Genetic diversity of wild soybean (<Emphasis Type="Italic">Glycine soja</Emphasis> Sieb. et Zucc.) and Japanese cultivated soybeans [<Emphasis Type="Italic">G. max</Emphasis> (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection

Wild soybeans, Glycine soja, are a source of genetic variation to improve soybeans. To improve the efficiency evaluation of conserved germplasm a core or mini-core collection approach that maximizes allelic diversity in a proportion of the whole collection has frequently been advocated. The genetic diversity of a wild soybean collection (1,305 accessions) plus Japanese cultivated soybeans (53 accessions) were analyzed at 20 SSR marker loci. Higher levels of allelic diversity were found in wild soybeans (28 alleles per locus) than Japanese cultivated soybean (five alleles per locus). The genetic distance between wild soybeans from different regions reflected their proximity. Accessions from Russia consisted of a diverse array of alleles resulting in accessions being spread further apart in a PCA plot than accessions from other regions. Accessions of wild soybean from Korea included many rare alleles and thus had a high representation in the core collection. The two core collections developed here, traditional and mini, consisted of 192 accessions with 97% of the allelic diversity (14% of the whole collection) and 53 accessions with 62.4% of the allelic diversity (5% of the whole collection), respectively.     

Determining Sources of Diversity in Cultivated and Wild <Emphasis Type="Italic">Lablab purpureus</Emphasis> Related to Provenance of Germplasm by using Amplified Fragment Length Polymorphism

To improve understanding of diversity of Lablab purpureus and establish relationships among 103 germplasm accessions collected from diverse geographic origins, amplified fragment length polymorphism markers were used. Four primer sets selected out of 16 produced 289 clear, repeatable polymorphisms. UPGMA analysis of similarity data clustered the accessions according to their subspecific taxonomic organization, i.e., subsp. purpureus and subsp. uncinatus, as well as to cultivated and wild forms. The well-represented landraces from Africa and Asia, belonging predominantly to subsp. purpureus, displayed moderate genetic diversity. Wild forms from Africa showed far greater levels of diversity that would justify taxonomic re-assessment of the wild subsp. uncinatus. The molecular analysis identified forms that were collected in the wild in India but were genetically placed intermediate between wild and cultivated forms. As these plant types did not exist among the African accessions, it is suggested that they might represent escapes from early attempts of domestication. These results support the suggested pathway of domestication and distribution of L. purpureus from Africa to Asia. Additional members to a previously published core collection of the species are proposed.     

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.     

Collection of Lupinus angustifolius L. Germplasm and Characterisation of Morphological and Molecular Diversity

Lupinus angustifolius L. is a Mediterranean species, domesticated in the 20th century, representing an important grain legume crop in Australia and other countries. This work is focused on the collection of wild germplasm and on the characterisation of morphological and molecular diversity of germplasm accessions. It reports the collection of 81 wild L. angustifolius accessions from the South and Centre of Portugal, available at the ‘Instituto Superior de Agronomia Gene Bank’, with subsequent morphological and molecular characterisation of a selection of these and other accessions. A multivariate analysis of morphological traits on 88 L. angustifolius accessions (including 59 wild Portuguese accessions, 15 cultivars and 14 breeding lines) showed a cline of variation on wild germplasm, with plants from Southern Portugal characterised by earlier flowering, higher vegetative development and larger seeds. AFLP and ISSR molecular markers grouped modern cultivars as sub-clusters within the wider diversity of wild germplasm, revealing the narrow pool of genetic diversity on which domesticated accessions are based. The importance of preserving, characterising and using wild genetic resources for L. angustifolius crop improvement is outlined by the results obtained.     

The use of characterisation data to establish the Indian mungbean core collection and assessment of genetic diversity

A representative core set of well characterised Indian mungbean collection was developed using information on passport, characterisation and evaluation data. Initial diversity groups of the accessions comprising the whole collection were formed based on six major crop growing zones and a separate group for a few accessions from diverse exotic sources. Principal components score strategy was found to be most useful in maximising the selection inertia than strictly random sampling in all individual groups. A total of 152 accessions were extracted and the validity of their representativeness was established by comparing its diversity with that of the whole collection. Shannon diversity index for qualitative characters and certain statistical parameters for quantitative variables were used for measuring the diversity of the accessions in the core set and that of the whole collection. The representative core set was subjected to multivariate analysis for assessment of genetic diversity and also the variation patterns for discriminating among accessions to facilitate the users for easy accessibility, and effective and efficient utilisation of the material.     

Realizing value of genetic resources of <Emphasis Type="Italic">Allium</Emphasis> in India

The genetic resources of Allium in India are potential source of genes for widening the crop genetic base. Despite their high economic value, limited number of germplasm accessions of wild species have been collected and conserved mainly due to difficult access to areas of occurrence. The present work mainly highlights information on species diversity distribution and utilization of wild Allium species to assess the value of Indian germplasm and prioritization for future collection and conservation programmes.     

Marker-assisted sampling of the cultivated Andean potato Solanum phureja collection using RAPD markers

The potato crop originated in the Andean highlands where numerous farmer's varieties and non-cultivated wild species exist. An Andean potato collection is held in trust at the International Potato Center (CIP) to preserve the biodiversity of this crop and ensure the supply of germplasm for potato improvement worldwide. A core collection representing the biodiversity of the Andean potato germplasm is under construction using morphological, molecular, and geographic data. One of the eight cultivated potato species, Solanum phureja, has been genotyped using the RAPD technique. A protocol suitable for large germplasm collection genotyping has been developed to process numerous samples at reasonable costs. From 106 RAPD primers evaluated, we have selected 12 primers yielding 102 polymorphic markers, which unambiguously discriminated all 128 accessions but 2 that are possible duplicates. The S. phureja germplasm collected throughout the Andean countries appears to have a homogeneous genetic constitution. There was no clear geographic pattern as indicated by cluster analysis of the RAPD data. A sub-group of 20 accessions has been identified on the basis of the marker data and selected to maximize molecular (RAPD) variance and polymorphism. The probability of capturing equal amounts of marker polymorphism in this sub-group of 20 accessions by random sampling is less than 40%. This set accessions represents our first group of accessions that may constitute a core of the S. phureja collection. This tentative core will be challenged for diversity content by alternate markers and agronomic traits. Hence, the methodology for sampling less than 10% of the base collection, proposed for core collections by Brown (1989), can be based on molecular marker data provided cost-efficient fingerprints are developed.     

Wild crop relative populations hot-spots of diversity are hot-spots of introgression in the case of pearl millet

Wild crop relatives are unique genetic resources for crop adaptation. Increasing pressure from agriculture threatens these populations both by reducing their habitats and by creating opportunities for wild-cultivated hybridization. In this study, we assessed the diversity of 38 wild pearl millet populations covering the whole known distribution of the species in Africa, which extends from Senegal to Sudan. Using genetic analyses of 10 cultivated varieties as control, we demonstrate the high diversity harbored by these wild populations. Diversity patterns suggest a diversity hot-spot in the southern part of the wild population’s range. However, this high wild genetic diversity could partly be explained by introgression from cultivated varieties. Such introgression is widespread in the Sahel. We validate the impact of cultivated introgression on the diversity of the wild population using a genetic introgression model. The introgression distorts the real assessment of the diversity of the wild population, and the burden of this gene flow compromises the long term survival of the wild populations’ original genome. Our study also questions the long term survival of the crop’s wild relatives.     

Genetic differentiation and geographical distribution of barley germplasm based on RAPD markers

Random amplified polymorphic DNA (RAPD) analysis was used to characterize barley germplasm genetic diversity. For the analysis 303 morphologically distinctive accessions were selected from the VIR germplasm collection, St. Petersburg, Russia and the MAFF Genebank, Tsukuba, Japan to represent the principal regions of barley cultivation. A total of 93 polymorphic bands scored from RAPD patterns were used to generate a genetic distance matrix, which was used in both cluster and principal coordinate analysis. Both analysis clearly separated barley cultivars and local populations into three distinctive groups, which evidently reflect different directions in evolution and geographical distribution of barley. The hierarchy of accessions clustering in the first group indicates the westward distribution of barley from West Asia to Europe and New World across Ethiopia and then Mediterranean region. The principal breeding trends based on spike morphology are also observed in this group. The second group is associated with eastward distribution of the crop and represents a unified genetic group, which consists of East Asian and Central Asian accessions. The third distinctive group identified is connected with the evolution and dissemination of hulless forms in Central Asia and the Caucasus region. The conformity of identified genetic groups and clusters with the global centers of crops diversity (gene centers) determined by Vavilov (1926) and modern ecogeographical classification of barley is discussed.     

A problem of the rich: Prioritizing local plant genetic resources for ex situ conservation in Israel

A priority list of 323 plant species was created through a consultative process for ex situ conservation in the recently inaugurated Israel Plant Gene Bank (IGB). The IGB is set up to preserve plant genetic resources and the endangered genetic variability of the Israeli flora. Upon its inauguration, we consulted with the country’s leading plant breeders and botanists in an attempt to create a list of the most important plant species to be included in the initial collections. The list includes crop wild relatives (CWRs), selected according to their contribution to humans: edible plants (grains, vegetables, oil); forage plants; species with potential industrial and biotechnological applications (e.g. spices, medicinal plants, aromatic plants, fibers, dyes), and species with horticultural and forestry potential. We further ranked the species on the basis of assessed values for each of seven characteristics: distribution range in the country; abundance; rarity of the growing habitats; endemism; red number index—representing imminent threat of extinction; availability of samples in Israeli collections, and genetic relationship to cultivated crops. The sum of the assessed values for these seven characteristics was used to group the species on the list into four main prioritized-collection schemes. Statistical analysis indicated that all attributes had similar influence on the collecting prioritization scheme. In general, rare species with low abundance in their growing habitats were ranked in the highest priority group, while highly distributed species were sorted together into a lower priority group. The prioritization scheme will be used to optimize the collection in the IGB with the aim of establishing its collecting activities.     

Development of an algorithm identifying maximally diverse core collections

The development of a core collection, one which represents the genetic diversity of a crop with minimal redundancy and increases utility of the collection as a whole, is especially important as the funding for germplasm collections decreases. With limited resources, it is difficult to manage large germplasm collections and disperse genetically diverse germplasm to plant breeders. An algorithm was developed to assist in selection of core collections based on estimates of genetic distance. The criteria for selection of the maximum genetically diverse set were based on rankings of genetic distance between an accession with respect to all other accessions. Depending on the size core which a user wished, a zone around each selected accession was determined and no other accession within these limits was selected. The premise for the algorithm was that the genetic variability represented in the core must be representative of the distribution of genetic distances within the population of interest. In the present study, the algorithm was used with RAPD-marker-based estimates of genetic distance for 270 Theobroma cacao L. accessions and 134 Capsicum accessions that chose a set representing 18.5% of the population and representing the breadth of RAPD-based variation.     

Population genetic structure of in situ wild Sorghum bicolor in its Ethiopian center of origin based on SSR markers

In situ population studies of wild relatives of crops are crucial for the conservation of plant genetic resources, especially in regions with high genetic diversity and a risk of local extinction. Ethiopia is the center of origin for sorghum, yet little is known about the genetic structure of extant wild populations. Using 9 Simple Sequence Repeat loci, we characterized 19 wild populations from five regions, 8 local cultivar populations from three regions, and 10 wild sorghum accessions from several African countries. To our knowledge, this is the most comprehensive study to date of in situ wild sorghum populations in Africa. Genetic diversity corrected for sample size was significantly greater in the wild populations in situ than in local cultivars or the accessions. Approximately 41 % of the genetic variation in the wild plants was partitioned among populations, indicating a high degree of differentiation and potential value for germplasm conservation, and the average number of migrants (N_m) per generation was 0.43. Cluster analyses showed that some wild populations were grouped by geographic region, whereas others were not, presumably due to long-distance seed movement. Four wild populations from disjunct regions formed a unique cluster with an Ethiopian accession of subsp. drummondii and probably represent a weedy race. STRUCTURE and other analyses detected evidence for crop-wild hybridization, consistent with previous molecular marker studies in Kenya, Mali, and Cameroon. In summary, in situ wild sorghum populations in Ethiopia harbor substantial genetic diversity and differentiation, despite their close proximity to conspecific cultivars in this crop/wild/weedy complex.     

Establishment of sesame germplasm core collection in China

A sesame core collection containing 453 accessions was established by assessing genetic diversity of 4251 accessions collected in China. The accessions in the whole collection were grouped based on their origin, varietal and agro-ecological type. A computer program was used to cluster the data of 14 traits from the random small sample. Ward's method was chosen as the desirable method for clustering sesame germplasm resources. A set of technical methods for establishing core collection has been developed through determining the number of selected accessions based on the diversity distribution. The agronomic traits of the pre-selected core collection were investigated and tested in three ecological locations in China for two years. Among six qualitative traits, including plant type and flower color in a total of 5304 accessions, 97.85% was completely the same as the original data, and three quantitative traits, including growth period and plant height, were significantly and positively related with the original data. The representativeness assessment of the final core collection indicated that 35 phenotypes of 10 qualitative traits in the core collection were basically similar to those of the pre-selected core collection. Six feature values such as mean, standard deviation etc. of four quantitative traits including oil content and 1000-seed weight were close to those of the pre-selected core collection. The final core collection possessed a fair representativeness of the pre-selected core collection.     

Pattern of genetic diversity of cultivated and non-cultivated mashua, <Emphasis Type="Italic">Tropaeolum tuberosum</Emphasis>, in the Cusco region of Perú

This paper analyzes the genetic diversity of mashua cultivars grown in six communities in the Cusco region of Perú, of non-cultivated forms collected in the same region, and a sample of cultivars from the germplasm collection at the International Potato Center (CIP). From the DNA fingerprinting generated by SRAP markers, it is clear that mashua is a genetically variable crop with a range of similarity ranging from 65 to 99%. The widest range of variation was found for the most isolated community, Sayllafaya. Another important finding was that most of the non-cultivated accessions are likely feral races resulting from escape to cultivation rather than wild relatives. In general the range of variation of the cultivars from the communities and their feral relatives are not represented in the cultivars sampled of the collection maintained at the International Potato Center, Perú.     

Genetic diversity in the Lima bean (Phaseolus lunatus L.) as revealed by chloroplast DNA (cpDNA) variations

Genetic diversity in the Lima bean (P. lunatus L.) was assessed bymeans of two chloroplast DNA probes. Based on data obtained from 152accessions including wild forms and landraces, the two separateMesoamerican and Andean groups were confirmed and a transition poolof genetic diversity was observed in the two botanical formsconsistent with their distribution range. Three primary centres ofgenetic diversity and one secondary diversification spot are proposedfor the wild Lima bean whereas only two domestication sites areunderlined for the landraces. The importance of human intervention inwidening the distribution range and the genetic diversity inlandraces is discussed.