Rice genetic resources: history,conservation, investigative characterization and use in Japan

Rice has been grown in Japan for about 3000 years. Although both japonica and indica varieties have been grown in Japan, now japonica rices are grown. Japanese rice breeding has used an ecological breeding approach. While emphasis in rice breeding in the 1940's and 1950's focussed on yield in recent decades quality has been of major importance. Consumer preference and name recognition of high quality varieties, such as Koshihikari, has resulted in slow acceptance of new varieties.Rice germplasm was systematically collected throughout Japan between 1962 and 1963. Subsequent acquisition and collecting, in Japan and other countries, has resulted in 28,000 accessions being conserved in the National Genebank, based at the National institute of Agrobiological Resources (NIAR).Research on genetic diversity of rice using a range of techniques, for example esterase isozymes, has revealed clinal variation in rice radiating from the center of diversity of rice in and around southwest China. Newly found genes in traditional rice germplasm, such as genes for non-elongating mesocotyl, are now routinely identified on the rice genome. Pioneering studies on eco-genetic differentiation of species in the genus Oryza in Japan has revealed much about the complex genepool for which rice evolved.Pest and disease resistance sources, particularly to blast, bacterial blight and brown plant hopper, from many countries have been incorporated into Japanese varieties. Cold tolerance at the booting stage was found in the Indonesian variety Silewah. In the future in characterisation of rice germplasm and interaction between rice germplasm specialists and rice molecular scientists, both in Japan and internationally, will be corner stones to securing rice genetic diversity and rice improvement in the next century.     

我国作物种质资源保存研究与展望

我国于１９８４年１９８６年在北京建成两座国家种质库,９０年代初又在青海建立一座复份库,形成了国家库中,长期配套和异地结合的种质资源保存体系。截止１９９３年底,国家库保存种质资源达２７万余份,到１９９５年保存总数将达到３０余万份。与种子入库时,在国家库的管理,种子质量检测,种子干燥以及低温保存技术研究等方面取得一定进展,今后将继续扩大种质贮存、加强贮存种子生活力跟踪监测,无破坏性检测技术,贮存生理和     

Animal genetic resources and domestic animal diversity in Nepal

Domestic livestock in Nepal belong to 17 species, including five Bovidae (and interspecific hybrids of two of them), seven Aves, two Equidae (not including mules), pig (Sus scrofa), rabbit (Oryctolagus cuniculus) and elephant (Loxodonta africana). Cattle (Bos taurus and Bos indicus) are the most numerous quadruped, followed by goats (Capra hircus), buffalo (Bubalus bubalis) and sheep (Ovis aries). Domestic fowl (Gallus domesticus) are the most common poultry, followed by pigeons (Columba livia) and ducks (Anas platyrhyncos). Government policy is to upgrade and replace local types with improved stock. This policy has had limited success through lack of funding, inconsistent long-term objectives and an inability to pursue programmes in traditional farming systems. The purity of native types is being lost in some areas due to informal programmes by farmers themselves. Except for one type of goat there are no conservation programmes for native breeds. Wild relatives of livestock, including arnee (Bubalus arnee), gaur (Bibos gaurus), wild boar (Sus scrofa), jungle fowl (Gallus gallus) and rock dove (Columba livia), are being infiltrated by genes of domestic animals. Little has been done to characterize Nepal's livestock resources yet continuous attempts have been made to replace them. Conservation needs are to: (i) identify all genetic resources comprising the gene pool of species used as domestic livestock; (ii) develop and use the associated diversity to increase production, achieve sustainable systems and meet demands for particular products; (iii) monitor resources represented by small numbers or that are being displaced; and (iv) preserve resources not in current demand. A start has been made on this by Nepal's membership of a regional network.     

Strategies for genetic conservation of trees in the Peruvian Amazon

Forestry practices and high rates of land clearance for agriculture are causing genetic erosion of valuable tree species in the Peruvian Amazon, thereby endangering the economic sustainability of rural communities and limiting Peru's opportunities for the development of new timber and non-timber forest products. The potential utility and limitations of six low-input interventions to help forestall further genetic erosion in the region are discussed, with a focus on local community involvement. Improved agroforestry systems may help reduce deforestation by increasing farm productivity, although methods to increase the currently low adoption rate of these technologies need to be developed. Use of strategic tree domestication techniques can also improve farm productivity and prevent inadvertent genetic drift and inbreeding associated with traditional domestication practices, although to have a major impact, current programs need to be extended across the region. Woodlot forestry could supplant selective extraction of timber and offers an attractive opportunity for poverty alleviation if appropriate credit and land tenure policies can be developed. However, it may also result in increased deforestation if activities on public land cannot be controlled. The implementation of improved seed collection systems and simple seed transfer guidelines would help to reduce the collection of seed of poor quality and low genetic diversity, and avoid maladapted plantings, although such programs are difficult to monitor and seed costs may increase. Strategic identification and design of in situ conservation areas would help to ensure the viability of conserved populations, but requires the forfeiture of significant revenue from timber concessions.     

Importance of genetic characterization and conservation of plant genetic resources: The breeding system and genetic diversity of wild soybean (Glycine soja)

Abstract Plant genetic resources play an important role in the improvement of cultivated plants. To characterize and evaluate the ecological and reproductive features of wild soybean ( Glycine soja Sieb. et Zucc.), which is the most probable ancestor of cultivated soybean ( G. max (L) Merr.), the breeding system and genetic diversity of G. soja were investigated. The extent of natural cross-pollination of G. soja was estimated in four populations along the Omono River in Akita Prefecture, Japan by examining allozyme variation. Although it has been previously believed that G. soja is autogamous, as is cultivated soybean, the mean multilocus outcrossing rate ( t m) estimate was 13%. These values are much higher than the outcrossing rate previously reported for both G. soja and G. max . Frequent visits by honeybees and carpenter bees to flowers were also observed, which supported this conjecture. Furthermore, to evaluate the genetic variation of G. soja as a genetic resource, the genetic structure of 447 populations over Japan were analyzed. Wild soybean populations had a higher degree of variation of isozyme loci. The G ST coefficient of gene differentian values among the sites within the district were particularly high, revealing that the isozyme genotype was greatly different among site populations and homogeneous within the sites. The genetic differentiation among nine districts was observed in the allele frequencies of a few loci, indicating that geographic isolation in the wild soybean population was effectively created through the distance between the districts. The difference in the allele frequency among the districts may be produced under genetic drift. Finally, the importance of the preservation of natural plant populations and the habitats of wild progenitors (i.e. the in situ conservation of plant genetic resources) was emphasized.     

Impact evaluation to communicate and improve conservation non-governmental organization performance: the case of Conservation International

The rising prominence of more rigorous approaches to measuring conservation outcomes has included greater adoption of impact evaluation by conservation non-governmental organizations (CNGOs). Within the scientific literature, however, little consideration has been given to the unique and specific roles of CNGOs in advancing impact evaluation. We explore these issues in the context of one CNGO—Conservation International (CI)—and its experiences producing, using and funding impact evaluations over the past decade. We examine the contributions of impact evaluation to CI''s mission at three different stages of CI''s strategy: innovation, demonstration and amplification. Furthermore, we review incentives and barriers encountered by CI in its 10+ years'' experience in impact evaluation. More coordinated and strategic use of impact evaluation by CNGOs would facilitate learning and promote accountability across the conservation community.     

Ex-situ conservation of wheat genetic resources from Saudi Arabia

Wheat (Triticum L.) is one of the major food crops of the world, and an important component of food security. The aim of this study was to collect and preserve seeds of wheat growing in eight regions of the Kingdom of Saudi Arabia (Al-Qassim, Asir, Al-Taif, Najran, AL-Baha, Jazan, Al-Madinah and Wadi Al-Dawasir) where wheat has been cultivated since ancient times. Sixty-one accessions/samples of wheat (Triticum aestivum) were collected and placed in dry storage (ex-situ conservation) at −18 °C (i.e. permanent storage). The accessions of local wheat have the ability to grow under harsh environmental conditions such as (high temperature, drought and salinity). Most of these samples were collected directly from farms, but a few were collected from markets. The most important criteria for ex-situ conservation is that seeds need to have a low moisture content (MC) and a high percentage viability. Seed MC was measured for all 61 accessions by the oven-drying method and seed viability was tested in three ways: percentage of germination, tetrazolium chloride testing, and X-ray radiography.The seed MC of the 61 accessions was uniformly very low (0.10–0.12%), and 97 to 100% of the seeds were viable. Thus, all 61 wheat accessions collected in this study have the initial requirements to remain viable for long periods of time in ex-situ conservation in the gene seed bank.     

Conservation priorities of genetic diversity in domesticated metapopulations: a study in taurine cattle breeds

We estimated neutral diversity of 21 European cattle breeds with 105 microsatellites. Nine of them resembled unselected Balkan Buša strains with diffuse breeding barriers and the 12 others were strongly differentiated, isolated breeds. Because of the impact of neutral genetic diversity on long-term population adaptive capacity, we discuss the long-term outcome of different conservation priorities in a subdivided metapopulation of the investigated cattle breeds. The optimal contribution to a pool of total genetic diversity allocated more than 95% of long-term relevant neutral diversity to virtually unselected strains of the Balkan Buša, while the maximization of total variance preferred inbred breeds. Current artificial selection methods, such as genomic selection sped up and a recovery of underestimated traits becomes quickly impossible. We emphasize that currently neutral and even deleterious alleles might be required for future genotypes in sustainable and efficient livestock breeding and production systems of a 21st century. We provide cumulative evidences that long-term survival relies on genetic complexity and complexity relies on allelic diversity. Our results suggest that virtually unselected, nonuniform strains harbor a crucial proportion of neutral diversity and should be conserved with high global priority. As one example, we suggest a cooperative maintenance of the nondifferentiated, highly fragmented, and fast vanishing metapopulation of Balkan Buša.     

PlantGM: a database for genetic markers in rice (Oryza sativa) and Chinese cabbage (Brassica rapa)

The Plant Genetic Map Database (PlantGM) has been developed as a web-based system which provides information about genetic markers in rice (Oryza sativa) and Chinese cabbage (Brassica rapa). The database has three major parts and functions; (1) Map Search, (2) Marker Search, and (3) QTL Search. At present, the database provides characterization information for about 3258 genetic markers. It has 2800 RFLP and 112 QTL markers related to rice in addition to 321 RFLP and 25 PCR-based markers for Chinese cabbage. In addition, a genetic linkage map was also constructed by using 1,054 markers from 2,912 markers in rice.

Availability

The database is available for free at http://www.niab.go.kr/nabic/PlantGM     

Genetic diversity and conservation and utilization of plant genetic resources

Biodiversity refers to variation within the living world, while genetic diversity represents the heritable variation within and between populations of organisms, and in the context of this paper, among plant species. This pool of genetic variation within an inter-mating population is the basis for selection as well as for plant improvement. Thus, conservation of this plant genetic diversity is essential for present and future human well-being. During recent years, there has been increasing awareness of the importance of adopting a holistic view of biodiversity, including agricultural biodiversity, conservation for sustainable utilization and development. These principles have been enshrined in the Convention on Biological Diversity and the Global Plan of Action of the Food and Agriculture Organization of the United Nations. The emphasis is now to understand the distribution and extent of genetic diversity available to humans in plant species, so that the genetic diversity can be safely conserved and efficiently used. It is generally recognized that plant genetic diversity changes in time and space. The extent and distribution of genetic diversity in a plant species depends on its evolution and breeding system, ecological and geographical factors, past bottlenecks, and often by many human factors. Much of the large amount of diversity of a species may be found within individual populations, or partitioned among a number of different populations.A better understanding of genetic diversity and its distribution is essential for its conservation and use. It will help us in determining what to conserve as well as where to conserve, and will improve our understanding of the taxonomy and origin and evolution of plant species of interest. Knowledge of both these topics is essential for collecting and use of any plant species and its wild relatives. In order to mange conserved germplasm better, there is also a need to understand the genetic diversity that is present in collections. This will help us to rationalize collections and develop and adopt better protocols for regeneration of germplasm seed. Through improved characterization and development of core collections based on genetic diversity information, it will be possible to exploit the available resources in more valuable ways.     

The combined use of embryos and semen for cryogenic conservation of mammalian livestock genetic resources

The objective of this empirical simulation study was to evaluate the use of a combination of semen and embryos in the creation of gene banks for reconstruction of an extinct breed. Such an approach was compared for banks with varying proportions of embryos on the basis of the amount of the material to be stored, time for reconstruction, maintenance of genetic variability, and probability of failure during reconstruction. Four types of populations were simulated, based on reproductive rate: single offspring, twinning, enhanced reproduction, and litter bearing. Reconstruction was simulated for banks consisting of different combinations of semen and reduced numbers of embryos (expressed as a percentage of the material needed for a bank containing exclusively embryos and ranging from 10 to 90%). The use of a combination of semen and embryos increased the number of insemination cycles needed for reconstruction and the level of genetic relatedness in the reconstructed population. The risk for extinction was unacceptably high when a very low proportion of embryos (< 20%) was used. However, combining semen with embryos could decrease costs, allowing for the conservation of more breeds, and specific strategies for semen use could decrease the level of relationships in the reconstructed breed.     

Challenges in the conservation and sustainable use of genetic resources

The meeting on 'Genetic Resources in the Face of New Environmental, Economic and Social Challenges' held in Montpellier (France) from 20-22 September 2011 brought together about 200 participants active in research and management of the genetic diversity of plant, animal, fungal and microbial species. Attendees had the rare opportunity to hear about agronomy, botany, microbiology, mycology, the social sciences and zoology in the same conference. The research teams presented the results of about 50 projects funded by the French Foundation for Research on Biodiversity to preserve genetic diversity carried out in Africa, Asia, Europe and the Americas. These projects aimed to better understand and manage genetic resources in a rapidly changing world (e.g. structural changes in the agricultural industry, the need for climate change mitigation and adaptation, the challenge of achieving food security despite the growing world population and changing dietary habits, the opportunities provided by the many new molecular biology tools, the problems caused by widespread scientific budget cuts). The meeting also hosted some roundtables open to all participants which provided a forum to establish a much needed dialogue between policy-makers, managers and researchers.     

Characterisation of Chinese elite cultivars and genetic resources of chestnut by AFLP

We selected a informative set of twelve amplified fragment length polymorphism (AFLP) primer pairs suitable for evaluation of Chinese chestnut (Castanea mollissima Blume) genotypes. Cluster analysis based on 198 polymorphic AFLP amplified by these 12 primer pairs clearly divided investigated genotypes according to their place of origin. We showed, that genetic basis of modern genotypes is narrow also in the case of this species.     

Genetics of species re-introductions: Applications of genetic analysis

The value of obtaining genetic information as a prerequisite to management decisions regarding rare plant species is assessed using specific examples. The conclusions derived indicate that specific genetic information can help direct planning, strategy and development and the allocation of resources. However, such information can also be valueless in management terms because the information obtained, by its nature, cannnot always be interpreted unambigously, and thus is unable to provide the predictive certainty that is often required or expected by management personnel. It is important that such caveats be clear to management personnel before applying genetic studies for applied purposes.     

Conservation of rare species with island-like distributions: A case study of Lasthenia conjugens (Asteraceae) using population genetic structure and the distribution of rare markers

Californian vernal pools, a patchy, island-like habitat, are endangered as a result of habitat destruction. Conservation of the remaining vernal pool habitat is essential for the persistence of several endangered species. We present the first study examining DNA-level genetic diversity within and among populations of a vernal pool plant species. We investigated genetic variation across eight populations of the US federally endangered vernal pool endemic Lasthenia conjugens (Asteraceae) using intersimple sequence repeat (ISSR) markers. Genetic diversity within the species was high (Nei's gene diversity estimate was 0.37), with moderate differentiation among populations (Bayesian F _ST analog of 0.124). Using an amova analysis, we found that the majority of the genetic variation (84%) was distributed within populations. There is a significant relationship between geographical distance and pairwise genetic differentiation as measured by the Bayesian estimate θ^B. The alternative hypotheses of historic geological processes within the Central Valley and contemporary gene flow are discussed as explanations of the data. Because of the vulnerability of the populations, we calculated a probability of loss for rare alleles (fragments) in the populations. Calculations show that sampling only one of the eight populations for ex-situ conservation or restoration will capture approximately 54% of the sampled rare fragments. We believe that one of the sampled populations has become extinct since it was sampled. When removing this population from the above-mentioned calculations, sampling one population will capture only 41.3% of the sampled rare fragments. We recommend sampling strategies for future conservation and restoration efforts of L. conjugens.     

Conservation implications of genetic variation in three rare species endemic to Florida rosemary scrub

Habitat conversion and fire suppression during the last 50 yr have greatly reduced and altered Florida scrub vegetation, resulting in threats to the persistence of its unique flora. As part of a larger conservation project, we investigated patterns of isozyme variation in three rare perennial scrub plants with overlapping ranges endemic to Florida rosemary scrub on the Lake Wales Ridge. All three species have low levels of genetic variation, comparable to or lower than those generally reported for rare plants with restricted geographic ranges. Liatris ohlingerae has more than twice the expected heterozygosity of the other two species, with little population differentiation. In contrast, Hypericum cumulicola has highly differentiated populations with little apparent interpopulation gene flow and heterozygote deficiencies indicative of inbreeding. Eryngium cuneifolium, the species with the narrowest range and fewest populations, has intermediate values for genetic parameters. Although the three species have narrow and overlapping geographic ranges and similar habitat specificity, we discuss how optimal conservation of each species differs.     

The genetic rescue of the Florida panther

We examine the consequences of panthers introduced from Texas into south Florida, an area housing a small, isolated, inbred and distinct subspecies ( Puma concolor coryi ). Once part of a continuous, widespread population, panthers became isolated in south Florida more than a century ago. Numbers declined and the occurrence of genetic defects increased. Hoping to reverse the genetic damage, managers introduced eight female panthers from Texas into south Florida in the mid-1990s. This action was highly controversial and we explain the arguments for and against the intervention. We synthesized data systematically collected on the Florida panthers from before, during and after this management intervention. These data include information on movements, breeding, mortality, survivorship and range. There is no evidence that purebred Florida females produce fewer kittens at a later age or less often than do hybrid cats (i.e. those with a Texas ancestor). Hybrid kittens have about a three times higher chance of becoming adults as do purebred ones. Hybrid adult females survive better than purebred females; there is no obvious difference between the males. Males die younger than females, are more often killed by other males and are more likely to disperse longer distances into habitats that are dangerous to them. Hybrids are expanding the known range of habitats panthers occupy and use.     

Seeing the Forest for the Trees: Integrated Conservation and Development Projects and Local Perceptions of Conservation in Madagascar

This paper explores local perceptions of internationally financed conservation and development projects in Madagascar and the success of these projects at influencing perceptions. Interviews, surveys, and focus group sessions were conducted in the peripheral zones of three Malagasy national parks: Ranomafana, Andohahela, and Masoala. Relevant questions explored community demographics, socioeconomic status, and local perceptions of the parks. The principal finding is that while a majority of people living in the peripheral zones do find conservation a valuable goal, they see it as a luxury they cannot afford. Despite their efforts and innovation, conservation and development projects have had a minimal impact on socioeconomic or associational life in the Ranomafana and Andohahela peripheral zones, and a significant but modest impact in the Masoala peripheral zone, by providing economic alternatives to destructive resource use. As a result, they are limited in their success at promoting conservation outcomes.