Genetic diversity of cowpea [<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.] in four West African and USA breeding programs as determined by AFLP analysis

Cowpea is an important grain legume and hay crop of many tropical and subtropical regions, especially in the dry savanna region of West Africa. The cowpea gene pool may be narrow because of a genetic bottleneck during domestication. Genetic variation within specific breeding programs may be further restricted due to breeding methods, ‘founder effects’ and limited exchange of germplasm between breeding programs. Genetic relationships among 60 advanced breeding lines from six breeding programs in West Africa and USA, and 27 landrace accessions from Africa, Asia, and South America were examined using amplified fragment length polymorphism (AFLP) markers with six near infrared fluorescence labeled EcoRI + 3/1bases/MseI + 3/1bases primer sets. A total of 382 bands were scored among the accessions with 207 polymorphic bands (54.2%). Despite a diverse origin, the 87 cowpea accessions shared a minimum 86% genetic similarity. Principal coordinates analysis showed clustering of breeding lines by program origin, indicating lack of genetic diversity compared to potential diversity. Accessions from Asia and the Americas overlapped and were distinct from West African breeding lines, indicating that germplasm from Asia and the Americas have common origins outside West Africa. US and Asian breeding programs could increase genetic variability in their programs substantially by incorporating germplasm from West Africa, while national programs in West Africa should consider introgression of Asian germplasm and germplasm from other parts of Africa into their programs to ensure long-term gains from selection.     

Genetic relationships within Vigna unguiculata (L.) Walp. based on isozyme analyses

Summary Isozyme analyses of genetic diversity in Vigna unguiculata were performed to determine genetic relationships and level of genetic diversity between wild and cultivated cowpea. Thirty-four cultivated accessions of V. unguiculata, 56 wild accessions of V. unguiculata, and six accessions representing five related wild Vigna species were analyzed. Ten enzyme systems were polymorphic within Vigna unguiculata: AAT, ACO, G6PDH, DIAP, LAP, MUE, ME MDH, PRX, and SOD. Fourteen of 24 putative loci (58%) were polymorphic within wild V. unguiculata, but only one locus (4%) was polymorphic within cultivated cowpea; when five related Vigna species were examined, 21 of the 24 bands of activity showed polymorphisms (88%) adding 33 alleles to the 48 identified within V. unguiculata. In one F₂ population of 68 plants (UCDVg 36 × UCDVg 21) a loose linkage was indicated between Diap-2 and G6pd-1 (² = 15.39; p = 0.004) with an estimated distance of 36.0 cM ± 5.02 (recombination (r) = 0.31). Also in another F₂ population of 38 plants (CB 88 × UCDVg 21) a loose linkage was indicated between Lap-1 and Prx (\gC² = 9.62; p = 0.047) with an estimated distance of 39.8 cM ± 7.0 (r = 0.33). Total genetic diversity (H_T) was 0.085 over all of the accessions including the one classified as V. nervosa. Within accession diversity (H_s) approached zero and between accession diversity (D_si) was responsible for all of the genetic diversity present. Therefore the coefficient of gene differentiation (G_ST = D_STII_T) approached 1. Absolute gene differentiation (D_m) was 0.087. Two of the nine segregations in this study were skewed. In general, results of this study concurred with the taxonomic classification within V. unguiculata and provided a strong indication that a severe genetic bottleneck occurred during the domestication process of cowpea.Abbreviations AAT aspartate amino-transferase - ACO aconitase - ALD aldolase - AUS Australia - BDI Burundi - BWA Botswana - CHN China - CMR Cameroon - DIAP diaphorase - DZA Algeria - ETH Ethiopia - G6PDH glucose-6-phosphate dehydrogenase - GDH glutamate dehydrogenase - GHA Ghana - GUY Guyana - IDH isocitrate dehydrogenase - IND India - KEN Kenya - LAO Laos - LAP leucine aminopeptidase - MDH malate dehydrogenase - ME malic enzyme - MEX Mexico - MOZ Mozambique - MUE methylumelliferyl-esterase - MWI Malawi - MYS Malaysia - NER Niger - NGA Nigeria - PRX peroxidase - RBSC ribulose-bisphosphate carboxylase - SEN Senegal - SLE Sierra Leone - SOD superoxide dismutase - TGO Togo - TZA Tanzania - USA United States of America - XDH xanthine dehydrogenase - ZAF South Africa - ZAR Zaire - ZIM Zimbabwe - ZMB Zambia     

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 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 in sweetpotato [Ipomoea batatas (L.) Lam.] in relationship to geographic sources as assessed with RAPD markers

Available evidence shows that sweetpotato originated from either Central or South American lowlands with subsequent dispersal to North America, Europe, Africa, Asia and the pacific islands. A total of 71 polymorphic RAPD molecular markers were used to assess the genetic relationships amongst 74 sweetpotato varieties originating from a total of 23 sweetpotato producing countries within six geographical regions, namely, South America, Central America/Caribbean, United States of America (USA), East Africa, Asia and Oceania. An Analysis of Molecular Variance (AMOVA) indicated that 93.4% of the total variance was due to the differences between genotypes within regions. The difference between regions was significant (P < 0.001) but only contributed 6.6% to the variance. Genetic distance (PhiST) calculated with AMOVA and multidimensional scaling (MDS) revealed that the South American and the Central American/Caribbean genotypes formed two separate clusters. East African varieties, which have unique characteristics from other traditional varieties, were distinct from other traditional varieties from South America and Oceania. These results support the reported hypothesis of the origin and dispersal of the sweetpotato and indicate that the primary centre of diversity probably has two distinct genepools. It is proposed that the dispersal of the sweetpotato from its origin may have mainly involved varieties from Central America/Caribbean as opposed to varieties from South America. There is an indication that new genepools may be evolving in Africa and Asia due to hybridisation and adaptation to the local environments.     

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 diversity and phylogeny of indigenous rhizobia from cowpea [<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.]

16S rRNA RFLP, 16S rRNA sequencing, 16S-23S rRNA Intergenetic Spacer (IGS) RFLP and G-C rich random amplified polymorphic DNA (RAPD) assays were conducted to genetically characterise indigenous cowpea [Vigna unguiculata (L.) Walp.] rhizobia from different geographic regions of China. Isolated cowpea rhizobia comprised six 16S rRNA genospecies. Genotype I was composed of 14 isolated strains and the reference strains of B. japonicum and B. liaoningense. This group was divided into two sub-groups respectively related to B. japonicum and B. liaoningense by 16S rRNA sequencing, IGS restriction fragment length polymorphism and RAPD assays. Genotype II composed of 27 isolates from a variety of geographic regions. Four different assays confirmed this group was genetically distinct from B. japonicum and B. liaoningense and probably represent an uncharacterised species. Strains isolated from Hongan, Central China and B. elkanii were grouped to genotype III. Strain DdE4 was solely clustered into genotype IV and related to Rhizobium leguminosarum. Genotypes V and VI consisted of six fast-growing isolates and clustered with reference strain of Sinorhizobium fredii. Comparing with the miscellaneous slow-growing isolates, fast-growing isolates mainly isolated from cowpea cultivar Egang I exhibited strict microbe–host specificity except SjzZ4. Nucleotide sequences reported were deposited in the GenBank with the accession numbers DQ786795–DQ786804.     

Genetic variability in dinitrogen fixation between cowpea [Vigna unguiculata (L.) Walp] cultivars determined using the nitrogen-15 isotope dilution technique

 N fixed in 16 cultivars of cowpea [Vigna unguiculata (L.) Walp] inoculated with effective Bradyrhizobium strains collected from the West African MIRCEN culture collection was measured by ¹⁵N isotope dilution technique. In all plant parts, significant differences in the percentage of N derived from the atmosphere (%Ndfa) and the amount of Ndfa occurred between the cultivars. Ndoute variety exhibited the highest %Ndfa (74.33% in shoots; 60.90% in roots) and accumulated more fixed N (960 mg N plant^–1 and 38 mg N plant^–1 in shoots and roots, respectively). Therefore this cultivar should be selected as the highest N-fixing cowpea cultivar. It also should be used in a breeding programme to contribute to the development of cultivars that could stimulate an intensive use of cowpea in many different cropping systems in Africa with a view to maintaining soil fertility. Received: 14 June 1999     

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.     

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.     

Microsatellites and RAPD Markers to Study Genetic Relationships Among Cowpea Breeding Lines and Local Varieties in Senegal

Genetic diversity in local cowpea varieties and breeding lines from Senegal were studied using random amplified polymorphic DNA (RAPD) and microsatellite (SSR) techniques. Among the 61 RAPD primers used, twelve show polymorphism. Fifteen of the 30 microsatellite primer pairs were polymorphic, detecting one to nine alleles per locus. The RAPD and SSR data were analyzed both separately and in combination to assess relationships among genetic lines. Although RAPD provided information on levels of genetic diversity, microsatellite markers are most effective in determining the relationship among cowpea accessions and varieties. The SSR results support the genetic diversification of cowpea in Senegal and underscore their potential in elucidating patterns of germplasm diversity of cowpea in Senegal. An erratum to this article is available at .     

Sources of nitrogen and yield advantages for monocropping and mixed cropping with cowpeas (Vigna unguiculata L.) and upland rice (Oryza sativa L.)

Summary Sources of N used by cropped and intercropped cowpeas and rice were determined by the ¹⁵N isotope-dilution technique. The biological efficiency of intercropping cowpeas and rice was assessed by calculating the land equivalent ratio of dry matter yield, total N, and uptake of N. A reduced N uptake by both cowpeas and rice during mixed cropping was attributed to mutual competition, with both crops competing effectively for the scarce environmental resources. The lack of a significant difference in the uptake of fertilizer and soil N by mixed-crop rice and cowpeas is an indication that the soil N was sufficient and that the mixed cropping did not create any imbalance in soil and fertilizer N uptake. The land equivalent ratio ranged between 120% and 180% for shoot dry matter and total N, showing that biological efficiency was increased by intercropping cowpeas with rice. The proportion of N derived from the atmosphere by mono- and intercropped cowpeas was not significantly different, showing that the potential of cowpeas to fix N₂ was independent of the cropping system, since the rice did not stimulate the cowpeas to fix more N₂.     

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.     

Genetic diversity among varieties of Chia (Salvia hispanica L.)

Chia, Salvia hispanica L., was a staple crop in pre-Columbian Mesoamerica. Despite the great potential of the species as an oilseed crop, little research related to domesticated and wild varieties exists. A study was undertaken to assess genetic diversity among 38 wild and domesticated accessions of S. hispanica collected throughout Mesoamerica by using RAPD markers. Genetic diversity was higher among wild varieties (H _G= 0.15) than all domesticated varieties (H _G= 0.10) and modern commercial domesticated varieties (H _G= 0.02), suggesting a slight loss of diversity accompanying domestication and a near lack of diversity in modern commercial varieties. In addition, the preliminary results indicate that the center of genetic diversity is in the highlands of western Mexico.     

Genetic diversity and relationships among cultivated and wild accessions of tartary buckwheat (Fagopyrum tataricum Gaertn.) as revealed by RAPD markers

The methodology of sampling and the selection of a proper marker systemfor the analysis of accessions are major concerns in the evaluation of gene bank material. In our study the RAPD analysis of bulked DNA samples and single seedsDNA was successfully employed to evaluate intra- and inter-population geneticvariability of cultivated and wild tartary buckwheat accessions. The bulkingapproach enabled the distinction of all 40 analysed accessions and theirseparation into geographically well defined clusters. Three wild populations,two from Sichuan and one from Qinghai, formed a group that was geneticallyrelatively distant from wild populations from Tibet and all cultivatedlandraces which, on the other hand, exhibited very close relationships. Thesingle seed study that was used after bulked DNA analysis provided detailedinformation of the genetic variation present within some accessions of specialinterest. A moderate level of genetic variability was detected betweenaccessions and the variability was partitioned into between- andwithin-population components. On average, most of the detected variation ispresent between F. tataricumpopulations. The genetic and geographic distribution of variability is furtherdiscussed. We demonstrated the usefulness of combining bulking and single seedstudy approaches for the effective evaluation of genetic variability inF. tataricum accessions that couldalso have wider applicability in the management of plant genetic resources andphylogenetic studies.     

Genetic diversity and differentiation in Ethiopian populations of Phytolacca dodecandra as revealed by AFLP and RAPD analyses

Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) analyses were performed on six populations (a total of 89 individuals) of Phytolacca dodecandra (endod) collected in Ethiopia. The populations were selected based on our previous investigation to represent two altitude groups: lowland/central-highland (1600–2500 m) and highland (2501–3000 m). A total of 197 AFLP and 68 RAPD markers were scored from 5 primer pairs and 12 random primers, respectively. The overall patterns obtained for AFLPs and RAPDs from diversity, cluster and principal component analyses were very comparable. However, the moderate correlation (r = 0.56) between AFLP and RAPD similarity matrices as well as the discrepancies in diversity estimates between the two techniques in some populations and in the lowland/central-highland plants could be due to differences in sensitivity of reaction conditions, bias in scoring of bands, number of markers used for analyses, and/or parts of the genome surveyed. For both AFLP and RAPD, the lowland/central-highland populations showed higher polymorphism and Shannon information measure (H) than the highlands. Cluster and principal component analyses performed for both marker types have also clearly demonstrated the differentiation of all the lowland/central highland plants from those of the highlands, in agreement with our previous conclusion. Markers scored from any of the five AFLP primer pairs were sufficient to clearly distinguish the two altitude groups; with RAPD, selection of about 8 informative markers produced by seven random primers was needed for the same purpose.     

Morphological Diversity of Bambara Groundnut [Vigna subterranea (L.) Verdc.] Landraces in Tanzania

A field experiment was conducted in Tanzania for two seasons to assess the genetic diversity of bambara groundnut landraces based on morphological characters. One hundred accessions collected from a wide range of agricultural zones in the country were evaluated in a 10 × 10 triple lattice block design at Maruku station in Bukoba, Tanzania. For the qualitative characters evaluated, considerable morphological variations were observed for growth habit, pod shape and pod colour. Quantitative morphological characters such as peduncle length, number of leaves per plant, terminal leaflet width, terminal leaflet length, petiole length, plant spread, plant length, pod width, seed length, seed width, number of pods per plant, shelling percentage and days to 50% flowering showed significant variation among accessions for the two test seasons. Multivariate analysis for 15 quantitative morphological traits that showed significant variation indicated that the first four PCs with eigenvalues ≥1 accounted for 63.0 and 65.0% of the total variance among the accessions during the two test seasons, respectively. The most important loadings for PC1 and PC2 for the two seasons were terminal leaflet width, terminal leaflet length, petiole length, plant spread, plant height and pod length, pod width, seed length, seed width, numbers of pods per plant. Cluster analysis grouped bambara groundnut accessions into three major groups with respect to their geographic origins. Based on this present study, bambara groundnut landraces from Tanzania displayed a considerable diversity for morphological and agronomic traits useful for germplasm management and utilization into crop improvement.     

Cowpea [Vigna unguiculata (L.) Walp.] maternal lineages,chloroplast captures,and wild cowpea evolution

Genetic Resources and Crop Evolution - Vigna unguiculata is the major grain legume in Africa and is also important in South-East Asia as a vegetable. The wild relatives, present only in Africa, are...     

Genetic structure of quinoa (<Emphasis Type="Italic">Chenopodium quinoa</Emphasis> Willd.) from the Bolivian altiplano as revealed by RAPD markers

Quinoa (Chenopodium quinoa Willd.) is a pseudocereal originated from the Andes important for small farmers’ food security as well as for commercial production. Recently, it has been claimed that in Bolivia genetic erosion could result from the marginalization of the crop in the north and from its commercial standardization in the south. The aim of this study was to quantify the hierarchical structure of the genetic variation present in eight quinoa field populations, consisting of cultivated and weedy individuals, representative of the altiplano and interandean valleys of Bolivia. Randomly amplified polymorphic DNA markers show that quinoa has a strong population structure and a high intra-population variation. An effect of geographical structure of the populations was highlighted, due to population isolation, not simply linked to distance but more probably to climatic and orographic barriers present in the studied zone. The population structure is also reinforced by the limited seed exchanges among farmers as revealed by field interviews. This population structure appears related to three major biogeographic zones: the northern and central altiplano, the interandean valley, and the southern Salar. Intrapopulation genetic diversity was higher than that expected for a mainly autogamous species, and higher than that reported in anterior studies based on germplasm collections. These results are commented in view of current knowledge on phylogeny and reproductive biology of the species, and their implications regarding genetic resources 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.