Data analysis for molecular characterization of plant genetic resources

Characterizations of plant genetic resources based on molecular markers have been increased in the last years. Studies using a broad range of markers applied on hundreds of plant species are the theoretical basis for inferring genetic diversity to propose both breeding and conservation strategies. Despite increased importance of molecular characterization in plant genetic resources, there is scarce information about analysis of this type of data. To fill this gap of information, this review discuss the rationale behind analyses achieved to study genetic relationship among accessions (within and between groups) and to identify accession, and also discuss the adequacy of some analyses and/or parameters for specific purposes. Genetic diversity within groups may be either quantified for the whole group (parameters to choose will depend on type of marker), or quantified and visualized for the relationships among individuals. Quantification parameters will be chosen depending on type of marker, reproduction mode and relatedness of individuals. Visualization is achieved by hierarchical and non-hierarchical methods. Genetic diversity between groups should be quantified either by analysis of molecular variance, or Nei’s parameters, or Wright’s F-statistics. Efficiency of accession identification can be evaluated by maximal probability of identical match by chance and number of resolved genotypes.     

Isozyme analysis of genetic diversity in wild Sicilian populations of Brassica sect. Brassica in view of genetic resources management

In Sicily and in the small surrounding islands the section Brassica of the genus Brassica comprises five species, B. insularis Moris, B. incana Ten., B. macrocarpa Guss., B. rupestris Raf. and B. villosa Biv. These taxa represent a genetic resource as relatives of kale crops but some populations are endangered or threatened, thus isozyme analyses were performed to assess the genetic diversity degree at population and species levels in order to assist the design of conservation management programs.Eleven loci from five enzyme systems (aconitase, leucine aminopeptidase, 6-phosphogluconate dehydrogenase, phosphoglucoisomerase phosphoglucomutase) were analyzed in sixteen natural population (fifteen from Sicily, one from Calabria). Mean within-population genetic diversity was moderate (P = 41%, A = 1.54, H = 0.16). In some cases a great number of heterozygous individuals were detected, in other cases fixation index (F) deviated significantly from Hardy-Weinberg genotypic expectations.A total of 37 alleles was recognized, six of which resulted exclusive to single populations. The among-population component of the total genetic diversity (Gst mean values) for each species was 0.30–0.37, indicating genetic differentiation among populations.Among B. villosa and B. rupestris populations genetic distance values resulted rather low and they resulted high with B. incana and B. macrocarpa populations.The results are discussed with regard to the distribution of the genetic diversity level and the genetic resources management.     

Analysis of diversity in the fruit tree genetic resources from a Mediterranean island

A large number of genotypes of different fruit tree species have been described in Sardinia, where the plant species have evolved by adaptation to the Mediterranean environment. In this work results are summarized of a long-term survey carried out in the island by the authors since the early 1980s. Ten fruit tree species have been surveyed and collections of the traditional varieties were established. Some are major staple crops such as olive and grape, others such as almond, cherry, plum, fig, apple and pear are nowadays less cultivated, and still others have been more recently introduced like apricot and cactus pear. Data on the level of inter and intra-species diversity are given, as illustrated by representative morphological traits. The results of isozymes and RAPD-PCR analysis on the species Ficus carica genotypes are included, to assess genetic relationship among accessions. Observations on composition, as well as on state of conservation of selected traditional varieties are reported, and the main causes of genetic erosion are listed.     

Conservation strategies and management guidelines for wild Prunus genetic resources in Andalusia, Spain

Six species of the genus Prunus occur inAndalusia. Matters regarding their ecology, ethnobotanical aspectsand conservation are discussed, as well as knowledge about thegermplasm of those species with greater economic importance and theirdegree of conservation, namely: P.avium, P.mahaleb and P.insititia. Various conservation measures areproposed for wild germplasm and for the germplasm of local varieties:a) conservation efforts should target the best populations,except in the case of P.avium and P.insititia, where every individual should beaddressed, including both wild and local cultivars; b) theDehesa del Camarate (Sierra Nevada) is proposed as an areafor in situ germplasm conservation; c) theawareness of the importance of Prunus germplasmshould be increased among forest workers, environmental managers andthe public; d) some silvicultural techniques are proposed, suchas mixed Prunus patches, hedge treatment,Z-tree selection at the early stages and the protection ofroot suckers; e) improved, selected P.avium and P.mahaleb germplasm should be used at highlyproductive sites since these two species can be cultivated as highvalue timber trees; f) some Prunus speciescan also provide profitable NTFPs in the region. Details regardingdifferent collection areas are covered. Finally, some topics arerecommended for scientific research. Three tables and a distributionmap of Prunus species in Andalusia areincluded.     

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.     

The use of genetic resources in crop improvement: Lessons from China

The use of crop genetic resources in improvement programmes should be the ultimate objective of all undertakings in the field of germplasm resources. The present situation and future direction of the use of crop germplasm in China was assessed from responses to a questionnaire distributed to 165 plant breeders and curators nationwide. The general opinions for the limiting factors of germplasm utilization were also evaluated. Responses from the questionnaire indicated that the use of germplasm in breeding programmes is much more important than the direct use of germplasm in crop production as cultivars released. Among different types of crop genetic resources, released varieties and breeding lines contribute more to crop breeding. Wild relatives and genetic stocks, however, are expected to play a greater role in the future. Landraces will remain important in improvement. Limited useful germplasm available to breeders is the basic reason for the insufficient use of germplasm in crop breeding at present. The complex reasons which affect the availability of useful germplasm involve the research level, links between breeder and curator and others. To counter these, we propose some suggestions and measures which can be implemented in the near future.     

Farmers' valuation and conservation of crop genetic resources

This paper focuses on the value of landraces (traditional and local crop varieties) to farmers in centers of agricultural diversity. Additional information on the factors contributing to the private value which farmers assign to landraces may help to identify a strategy for ensuring the conservation of the crop genetic resources (CGRs) which are embodied in landraces while at the same time minimizing the costs. Economic and ethnobotanical approaches for examining the value of landraces complement one another. A formal economic approach establishes a framework for quantitative analysis while ethnobotanical methods provide qualitative data for assessing the likelihood that particular farmers or farm sectors will maintain landraces. Our research synthesizes the two approaches in order to examine farmer selection of local wheat landraces in relation to that of modern varieties in three provinces in western Turkey. Multiple farmer concerns (e.g. yield, risk, quality), environmental heterogeneity, and missing markets contribute to the persistence of landraces. Household characteristics informing variety choice will also affect the household's perceptions of the importance and value of landraces.     

Rose (<Emphasis Type=Italic>Rosa</Emphasis> spp.) genetic resources of Lake Van basin,Turkey: endangered antic roses of old Van gardens

Anatolia has been an important gene center for the planting and improving of old garden roses until sixteenth century. The interest in old garden roses in Anatolia shifted to new modern roses raised in Europe after sixteenth century. Old garden roses have been able to survive in remote gardens of Anatolia such as Van gardens. In this study, the population status, flower characteristics and usage methods of old garden roses, which were planted in Van gardens and had a rich garden culture tradition since Urartu, have been investigated. As a result of this study which was carried out between 2004 and 2005, ten species, one being new, have been determined in gardens in and around Van. In terms of availability, four of these species were determined as being rare, four infrequent and two widespread in the area. The urban texture of Van has experienced a fast improvement in the last two decades as a result of modernism, and the old rose gardens, which were part of the local culture and genetic wealth, have been replaced by the big blocks of houses.     

水产种质资源地理信息系统设计与实观

水产种质资源地理信息系统是为了实现水产种质资源数据共享而开发的一个C/S模式共享平台。采用VB＋MapX的二次开发方式，实现了空间数据与属性数据互相查询、数据管理以及报表输出等功能，另外还绘制了水产物种地理的分布图和水系分布图。     

Low genetic diversity in wild emmer (T. turgidum L. subsp. dicoccoides (Körn. ex Asch. et Graebn.) Thell.) from South-eastern Turkey revealed by Restriction Fragment Length Polymorphism

The present work was carried out to study genetic diversity among 17 populations of wild emmer wheat sampled from South-eastern Turkey, considered to be an important region for domestication of wheat. Eleven RFLP clones and 4 restriction enzymes combinations were used to probe the genomic DNA. A total of 151 polymorphic loci were obtained from the enzyme-probe combinations. The Genetic Distance (GD) values were from 0.019 (Gaziantep-3 and Sanliurfa-4) to 0.200 (Gaziantep-1 and K. Maras). Cluster analysis results showed that populations formed 2 clades within the dendrogram. Population Gaziantep-1 was unique and genetically most diverse from the remaining 16 populations. The results of average genetic distance (GD) among populations suggested that narrow genetic variability exist among 17 populations in the present study.     

Conserving the genetic resources of crop wild relatives in European Protected Areas

European native plant diversity is currently suffering erosion and extinction and thus, it is crucial to improve conservation strategies to maintain this essential resource. If unchecked, this genetic erosion and species extinction will cause unnecessary and irreversible harm to the economy and social well being of Europe. Much plant biodiversity is undoubtedly found in the existing 9654 European protected areas that cover 1,066,358 km², but clearly targeted and active conservation of priority plant species is required within these protected areas. To help ensure more efficient long-term sustainable conservation, a novel approach to the in situ conservation of European plants, notably crop wild relatives, is suggested. The purpose of this approach is to know what plant genetic resources (PGR) we have, where they are located and to assess whether the current network of protected areas includes a representative sample of European PGR diversity. The generation of in situ conservation and management plans for PGR populations in existing protected areas can significantly improve the present conservation status. Additionally, the identification of gaps of certain PGR in current protected areas can provide the basis for the designation of new complementary PGR in situ reserves.     

Accessing genetic resources: international law establishes multilateral system

The International Treaty on Plant Genetic Resources for Food and Agriculture is rapidly gathering sufficient ratifications to become international law. Once it enters into force, it will define the rules for access and benefit-sharing associated with most genetic resources of major food crops. This paper explains how the new Multilateral System established by the Treaty will work, and points out a number of ambiguities and problems in the text. Despite these shortcomings, the Treaty provides the international community of researchers, plant breeders, and farmers with an opportunity to foster cooperation and further the conservation and use of plant genetic resources.     

A wide range of genetic diversity in pear (<Emphasis Type="Italic">Pyrus ussuriensis</Emphasis> var. <Emphasis Type="Italic">aromatica</Emphasis>) genetic resources from Iwate,Japan revealed by SSR and chloroplast DNA markers

Iwateyamanashi (Pyrus ussuriensis var. aromatica) is one of the Pyrus species which grows wild in Japan. The number of Iwateyamanashi trees has been decreasing, so conservation and evaluation is urgently needed. Over 500 accessions of Pyrus species collected from Iwate in northern Tohoku region are maintained at Kobe University as an Iwateyamanashi germplasm collection. In order to investigate the genetic diversity, five SSR (simple sequence repeat) markers, developed from Japanese and European pear were examined for 86 Pyrus individuals including 58 accessions from Iwate. These SSR loci could discriminate between all the Iwate accessions except for 10 that bear seedless fruit, as well as determine the genetic diversity in Iwateyamanashi germplasms. High levels of variation were detected in 41 alleles and the mean observed heterozygosity across 5 loci was 0.50 for the Iwate accessions. Seedless accessions sharing identical SSR genotype with the local pear variety “Iwatetanenashi” were supposed to have been propagated vegetatively via grafting. In an UPGMA phenogram, Japanese pear varieties (P. pyrifolia) were clustered into two groups with some Iwate accessions including seedless ones. Another 38 Iwate accessions were not clustered clearly, and there was no clear relationship between these accessions and geographical distribution or morphological characters. Allele frequency revealed that the Iwate accessions were genetically more divergent than the Japanese pear varieties. Most Japanese pears possessed a 219 bp deletion at a spacer region between the accD and psaI genes in the chloroplast DNA (cpDNA), but other Pyrus species and two Iwateyamanashi trees did not. In the Iwate accessions, 79.3% had a deletion type cpDNA and others had a standard type cpDNA without deletion. These results are indicative of the wide range of genetic diversity in the Iwate accessions which include Japanese pear varieties. A combination of SSR and cpDNA analyses revealed high heterogeneity in Iwateyamanashi and coexistence of Iwateyamanashi and hybrid progeny with P. pyrifolia. These could be reasons for the wide range of continuous morphological variation described previously.     

Diversity and genetic resources of wild <Emphasis Type="Italic">Vigna</Emphasis> species in India

Diversity in morphological characters of 206 accessions of 14 wild Vigna species from India was assessed. Of these, 12 species belonged to Asian Vigna in the subgenus Ceratotropis and two were V. vexillata and V. pilosa belonging to subgenus Plectotropis and Dolichovigna, respectively. Data on 71 morphological traits, both qualitative and quantitative, were recorded. Data on 45 qualitative and quantitative traits exhibiting higher variation were subjected to multivariate analysis for establishing species relationships and assessing the pattern of intraspecific variation. Of the three easily distinguishable groups in the subgenus Ceratotropis, all the species in mungo-radiata group, except V. khandalensis, viz. V. radiata var. sublobata, V. radiata var. setulosa, V. mungo var. silvestris and V. hainiana showed greater homology in vegetative morphology and growth habit. The species, however, differed in other plant, flower, pod and seed characteristics. Within species variation was higher in V. mungo var. silvestris populations and three distinct clusters could be identified in multivariate analysis. V. umbellata showed more similarity to V. dalzelliana than V. bourneae and V. minima in the angularis-umbellata (azuki bean) group. Within species variations was higher in V. umbellata than other species in the group. In the aconitifolia-trilobata (mothbean), V. trilobata populations, were more diverse than V. aconitifolia. The cultigens of the conspecific wild species were more robust in growth, with large vegetative parts and often of erect growth with three- to five-fold increase in seed size and seed weight, except V. aconitifolia, which has still retained the wild type morphology to a greater extent. More intensive collection, characterisation and conservation of species diversity and intraspecific variations, particularly of the close wild relatives of Asian Vigna with valuable characters such as resistance to biotic/abiotic stresses, more number of pod bearing clusters per plant etc. assumes great priority in crop improvement programmes.     

Agronomic evaluations of grass and legume forage species collected in the Xinjiang Autonomous Region of the People's Republic of China and Mongolia

Because rangelands in the Xinjiang Autonomous Region of thePeople's Republic of China (PRC) and Mongolia are typicallyseverely overgrazed, bilateral (U.S./ PRC, U.S./Mongolia)efforts have been initiated to expedite capture of the remaining geneticdiversity. The current study was designed to evaluate selected germplasm of thefollowing forage species collected in these threatened areas: Bromusinermis Leyss., Dactylis glomerata L.,Festuca arundinacea Schreb., Festucaovina L., Festuca rubra L., Phleumphleoides (L.) Karsten, Phleumpratense L., Poa palustris L., Poapratensis ssp. angustifolia (L.) H.Lindb., Medicago sativa ssp. falcataArcengeli, Medicago sativa L. ssp. sativa, Medicago lupulina L.,Medicago ruthenica (L.) Ledebour,Trifolium fragiferum L., Trifoliumlupinaster L., Trifolium pratense L., andTrifolium repens L. Accessions were evaluated in the fieldat Beltsville MD (USA) on an Iuka sandy loam(coarse-loamy, siliceous, acid, thermic, Aquic Udigluvent; pH6.5) in a two-year study. Comparative check cultivars were included.There was significant variation in days to 50% heading (grassspecies) or flowering (legume species), leaf texture (grassspecies), growth habit, spring vigor, and dry matter yield among accessionsof at least some genera. Accessions did not demonstrate higher diseasesusceptibility relative to check cultivars, except in the case of severalF. arundinacea and oneM. sativa ssp.falcata entries. There was no significant variation in leafshape among the legume accessions, nor were leaf shapes significantly differentfrom those of the check cultivars. Several F.ovina, F. rubra,and Poa pratensis accessions may have potential in turfgrass breeding programs. There were apparent positive relationships amongupright growth habit, spring vigor, late development, and yield.     

Use of megagametophyte storage proteins as markers of the genetic diversity in stone pine (Pinus pinea L.) in Andalucia, Spain

Stone pine (Pinus pinea L.) is a Mediterranean species of interest for the traditional use of his edible kernel. Its area of distribution includes all the Mediterranean area, including the Iberian Peninsula where this tree presents the most extensive natural stands. Since land reforestation has become a high-priority of European policy, there is an increased interest in the characterisation of the germplasm of this species. In this study, the globulins from the megagametophyte were used for analysis of the variability and genetic diversity in 20 populations from Andalucia. Because of the complex profile, these proteins were analysed as blocks, corresponding each to a different range of molecular weight. Polymorphisms were observed in each of the five blocks. The diversity data showed that these populations present a high degree of variation, which suggest that this technic could be useful to analyse of the genetic diversity in this species.     

Genetic resources for improving nitrogen fixation in legume-rhizobia symbiosis

Leguminous crops are genetically polymorphous for the balance between symbiotrophic and combined types of nitrogen nutrition. In pea, polebean, alfalfa and fenugreek the wild-growing populations and local varieties exceed the agronomically advanced cultivars in the activity of N₂ fixation that occurs in symbiosis with nodule bacteria (rhizobia). Combined nitrogen nutrition ensures higher productivity than symbiotrophic one in the old leguminous crops (pea, alfalfa, common vetch, polebean, soybean), while the symbiotrophic type dominates in some young crops (hairy vetch, kura clover, goat's rue). An importance is emphasized of using the symbiotically active wild-growing genotypes as the initial material for breeding the legume cultivars. The data on high heritability (broad sense, narrow sense, realized) of the legume symbiotic activity demonstrate that the plant selection for this activity may be highly effective. A range of methods to select the legumes for an improved symbiotic activity is available including plant growth in N-depleted substrates, analysis of nodulation scores, direct (isotopic) and indirect (acetylene reduction) estimation of nitrogenase activity. Analysis of the specificity of interactions between different plant genotypes and bacterial strains (via two-factor analysis of variance) demonstrates the strain-specific plant polygenes are of a special importance in controlling the intensity of nitrogen fixation. Therefore, a coordinated plant-bacteria breeding is required to create the optimal combinations of partners' genotypes. Selection and genetic construction of the commercially attractive rhizobia strains should involve improvement of nitrogen fixing, nodulation and competitive abilities expressed in combination with the symbiotically active plant genotypes, Breeding of the leguminous crops for the preferential nodulation by highly active rhizobia strains, for the ability to support N₂ fixation under moderate N fertilization levels and to ensure a sufficient energy supply of symbiotrophic nitrogen nutrition is required     

Sampling variation in genetic resources of seed crops: a review

Summary The first explorations for the collection of genetic resources of crop plants took place in areas designated as centers of origin. Later, important characters were found to be present in areas other than those indicated by Vavilov. Hence collection missions were extended to cover other areas in addition to the centers of diversity with different ecogeography and agromorphological features. Collecting activities were aimed not only at providing germplasm for immediate use in breeding but also at conserving genetic variation for future contingencies. The analysis of the collected material has revealed the complex nature, amount and distribution of genetic variation present in natural populations as well as in landraces, old varieties and primitive forms. The study of variation for characters from different regions indicated that it is possible to select certain characters for detecting variability in the populations and establishing the minimum number of genotypes to be sampled. A minimum number of 20–130 plants per sample, depending on the crop, is recommended in order to capture 95% of the total variation in the field. However, it has been emphasized that the number of different populations sampled rather than the sample size per population determines the overall efficiency of a collection. The findings reported allow better utilization of the collected material and formulation of optimal and cost-effective sampling strategies for the future.