns. A total of 61 DNA fragments were detected in 90 individuals of L. terrestris from five sampling sites with 49 (80.3%) RAPD markers being polymorphic. The genetic similarities within (band sharing rates between 0.756 and 0.795) and among the L. terrestris populations (0.635) were similar even at widely separate locations. Inter-population variation in the RAPD pattern for all five earthworm populations accounted for 37.9% of the total variation, while intra-population variation for three adjacent Saarland populations accounted for only 18.0% of the total variation. Principal component analysis (PCA) and the genetic distances of the populations confirm these results. Twenty-four percent of the genetic distance is caused by geographical isolation as shown by a test for isolation by distance. These results show that L. terrestris fulfils the genetic qualifications for a bio-indicator particularly at closely located sampling sites. However, the results also suggest that earthworm studies of widely separated locations should include genetic characterisation of the earthworm samples.     

Genetic diversity and relationships among safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis> L.) analyzed by inter-simple sequence repeats (ISSRs)

Genetic diversity and relationships among 48 safflower accessions were evaluated using 22 inter-simple sequence repeats (ISSR) primers. A total of 429 bands were amplified, and 355 bands (about 82.7%) were polymorphic. Five to forty-one polymorphic bands could be amplified by each primer, with an average of 16.1 polymorphic bands per primer. The results showed that the polymorphism of the safflower germplasm was higher at the DNA level. All the 48 accessions could be distinguished by ISSR markers and were divided into 9 groups based on ISSR GS by using UPGMA method. The genetic relationships among the accessions from different continents were closer. Comparatively, the genetic diversity of the accessions originated from Asia was higher, from Europe assembled. The results also showed that the genetic variation of accessions from Indian and Middle Eastern safflower diversity centers were relatively higher. ISSR is an effective and promising marker system for detecting genetic diversity among safflower and give some useful information on its phylogenic relationships.     

Genetic diversity of <Emphasis Type="Italic">Guizotia abyssinica</Emphasis> (L. f.) Cass. (Asteraceae) from Ethiopia as revealed by random amplified polymorphic DNA (RAPD)

Genetic diversity of 70 populations of niger (Guizotia abyssinica) representing all its growing regions in Ethiopia was investigated using random amplified polymorphic DNA (RAPD) to reveal the extent of its populations genetic diversity. Ninety-seven percent of the loci studied was revealed to be polymorphic for the whole data set. The within population diversity estimated by Shannon diversity index and Nei gene diversity estimates was revealed to be 0.395 and 0.158, respectively. The extent of genetic variation of populations from major niger producing regions was significantly lower than that of populations from other regions; however, it is distributed regardless of altitude of growth. Genetic differentiation between populations was estimated with Shannon index as G^′ _ST (0.432), Nei’s G _ST (0.242) and AMOVA based F _ST (0.350) and appears to be equivalent to the average values calculated from various RAPD based studies on outcrossing species. Higher proportion of the variation detected by AMOVA resided within populations (64.58%) relative to the amount of variation among populations (35.42%). UPGMA cluster analysis showed that most of the populations were clustered according to their region of origin. However, some populations were genetically distant from the majority and seem to have unique genetic properties. It is concluded that the crop has a wide genetic basis that may be used for the improvement of the species through conventional breeding and/or marker assisted selection. Collection of germplasm from areas not yet covered and/or underrepresented is the opportunity to broaden the genetic basis of genebank collection.     

Genetic and Phenotypic Diversity in Downy-mildew-resistant Sorghum (Sorghum bicolor (L.) Moench) Germplasm

Genetic and phenotypic diversity among randomly selected 36 downy-mildew-resistant sorghum accessions were assessed, the former using 10 simple sequence repeat (SSR) marker loci and the latter using 20 phenotypic traits. The number of alleles (a _j ) at individual loci varied from five to 14 with an average of 8.8 alleles per locus. Nei's gene diversity (H _j ) varied from 0.59 to 0.92 with an average of 0.81 per locus. High gene diversity and allelic richness were observed in races durra caudatum (H _j = 0.76, a _j = 4.3) and guinea caudatum (H _j = 0.76, a _j = 3.8) and in east Africa (H _j = 0.78, a _j = 7.2). The regions were genetically more differentiated than the races as indicated by Wright's F _st. The pattern of SSR-based clustering of accessions was more in accordance with their geographic proximity than with their racial likeness. This clustering pattern matched little with that obtained from phenotypic traits. The inter-accession genetic distance varied from 0.30 to 1.00 with an average of 0.78. Inter-accession phenotypic distance varied from 0.01 to 0.55 with an average of 0.33. Eleven accession-pairs had phenotypic distance of more than 0.50 and genetic distance of more than 0.70. These could be used as potential parents in a sorghum downy mildew resistance-breeding program.