Assessing the Genetic Diversity in the International Cocoa Genebank,Trinidad (ICG,T) using Isozyme Electrophoresis and RAPD

Random amplified polymorphic DNA (RAPD) and isozyme electrophoresis (IE) techniques were used to estimate the level of genetic diversity in a sample of cacao germplasm existing at the International Cocoa Genebank, Trinidad. Twenty-six cocoa populations represented by 459 cocoa genotypes were analysed using IE and 22 populations represented by 353 cocoa genotypes were analysed using RAPD. Despite few differences in the classification of the populations, both techniques revealed three major groups: the indigenous trees, the cultivated Trinitario and the cultivated trees from Ecuador. Two-thirds of the partitioned diversity were found within populations and one-third between the populations, with both techniques.     

Allelic Size Standards and Reference Genotypes to Unify International Cocoa (Theobroma cacao L.) Microsatellite Data

Standardisation of microsatellite allele profiles between laboratories is of fundamental importance to the transferability of genetic fingerprint data and the identification of clonal individuals held at multiple sites. Here we describe two methods of standardisation applied to the microsatellite fingerprinting of 429 Theobroma cacao L. trees representing 345 accessions held in the worlds largest Cocoa Intermediate Quarantine facility: the use of a partial allelic ladder through the production of 46 cloned and sequenced allelic standards (AJ748464 to AJ48509), and the use of standard genotypes selected to display a diverse allelic range. Until now a lack of accurate and transferable identification information has impeded efforts to genetically improve the cocoa crop. To address this need, a global initiative to fingerprint all international cocoa germplasm collections using a common set of 15 microsatellite markers is in progress. Data reported here have been deposited with the International Cocoa Germplasm Database and form the basis of a searchable resource for clonal identification. To our knowledge, this is the first quarantine facility to be completely genotyped using microsatellite markers for the purpose of quality control and clonal identification. Implications of the results for retrospective tracking of labelling errors are briefly explored.     

Morphological Variability of Prosopis cineraria (L.) Druce, from the Cholistan Desert, Pakistan

Sixty-two accessions of Prosopis cineraria, collected from different areas of the Cholistan desert and from the vicinity of Islamia University, Bahawalpur during June, 2002 were evaluated for agro-morphological diversity. Data collected revealed considerable variation for pod length, pod thickness, number of seeds per pod, pod weight, 100-seed weight, seed size, number of pinnules, length of pinnae, length of the pinnulae, and breadth of the pinnulae. Accessions GD-1 and GD-2, collected from Gadhen Wala Toba, KWT-1, KWT-3, KWT-4, KWT-6, from Khokhran Wala Toba, TWT-2, TWT-7, TWT-8, from Taraway Wala Toba, CSW-2, CSW-7, CSW-8, from Chah Sulleh Wala, and IUB-5, IUB-9, from Islamia University, Bahawalpur, showed very high variation. Overall, accessions KWT-6 from Khokhran Wala Toba, and TWT-7, from Taraway Wala Toba, (both from Cholistan desert), appeared as best genotypes based on their morphological variation detected in this study.     

Effect of fertilizer and endomycorrhizal inoculum on growth and nutrient uptake of cocoa (Theobroma cacao L.) seedlings

Summary A greenhouse experiment was carried out to evaluate the influence of vesicular-arbuscular mycorrhiza (VAM) on growth and nutrient uptake of cocoa seedlings treated with five levels of palm oil mill effluent, in an unsterilized Oxisol and an Ultisol, either with or without addition of the VAM fungus Scutellospora calospora (Nicol. & Gred.) Walker and Sanders. Inoculation with the VAM fungi significantly increased nutrient uptake and plant growth in both soils. The dry matter yield, and the tissue N and K concentration in the plant tops increased significantly with increasing levels of palm oil mill effluent applied to both the Oxisol and the Ultisol. The maximum tissue P concentration, however, was obtained from plants grown in the Ultisol that was given 50.0 g palm oil mill effluent per kg while the maximum P recovery of 26% was obtained from plants given only 16.7 g effluent per kg. Overall, the percentage of P recovery decreased with the addition of increasing levels of palm oil mill effluent. In the Oxisol, the tissue P concentration increased with the addition of increasing levels of palm oil mill effluent, but the maximum recovery of P was recorded from plants given only 0.3 g effluent per kg. The percentage P recovery decreased with subsequent additions of the effluent.     

The Effect of Liming on the Availability of Cadmium in Soils and Its Uptake in Cacao (Theobroma c acao L.) In Trinidad & Tobago

ABSTRACT

Cadmium (Cd) is absorbed and bio-accumulated by cacao (Theobroma cacao L.) trees, resulting in unacceptably elevated levels in cocoa beans, necessitating measures to reduce its uptake from soils. A field experiment, lasting 18 months, was carried out to assess the effectiveness of liming on pH, bioavailability of Cd in soils and its uptake in cacao tissues. The treatments were: (a) control (untreated) and (b) lime-treated trees. Results demonstrated a significant (P < 0.05) increase in the soil pH (lime treated) and a natural fluctuation in pH for the control. For the lime-treated trees, bioavailable Cd levels generally stabilized with no significant change (P > 0.05) compared to the significant (P < 0.05) increase showed by control trees. The Cd levels in the leaves of both treatments decreased, however, the rate of decline in leaf Cd concentrations for lime-treated trees (?0.1378) was 3x faster than control (?0.0497) trees demonstrating the effectiveness of liming.     

Relationships Among <Emphasis Type="Italic">Brassica napus</Emphasis> (L.) Germplasm from Spain and Great Britain as Determined by RAPD Markers

The genetic diversity and the relationships among a collection of Brassica napus L. European populations were evaluated using random amplified polymorphic DNA markers. The study included 33 accessions of B. napus collected from Galicia (northwestern Spain) and 18 British cultivars, 16 accessions of B. napus and two accessions of Brassica oleracea L. used as controls. DNA from 25 individuals per population was analyzed using 18 decamer primers. One hundred thirty-eight amplification products were scored of which 105 were polymorphic. These bands ranged in size from 350 to 2500 base pairs. Similarity coefficients and cluster analysis were computed and six groups were obtained. Cluster I was the largest and included all the landraces from northwestern Spain, except two accessions that grouped separately into Clusters III and IV, respectively. A low level of genetic variability was detected among the B. napus Spanish genotypes, while considerable diversity was present among the British ones, which grouped into three groups, two main clusters and one group formed by one accession. Cluster II included all commercial varieties grown in Great Britain whereas Cluster V grouped local varieties maintained by the growers for many years. Cluster VI was a singularity formed by one entry. British accessions of B. oleracea had the greatest dissimilarity with all the other populations and grouped separately in Clusters VII and VIII. As conclusion, B. napus landraces used in northwestern Spain as leafy-green vegetable probably have an independent origin from B. napus crops grown in other European regions. Besides, separate domestication in northwestern Spain and Great Britain for a different end use might have led to two distinct gene pools.     

Patterns of Phenotypic Variation in a Germplasm Collection of Carthamus tinctorius L. from the Middle East

Phenotypic diversity was assessed for quantitative and qualitative traits in a salt-tolerant subset of the international safflower (Carthamus tinctorius L.) germplasm collection originating from 11 countries in three regions (Central Asia, Southwest Asia and Africa) of the Middle East. Phenotypically, the germplasm, among and within regions, was highly variable, especially for rosette- and yield-related traits. Frequency of desirable variants of seven agronomically important traits ranged from 14% for long rosette period to 50% for no or few spines. Level of population differentiation was high for number of capitula per plant (30%), whereas most traits partitioned their diversity (82–87%) within populations. Region-specific nonrandom associations among sets of qualitative traits and the existence of broad morphological and phenotypic diversity in this germplasm were supported by the large number of log-linear models needed to describe qualitative trait associations, the high number of principal components needed to account for total variability, and the low discriminatory power of phenotypic traits among germplasm from regions and countries in the Middle East. These results suggest that adaptation of the species to the wide spatial and temporal variation in the Middle East resulted in a multitude of ecotypes and in enormous amount of local variation. A multivariate selection criterion for high biological and seed yield, long rosette period and no or few spines identified five accessions from Southwest Asia that can be introduced into subsistence farming systems as a multipurpose crop under saline agriculture.     

Collection, evaluation and classification of Greek populations of faba bean (Vicia faba L.)

Fifty-five Greek Vicia faba L. populations, collected from diverse areas, were planted at two dry and low fertility sites for evaluation and classification. Yield evaluation, which was carried out by Principal Component Analysis (PCA) on the basis of seven yield traits, showed the number of pods per plant, number of ovules and seeds per pod, and branching from the basal nodes to be the most important traits for population evaluation regarding yield. For population classification, four dissimilarity coefficients (Manhattan, Average Taxonomic Distance, Euclidean distance and squared Euclidean distance) and four multivariate methods (PCA, UPGMA, Neighbor-joining and Principal Coordinate Analysis) were evaluated using fifteen morphological and seven yield traits. Neighbor-joining was chosen as the most suitable multivariate method. This method combined with PCA for the seven yield traits, placed the populations into six groups. As revealed by the application of PCA on all twenty-two traits the grouping was based mainly on pod characteristics, stem thickness, plant height, 1000 seed weight and branching from basal nodes. Based on the results of the present study, a model is proposed for conserving cross-pollinated species, such as faba bean.     

Variation of cultivated flax (Linum usitatissimum L. subsp.usitatissimum) and its wild progenitor pale flax (subsp.angustifolium (Huds.) Thell.)

The domestication of cultivated flax (Linum usitatissimum L. subsp.usitatissimum) is briefly discussed. Using data documented as a matter of routine in genebank work, 63 accessions of cultivated flax from the flax germplasm collection of the Gatersleben Genebank are compared with 73 accessions of its wild progenitor pale flax (subsp.angustifolium (Huds.) Thell.), which have been observed in systematic field trials. Range of variation, genetically based variation, heritability and correlation of several characters are considered, especially with respect to the influence of domestication. Cultivated flax shows higher variation in the characters of generative plant parts, while pale flax varies more in the vegetative parts of the plant. The character correlations are similar in both subspecies. Of the 29 characters studied in pale flax the parameters describing tillering, height of plant, weight of seeds, width of petals and width of leaves are especially suitable for distinguishing between different accessions. In spite of the high heritabilities of most of the characters, the influence of the environment is significant in most cases.     

Genetic Relationships and Variation among Biotypes of Dallisgrass (Paspalum dilatatum Poir.) and Related Species Using Random Amplified Polymorphic DNA Markers

The genus Paspalum L. consists of more than 400 species. Around twenty-five informal groups of species are recognized in Paspalum and the Dilatata group is of special interest because its members are excellent potential forage grasses. Seventy-five germplasm accessions, representing 15 taxa, were analyzed using randomly amplified polymorphic DNA (RAPD). Polymorphisms were observed with twenty-two primers in the Dilatata group and 16 of those were analyzed. Four hundred and four different RAPD fragments were generated, resulting in an average of 25.2 bands per primer. Among the 404 markers analyzed, 48 (11.88%) were exclusive for the P. dilatatum Poir. biotypes, 31 (7.67%) were exclusive to taxa belonging to other groups included in this study, 28 markers (6.93%) were diagnosed for other species of the Dilatata group and 16 (3.96%), for natural hybrids. Extensive RAPD variation was found among the species studied. Inter- and intra-taxonomic polymorphisms were detected. A dendrogram based on the RAPD data shows some clusters corresponding to the same taxa. However, the biotypes of P. dilatatum do not form a cluster. The present work confirms that the RAPD technique can be used to determine genetic relationships between the taxa belonging to the Dilatata group.     

Phenotypic Variation and Relationships in Landraces and Improved Varieties of Rye (Secale cereale L.) from Northern Europe

Phenotypic diversity for agronomic characteristics was determined in an experiment with 29 landraces and 14 improved varieties of rye from the Nordic area, Germany and Poland. The accessions were scored for 12 characters. Effects of the location, year, type, and country of origin for landraces were investigated with analysis of variance. Phenotypic variations for the traits were estimated using the Shannon–Weaver diversity index. The genetic variation was high, with an average of H ₀ = 0.566. The landraces from Norway, Sweden and Finland showed the highest variation, whereas the improved varieties had the lowest. The German material also had low variation but the status of this material is uncertain. The genetic diversity showed that 70% of the variation was found within the accessions. A cluster analysis was carried out to identify the relationship between the accessions. The material grouped into eight clusters, where clusters I to V included landraces from Sweden, Finland and Norway, except for cluster III, which included one improved variety from Denmark. Cluster VI comprised a single Swedish landrace from Gotland. Most of the improved varieties were in cluster VII and the last cluster contained accessions from Germany and Sweden.     

Variation of morphological and adaptive traits in subterranean clover populations from Sardinia (Italy)

Variation was studied in subterranean clover for two morphological and four adaptive characters on genetically complex populations from Sardinia. The aim was to assess the population genetic structure in this almost completely inbred species, and to verify whether or not similar levels of diversity occurred at distinct sites of origin. Differences were found among populations for the class frequencies of the two morphological characters and for the subsequent level of intrinsic diversity measured by the Shannon-Weaver index. The variation among and within populations found for the other four characters suggested thatpopulations adjust in the long term their adaptive features to the environmental conditions but maintain contextually high levels of intra-population variation, which, in turn, is a primary factor of adaptation in environments that are seldom uniformspatially and temporally. A principal component analysis executed on the important traits for adaptation showed that these features could be combined, on the average, in different ways in the genetically complex populations here examined. Similarities or differences among populations were not necessarily related to geographic distances ofthe respective collection sites.     

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.     

Diversity Analysis of Garlic (Allium sativum L.) Germplasms Available in Nepal Based on Morphological Characters

A total of 179 garlic (Allium sativum L.) accessions were collected from various parts of Nepal in 2000. Each accession was planted in each of a plot of 2.25 m² at the Institute of Agriculture and Animal Science (IAAS) Horticulture farm (225 m asl) and at the Agriculture Research Station, Dailekh (1400 m asl) of Nepal Agriculture Research Council (NARC) in the first week of November 2000. All accessions were characterized for leaf erectness, leaf color, leaf wax, leaf cross section, bulb regularity, bulb skin color, bulb outer scales number, days to emergence, bulbing period, number of green leaves at 135 days after planting, days to maturity, plant height, bulb weight, bulb diameter, number of cloves per bulb, clove diameter and bulb yield. Data were analyzed by using principal component and cluster analysis procedures to reveal three major clusters. Four principal components were identified explaining more than 86% of total variation. Major characters included in the principal components were bulb weight, diameter, yield, number of cloves per bulb, maturity, plant height, number of green leaves at 135 days after planting, and bulbing period. The level of variation found in the collection showed the great potentiality of improving agronomic characters in garlic.     

Study of a germplasm collection of loquat (Eriobotrya japonica Lindl.) by multivariate analysis

Loquat species (Eriobotrya japonica Lindl.) originated in China, later was introduced in Japan. However, introduction in Europe occurred much later, in 18th century, it was introduced as an ornamental tree. Since then, the species was very well adapted to the Mediterranean climate, mainly in South East of Spain, where is located more than 50% of total European crop production. A European Project titled ‘Conservation, evaluation and collection of underutilized fruit species’ supported surveys and collection of plant material from these species in the Mediterranean basin countries. One of these surveys resulted in a germplasm collection of loquat established at IVIA, Valencia, Spain. This collection is being extended with new accessions collected across the world, currently the collection have 123 accessions under study. Germplasm management needs first a characterization of the plant material introduced and second diversity studies into the collection that could point out the variability pattern, to establish groups of accessions with similar traits and the most significant variables. These results allow organizing the information gathered for further uses. In this paper, 62 accessions from the IVIA germplasm collection were studied. Results from 43 variables were gathered and data studied by multivariate analysis. The analysis allowed summarizing the data tables with new variables containing most of the information. These results along with those obtained in the coming years will allow define a nuclear collection (minimum number of accessions that contained all the variability present in the collection).     

Development of Core Collection in Pigeonpea [<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millspaugh] using Geographic and Qualitative Morphological Descriptors

Pigeonpea is an important pulse crop grown by smallholder farmers in the semi-arid tropics. Most of the pigeonpea cultivars grown to date are selections from the landraces, with a narrow genetic base. With the expansion of the crop to newer areas, problems of local importance are to be addressed. Hence, an economically feasible and faster germplasm evaluation mechanism, such as a core collection, is required. This article describes the development of core collection from 12,153 pigeonpea accessions collected from 56 countries and maintained at ICRISAT, Patancheru, India. The germplasm accessions from 56 countries were placed under 14 clusters based primarily on geographic origin. Data on 14 qualitative morphological traits were used for cluster formation by Ward’s method. From each cluster ≈10% accessions were randomly selected to constitute a core collection comprising 1290 accessions. Mean comparisons using Newman–Keuls test, variances’ comparisons by Levene’s test, and comparison of frequency distribution by χ²-test indicated that the core collection was similar to that of the entire collection for various traits and the genetic variability available in the entire collection is preserved in the core collection. The Shannon–Weaver diversity index for different traits was also similar for both entire and core collection. All the important phenotypic associations between different traits available in the entire collection were preserved in the core collection. The core collection constituted in the present study facilitates identification of useful traits economically and expeditiously for use in pigeonpea improvement.