Parataxonomy,perceived dynamics and diversity of uses of two Detarium species in Benin (West Africa)

The contribution of species providing non-timber forest products to the livelihoods of local communities is well established. However, this contribution may be limited by the existence of confusion while dealing with close relative species. This is particularly the case for Detarium microcarpum Guill & Perr. and D. senegalense J.F.Gmel. The objectives of this study were to (1) identify the criteria used by local communities to differentiate D. microcarpum and D. senegalense, (2) determine local communities’ perception of the past dynamics of the two species and (3) assess the diversity of uses of both species. Data on differentiation criteria, perceived variation in the species abundance, and the different uses were collected using individual semi-structured interviews (n?=?914 informants). The relative frequency of citation and the use-value were calculated. The Chi-square test, correspondence analysis and generalized linear model were used for statistical analyses. Informants used fourteen criteria to differentiate the two species. The predominant criteria were the shape of the seed (87.86%) and the shape of the fruit (67.86%). Most of the informants reported that the populations of D. microcarpum (61.80%) and that of D. senegalense (60.12%) have regressed. In total, 168 use-reports were enumerated for the two species with 19 shared use-reports. We concluded that local communities use a variety of criteria to differentiate both species, the most popular being morphological traits of the fruits. Both species shared several use-reports (11.31%). However, their populations have declined. The documented uses for both species provide preliminary information for their future food uses and drug discovery.

     

Some factors affecting regional differentiation of the soils in the Republic of Benin (West Africa)

Spatial distribution of the parent materials, color, clay-eluviated horizon thickness, textural profile type, presence and position of the ferruginous nodules and ferricretes in the profile are analyzed at a small scale using the thematic information content of the published 1:200,000 soil map of Benin. Analyses indicate that there is a regional differentiation of the soil cover which is first drawn on that of the geological provinces, sedimentary basins, great morpho-structural units, and then determined by the factors that control the preservation or the transformation and erosion of an ancient lateritic mantle. These factors are directly influenced by differential changes of the local base levels.     

Genetic Nature of Yams (Dioscorea sp.) Domesticated by Farmers in Benin (West Africa)

‘Domestication’ is a traditional farmers’ practice reported for yams (Dioscorea sp.) in Benin (West Africa). It involves introducing ‘spontaneous’ (naturally occurring) yams, supposedly wild (D. abyssinica and D. praehensilis), in varieties of the D. cayenensis–D. rotundata cultivated species complex. In this study, we established the genetic nature of ‘predomesticated’ yam plants using the amplified fragment length polymorphism (AFLP) technique. A total of 213 accessions, consisting of 32 predomesticated yams, 70 D. cayenensis–D. rotundata, 86 D. abyssinica and 25 D. praehensilis yams were analysed. Using 91 AFLP markers, three groups of accessions were distinguished, broadly corresponding to the above botanical species. Of the 32 predomesticated accessions, 16% were clustered with D. praehensilis, 37% with D. abyssinica and the remaining 47% with D. cayenensis–D. rotundata. These results demonstrated the use of wild plants by farmers in their domestication process, and suggested that plants derived from intervarietal and interspecific hybridisation may also be subject to this process. This study has shown that through domestication farmers influence and increase the genetic diversity in yam by using sexual reproduction of wild and possibly cultivated yams.     

Dust characteristics and source-sink relations in eastern West Africa (SW-Niger and Benin) and South America (Argentinean Pampas)

In order to quantify dust input and to describe its characteristics under different environmental conditions, and to get information on source-sink relation, dust was collected monthly with bulk deposition samplers (open bucket type) in 2 and 4 m height over a 2—3 years period at different sites in West Africa (SW-Niger and Benin) and in the semi-arid Argentinean Pampas. Dust input, mineralogy (bulk and clay), chemical properties including total element content and particle-size distribution showed a clear seasonal pattern in eastern West Africa. Far-transported Saharan dust in the dry season could be distinguished from local material transported in the rainy season. In Argentina, high sand content of the samples pointed to an important participation of local components in the collected material. This was supported by higher contents of seaborne salts at the coastal sites, and the highest amounts of collected dust at the site of highest wind velocities. Due to the lack of seasonal differences in dust amount and its characteristics, and the aeolian genesis of the Pampas soils, a separation of local material and long-range dust was not possible.     

AFLP assessment of diversity in sweetpotato from Latin America and the Pacific region: Its implications on the dispersal of the crop

Although originally domesticated in tropical America, the sweetpotato [Ipomoea batatas (L.) Lam.] has a long history of cultivation in the Pacific region. While the post-Columbus dispersal of sweetpotato to Asia and the Pacific is well documented, the hypothesis that there was a prehistoric transfer of sweetpotato by Peruvian or Polynesian voyagers from Peru to Oceania has long been a controversial issue. The objective of this study was to assess the genetic diversity and interrelationships of sweetpotato landraces from the Pacific region and Latin America, and test the hypothesis of human transfer of this crop to the Pacific Island in prehistoric times. Seventy-five sweetpotato landraces from Peru, Ecuador, Mexico, the Philippines, Papua New Guinea (PNG) and 5 Oceania countries were analyzed using amplified fragment length polymorphism (AFLP). Multidimensional scaling (MDS) and analysis of molecular variance (AMOVA) revealed a large genetic variation in the Oceania gene pool, far greater than that in Peru-Ecuador. The Mexican cultivars were grouped together with those of Oceania. In contrast, there is little association between the Peru-Ecuador germplasm and that of Oceania. These results suggest that Peru-Ecuador may not be the source of the Oceania sweetpotato germplasm. Natural dispersal from Mesoamerica is an alternative explanation, to the Kumara hypothesis, for the origin of the Oceania sweetpotato.     

Genetic diversity within and among landraces of pearl millet (Pennisetum glaucum) under farmer management in West Africa

The influence of farmer management on pearl millet landrace diversity was determined by evaluating variation in individual farmers' populations from two villages in north-eastern Nigeria. The variability within and between landrace samples was estimated using variation at 163 amplified fragment length polymorphism marker (AFLP) loci. The data indicated that individual farmers' husbandry practices result in the isolation of their own group of ideotypes each in their own unique genetic backgrounds, thereby rendering landrace names inappropriate as indicators of a generic genetic identity. The implications of these findings for sampling strategies for genebanks and regional genetic evaluations are discussed.     

Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region

The Capsicum genus is native to tropical America and consists of 27 species, five of which are used as fresh vegetables and spices: Capsicum annuum L., Capsicum chinense Jacq., Capsicum frutescens L., Capsicum baccatum L. and Capsicum pubescens R. et P. The study of the relationships among species of cultivate Capsicum species will be useful for breeding new cultivars or hybrids. This study is focused on the genetic diversity and relationships of these species that were collected in the Andean region. Ten microsatellites and four AFLP combinations were used to characterize 260 Capsicum accessions. The AFLP tree turned out to be informative regarding relationships among species. The data clearly showed the close relationships between C. chinense and C. frutescens. Moreover, C. cardenasii and C. eximium were indistinguishable as a single, morphologically variable species. Our data showed C. baccatum and C. praetermissum to be distinct species that form a compact group. In the present work, AFLP fingerprinting indicated that C. chacoense was placed in the C. baccatum complex and showed C. tovarii as a separate species. In addition, SSR data indicated that there is intraspecific differentiation in the species C. chinense, C. baccatum and C. pubescens, as the PCoA-based clustering showed a clear geographic division related to country. Even though Bolivia is considered to be the nuclear area for these species, we have found similar variability in Ecuador and Peru for several Capsicum species.     

Microsatellite markers and genetic diversity assessment in Lolium temulentum

Lolium and Festuca are two important genera of cool-season forage and turf grasses worldwide. Lolium temulentum L. (darnel ryegrass) has been proposed as a model species for genomics studies of cool-season forage and turf grasses. A study with 41 darnel ryegrass, three tall fescue (Festuca arundinacea Schreb.), two tetraploid fescue (F. glaucescens), and two meadow fescue (F. pratensis) genotypes was initiated to (i) identify a set of microsatellite (simple sequence repeats) markers useful for L. temulentum L., and (ii) to utilize such markers for assessing the genetic variability of L. temulentum accessions collected from different geographical regions of the world. A total of 40 tall fescue (TF) EST-SSRs and 60 Festuca–Lolium (F × L) genomic SSRs were screened on a subset of eight genotypes. The selected 30 tall fescue EST-SSRs and 32 F × L genomic SSRs were used for further analysis of genotypes. The TF-EST- and the F × L genomic-SSRs identified 10.3 and 9.3 alleles per marker, respectively with an average polymorphic information content (PIC) value of 0.66. The phenogram based on 319 EST-SSR and 296 genomic SSR fragments, grouped L. temulentum accessions into three major clusters except for accession ABY-BA 8892.78. Lolium temulentum accession ABY-BA 8892.78 did not cluster with any other accession. The Festuca clusters were distantly related with darnel ryegrass clusters with a similarity coefficient of 0.26. The selected set of tall fescue EST- and F × L genomic SSRs were useful in assessing L. temulentum genetic diversity and could benefit the genetic improvement of members of the Festuca–Lolium complex.     

Assessing genetic diversity of sweet potato (Ipomoea batatas (L.) Lam.) cultivars from tropical America using AFLP

The sweet potato genebank at the International Potato Center (CIP) maintains 5,526 cultivated I. batatas accessions from 57 countries. Knowledge of the genetic structure in this collection is essential for rational germplasm conservation and utilization. Sixty-nine sweet potato cultivars from 4 geographical regions (including 13 countries) of Latin America were randomly sampled and fingerprinted using AFLP markers. A total of 210 polymorphic and clearly scorable fragments were generated. A geographic pattern of diversity distribution was revealed by mean similarity, multidimensional scaling (MDS), and analysis of molecular variance (AMOVA). The highest genetic diversity was found in Central America, whereas the lowest was in Peru-Ecuador. The within-region variation was the major source of molecular variance. The between-regions variation, although it only explains 10.0% of the total diversity, is statistically significant. Cultivars from Peru-Ecuador, with the lowest level of within region diversity, made the most significant contribution to the between region differentiation. These results support the hypothesis that Central America is the primary center of diversity and most likely the center of origin of sweet potato. Peru-Ecuador should be considered as a secondary center of sweet potato diversity.     

Bradyrhizobium sp. (Lupinus) in the winter rainfall region of South Africa

Widespread cultivation of lupin has resulted in the establishment of effective populations of Bradyrhizobium sp. (Lupinus) in the winter rainfall region of the Western Cape, South Africa. To determine whether inoculation increased yields of Lupinus angustifolius L., field trials were carried out at five sites in this region. Populations ranged from 380 rhizobia g^-1 in a moderately alkaline (pH 7.6) soil to >5,000 rhizobia g^-1 in four moderately acid (pH 5.5-5.8) soils. Soil isolates were generally similar to the inoculant strain WU425 in nitrogen-fixing effectiveness but several were significantly less effective. Average effectiveness of isolates from certain soils differed significantly. Although inoculation failed to appreciably increase nodule occupancy by WU425 in acid soils containing high populations of rhizobia, nodule occupancy was increased to 98% in the low population alkaline soil. The latter site was later abandoned because of disease. At the other sites, analysis of seed dry mass and protein content showed that yields were not significantly increased by either inoculation, nitrogen fertiliser (45 kg N ha^-1) or molybdenum applications. Analysis of genomic DNA by PCR fingerprinting showed that WU425 (isolated in Western Australia) and serologically related strains from other cultures clustered separately from the soil isolates. Isolates from the four acid soils were genomically diverse, whereas isolates from the alkaline soil formed a homogeneous cluster. Further investigation is required to determine the benefit of inoculation in alkaline soils of the winter rainfall region of the Western Cape.     

Identification of intra-accession genetic diversity in selfing crops using AFLP markers: implications for collection management

Germplasm conserved as seeds in genebanks requires regular regeneration. In this process, selection and genetic drift may cause loss of genetic diversity from accessions. In the case of selfing crops, separation of distinct lines into different accessions may be an efficient strategy to avoid these negative effects. In order to evaluate the applicability of this method for collection management, knowledge about the level of intra-accession genetic diversity is required. By means of AFLP analysis intra-accession variation was investigated in two cultivars, two landraces and two wild populations of ex situ conserved barley germplasm. In the total sample of 216 individuals analysed (36 per accession), 22 genotypes were observed based on 104 polymorphic loci. The number of genotypes detected ranged from 1 to 3 per accession, except for a Nepalese landrace that revealed 12 genotypes. An UPGMA cluster analysis grouped the genotypes unambiguously into the accession they belonged to and genotypes within accessions were generally found to be closely related. In order to determine the repeatability of the results obtained, 11 individuals belonging to 4 genotypes from the Nepalese landrace were scored for a second set of AFLP markers. Matrices of genetic distances calculated for the two AFLP datasets were found to be highly correlated (r = 0.9346, P < 0.001). Separation of genotypes into different accessions was considered a relevant option only for the Nepalese landrace. Analysis of molecular variance indicated that this accession could be well divided into 8 distinct lines. Further implications of the results for genebank practices are discussed.     

Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum L.) germplasm

The effective utilization of crop diversity held in genebanks depends on our knowledge of useful traits and available markers associated with the target traits. Target region amplification polymorphism (TRAP) was used to evaluate the genetic diversity and underlying relationships among 263 accessions of chickpea landraces maintained by the USDA-ARS Western Regional Plant Introduction Station in Pullman, WA, USA. Two-hundred sixty-two TRAP markers were amplified by eight primer combinations. Altogether, 110 (42 %) markers were polymorphic, the other 152 (58 %) displayed no variation. These polymorphic markers revealed important differences among the accessions, with an estimated, mean pair-wise genetic distance of 25.82 %, ranging from 2.8 to 50.0 %. Genetic distance analysis divided the accessions into two major groups, with 113 and 150 accessions each, and substantial association between molecular diversity and geographic origin was evident. Bayesian analysis of population structure revealed two groups (K = 2) with evidence for six sub-groups. Additionally, the population structure of a subset of 110 lines was determined (K = 3) for testing marker-trait associations (MTAs). Phenotypic traits included the concentrations of protein and nine mineral elements in the seeds. Two MTAs were significant (p < 0.01) for concentrations of Ca and K, and three MTAs were significant for Cu and Ni concentrations. The results indicate that this population is useful for genome-wide association studies on other economic traits given the level of genetic diversity uncovered and the marker-trait associations in seed minerals discovered.     

Diversity patterns of indigenous arbuscular mycorrhizal fungi associated with rhizosphere of cowpea (Vigna unguiculata (L.) Walp.) in Benin,West Africa

Assessment of diversity and understanding factors underlying species distribution are fundamental themes in ecology. However, the diversity of native arbuscular mycorrhizal fungi (AMF) species in African tropical agro-ecosystems remains weakly known. This research was carried out to assess the morphological diversity of indigenous AMF species associated with rhizosphere of cowpea (Vigna unguiculata (L.) Walp.) in different agro-ecological zones (AEZ) of Benin and to examine the effects of soil chemical properties, climatic factors and agricultural practices on this diversity. Results showed that, in Benin, cowpea was grown by farmers in very exhausted soils, where available phosphorus and potassium were deficient. The indigenous AMF spore density was on average 202 spores per 100 g dry soil and there was no difference in the density among the agro-ecological zones (P = 0.56). Fifteen AMF morphospecies belonging to eight genera (Gigaspora, Scutellospora, Racocetra, Acaulospora, Funneliformis, Rhizophagus, Glomus and Claroideoglomus) were detected. The computed species richness estimators indicated that a limited number of additional undetected morphospecies are probably present in cowpea fields. According to analysis of similarity (ANOSIM), the arbuscular mycorrhizas community composition of the Sudanian zone and Guinean zone were not significantly different (r = −0.01; P = 0.517). The diversity of AMF morphospecies in the fields was weak with prevalence of Glomeraceae (92%). Furthermore, AMF diversity and evenness indices were negatively correlated with annual rainfall (P < 0.01) and with available phosphorus (P < 0.05). However, no significant correlation was observed between AMF diversity indices and soil organic carbon. Ultimately, this study tends to confirm that soil management practices (tillage, soil disturbance) have negative effect on AMF diversity.     

Genetic diversity analysis of hulless barley from Shangri-la region revealed by SSR and AFLP markers

For adding the hulless barley resources of Shangri-la region to the global barley resource library, a basic work was done by us to assess their genetic diversity of this region. The genetic diversity of 60 hulless barley samples collected from three counties in Shangri-la region of Yunnan Province, were studied using SSR (simple sequence repeats) and AFLP (amplified fragment length polymorphism) markers. A total of 70 alleles were detected for 19 pairs of SSR primers, and 525 band containing 464 polymorphic bands were revealed for 5 pairs of AFLP primers. The value of polymorphism information content (PIC) ranged from 0.03 to 0.86 for SSR primers. The total numbers of alleles were 51, 55, 43 in three populations and the polymorphic bands were 188, 205 and 141. The genetic distances and genetic identity among the three populations showed their close relationship. The gene diversity among populations relative to the total population diversity (Gst) was 0.13 for SSR markers and 0.02 for AFLP markers and indicated that just 13 and 2% variations were among populations, respectively. The UPGMA cluster analysis revealed that all of the samples grouped randomly rather than clustered into distinct groups corresponding to their populations, row types and spring/fall types. We concluded that there was high genetic diversity in the population of Shangri-la region and the formation of diversity was related to complex environment and inhabitants’ traditional practices.     

Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP

Sweet potato (Ipomoea batatas L.) is the fifth most important crop in the developing countries after rice, wheat, maize and cassava. The amplified fragment length polymorphism (AFLP) method was used to study the genetic diversity and relationships of sweet potato accessions in the germplasm collection of Sokoine University of Agriculture, Morogoro and Sugarcane Research Institute, Kibaha, Tanzania. AFLP analysis of 97 sweet potato accessions using ten primer combinations gave a total of 202 clear polymorphic bands. Each one of the 97 sweet potato accessions could be distinguished based on these primer combinations. Estimates of genetic similarities were obtained by the Dice coefficient, and a final dendrogram was constructed with the un-weight pair-group method using arithmetic average. AFLP-based genetic similarity varied from 0.388 to 0.941, with a mean of 0.709. Cluster analysis using genetic similarity divided the accessions into two main groups suggesting that there are genetic relationships among the accessions. Principal Coordinate analysis confirmed the pattern of the cluster analysis. Analysis of molecular variance revealed greater variation within regions (96.19%) than among regions (3.81%). The results from the AFLP analysis revealed a relatively low genetic diversity among the germplasm accessions and the genetic distances between regions were low. A maximally diverse subset of 13 accessions capturing 97% of the molecular markers diversity was identified. We were able to detect duplicates accessions in the germplasm collection using the highly polymorphic markers obtained by AFLP, which were found to be an efficient tool to characterize the genetic diversity and relationships of sweet potato accessions in the germplasm collection in Tanzania.     

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

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