How Can We Strengthen the Global Genetic Resources' Conservation and Use System?

Genetic resources serve as the foundation of our food supply and are building blocks for the development of new crop varieties that support sustainable crop production in the face of climate change, as well as for the delivery of healthy diets to a continuously growing global population. With the encouragement of the FAO and with technical guidance and assistance from the International Board for Plant Genetic Resources (IBPGR), almost 2000 genebanks have been established worldwide for the ex situ conservation of genetic resources since the middle of the last century. The global genetic resources' conservation and use system has evolved over several decades and presents apparent weaknesses, without a clear blueprint. Therefore, a Special Issue (SI) of Plants on 'A Critical Review of the Current Approaches and Procedures of Plant Genetic Resources Conservation and Facilitating Use: Theory and Practice' was initiated. This SI comprises 13 review and research papers that shed light on the history and the political dimensions of the global system; its current strengths, weaknesses, and limitations; and how the effectiveness and efficiency of the system could be improved to satisfy the germplasm users (plant breeders, researchers) and benefit consumers and society at large. This SI provides insight into new approaches and technical developments that have revolutionised ex situ conservation and the use of germplasm and related information. It also reflects on complementary conservation approaches (in situ, on-farm, home gardens) to ex situ genebanks, as well as how-through new forms of collaboration at national, regional, and global levels and through stronger links between public genebanks-synergies between the private breeding sector and botanic garden community could be achieved to strengthen the global conservation and use system. Special attention has also been given to the governance of genetic resources and access and benefit-sharing issues that increasingly hamper the needed access to a wide range of genetic resources that is essential for plant breeders to fulfil their mission.

Collaboration between Private and Public Genebanks in Conserving and Using Plant Genetic Resources

Among the most important users of plant genetic resources, conserved predominantly in public genebanks around the world, are public and private plant breeders. Through their breeding efforts, they contribute significantly to global, regional, and local food and nutrition security. Plant breeders need genetic diversity to be able to develop competitive new varieties that are adapted to the changing environmental conditions and suit the needs of consumers. To ensure continued and timely access to the genetic resources that contain the required characteristics and traits, plant breeders established working collections with breeding materials and germplasm for the crops they were breeding. However, with the changing and increasingly more restrictive access conditions, triggered by new global legal instruments like the Convention on Biological Diversity/Nagoya Protocol and the International Treaty, plant breeders started to establish their own genebanks at the turn of the 21st century. This paper analyses the conditions that contributed to this situation as well as the historical ways that plant breeders used to acquire the germplasm they needed. Public genebanks played and continue to play a conducive role in providing genetic resources to users, including private-sector plant breeders. However, also the practices of the germplasm curators to collect and distribute germplasm were affected by the new legal framework that had been developed in global fora. It is against this background that the complementarity and collaboration between public and private sector genebanks have been assessed. Whenever possible, vegetable genetic resources and vegetable private breeding companies have been used to analyze and illustrate such collaboration. The authors look at reported successful examples of collaborative efforts and consider opportunities and approaches under which such collaboration can be established and strengthened to ensure the continued availability of the building blocks for food and nutrition security.

Critical Review of the Increasing Complexity of Access and Benefit-Sharing Policies of Genetic Resources for Genebank Curators and Plant Breeders-A Public and Private Sector Perspective

Plant breeders develop competitive, high-yielding, resistant crop varieties that can cope with the challenges of biotic stresses and tolerate abiotic stresses, resulting in nutritious food for consumers worldwide. To achieve this, plant breeders need continuous and easy access to plant genetic resources (PGR) for trait screening, to generate new diversity that can be built into newly improved varieties. International agreements such as the Convention on Biological Diversity (CBD), the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) and the Nagoya Protocol recognised the sovereign rights of countries over their genetic resources. Under the CBD/Nagoya Protocol, countries are free to establish specific national legislations regulating germplasm access and benefit-sharing to be negotiated bilaterally. Consequently, access to PGR became increasingly restricted and cumbersome, resulting in a decrease in germplasm exchange. The ITPGRFA attempted to ease this situation by establishing a globally harmonised multilateral system (MLS). Unfortunately, the MLS is (still) restricted to a limited number of food and forage crops, with very few vegetable crops. Easy and continuous access to genetic diversity combined with equitable and fair sharing of derived benefits is a prerequisite to breeding new varieties. Facilitated access contributes to sustainable crop production and food and nutrition security; therefore, access to and, consequently, use of PGRFA needs to be improved. Thus, the authors recommend, among others, expanding the scope of the ITPGRFA to include all PGRFA and making them and all related information accessible under a Standard Material Transfer Agreement (SMTA) combined, if necessary, with a subscription system or a seed sales tax. Such a transparent, functional and efficient system would erase legal uncertainties and minimise transaction costs for conservers, curators and users of genetic resources, thus aiding plant breeders to fulfil their mission.

Genebanks at Risk: Hazard Assessment and Risk Management of National and International Genebanks

Genebanks are crucial for safeguarding global crop diversity but are themselves exposed to several risks. However, a scientific basis for identifying, assessing, and managing risks is still lacking. Addressing these research gaps, this study provides risk analysis for three key risk groups: natural hazards, political risks, and financial risks, carried out on a sample of 80 important national and international genebanks, comprising at least 4.78 million accessions or roughly 65% of the reported total of ex situ conserved accessions worldwide. The assessment tool of Munich Re "Natural Hazards Edition" allowed a location-specific comparison of the natural hazard exposure. Results showed that genebanks in the Asia-Pacific region are most exposed to natural hazards, while institutions in African and some Asian countries are rather vulnerable to political risks. Financing is a major problem for national genebanks in developing countries, whereas the Global Crop Diversity Trust achieved considerable financial security for international genebanks. Large differences in the risk exposure of genebanks exist, making a location- and institution-specific risk assessment indispensable. Moreover, there is significant room for improvement with respect to quality and risk management at genebanks. Transferring risks of genebanks to third parties is underdeveloped and should be used more widely.

Crop genetic erosion: understanding and responding to loss of crop diversity

Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.

A Critical Review of the Current Global Ex Situ Conservation System for Plant Agrobiodiversity. II. Strengths and Weaknesses of the Current System and Recommendations for Its Improvement

In this paper, we review gene bank operations that have an influence on the global conservation system, with the intention to identify critical aspects that should be improved for optimum performance. We describe the role of active and base collections and the importance of linking germplasm conservation and use, also in view of new developments in genomics and phenomics that facilitate more effective and efficient conservation and use of plant agrobiodiversity. Strengths, limitations, and opportunities of the existing global ex situ conservation system are discussed, and measures are proposed to achieve a rational, more effective, and efficient global system for germplasm conservation and sustainable use. The proposed measures include filling genetic and geographic gaps in current ex situ collections; determining unique accessions at the global level for long-term conservation in virtual base collections; intensifying existing international collaborations among gene banks and forging collaborations with the botanic gardens community; increasing investment in conservation research and user-oriented supportive research; improved accession-level description of the genetic diversity of crop collections; improvements of the legal and policy framework; and oversight of the proposed network of global base collections.

A Critical Review of the Current Global Ex Situ Conservation System for Plant Agrobiodiversity. I. History of the Development of the Global System in the Context of the Political/Legal Framework and Its Major Conservation Components

The history of ex situ conservation is relatively short, not more than a century old. During the middle of last century, triggered by the realization that genetic erosion was threatening the existing landraces and wild relatives of the major food crops, global efforts to collect and conserve the genetic diversity of these threatened resources were initiated, predominantly orchestrated by FAO. National and international genebanks were established to store and maintain germplasm materials, conservation methodologies were created, standards developed, and coordinating efforts were put in place to ensure effective and efficient approaches and collaboration. In the spontaneously developing global conservation system, plant breeders played an important role, aiming at the availability of genetic diversity in their breeding work. Furthermore, long-term conservation and the safety of the collected materials were the other two overriding criteria that led to the emerging international network of ex situ base collections. The political framework for the conservation of plant genetic resources finds its roots in the International Undertaking of the FAO and became 'turbulent rapid' with the conclusion of the Convention on Biological Diversity. This paper reviews the history of the global ex situ conservation system with a focus on the international network of base collections. It assesses the major ex situ conservation approaches and methods with their strengths and weaknesses with respect to the global conservation system and highlights the importance of combining in situ and ex situ conservation.

Plant Biodiversity and Genetic Resources Matter!

Plant biodiversity is the foundation of our present-day food supply (including functional food and medicine) and offers humankind multiple other benefits in terms of ecosystem functions and resilience to climate change, as well as other perturbations. This Special Issue on 'Plant Biodiversity and Genetic Resources' comprises 32 papers covering a wide array of aspects from the definition and identification of hotspots of wild and domesticated plant biodiversity to the specifics of conservation of genetic resources of crop genepools, including breeding and research materials, landraces and crop wild relatives which collectively are the pillars of modern plant breeding, as well as of localized breeding efforts by farmers and farming communities. The integration of genomics and phenomics into germplasm and genebank management enhances the value of crop germplasm conserved ex situ, and is likely to increase its utilization in plant breeding, but presents major challenges for data management and the sharing of this information with potential users. Furthermore, also a better integration of in situ and ex situ conservation efforts will contribute to a more effective conservation and certainly to a more sustainable and efficient utilization. Other aspects such as policy, access and benefit-sharing that directly impact the use of plant biodiversity and genetic resources, as well as balanced nutrition and enhanced resilience of production systems that depend on their increased use, are also being treated. The editorial concludes with six key messages on plant biodiversity, genetic erosion, genetic resources and plant breeding, agricultural diversification, conservation of agrobiodiversity, and the evolving role and importance of genebanks.

Main Challenges and Actions Needed to Improve Conservation and Sustainable Use of Our Crop Wild Relatives

Crop wild relatives (CWR, plural CWRs) are those wild species that are regarded as the ancestors of our cultivated crops. It was only at the end of the last century that they were accorded a high priority for their conservation and, thus, for many genebanks, they are a new and somewhat unknown set of plant genetic resources for food and agriculture. After defining and characterizing CWR and their general threat status, providing an assessment of biological peculiarities of CWR with respect to conservation management, illustrating the need for prioritization and addressing the importance of data and information, we made a detailed assessment of specific aspects of CWRs of direct relevance for their conservation and use. This assessment was complemented by an overview of the current status of CWRs conservation and use, including facts and figures on the in situ conservation, on the ex situ conservation in genebanks and botanic gardens, as well as of the advantages of a combination of in situ and ex situ conservation, the so-called complementary conservation approach. In addition, a brief assessment of the situation with respect to the use of CWRs was made. From these assessments we derived the needs for action in order to achieve a more effective and efficient conservation and use, specifically with respect to the documentation of CWRs, their in situ and ex situ, as well as their complementarity conservation, and how synergies between these components can be obtained. The review was concluded with suggestions on how use can be strengthened, as well as the conservation system at large at the local, national, and regional/international level. Finally, based on the foregoing assessments, a number of recommendations were elaborated on how CWRs can be better conserved and used in order to exploit their potential benefits more effectively.

Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum.

Origins of food crops connect countries worldwide

Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.

Patterns of domestication in the Ethiopian oil-seed crop noug (Guizotia abyssinica)

Noug (Guizotia abyssinica) is a semidomesticated oil-seed crop, which is primarily cultivated in Ethiopia. Unlike its closest crop relative, sunflower, noug has small seeds, small flowering heads, many branches, many flowering heads, and indeterminate flowering, and it shatters in the field. Here, we conducted common garden studies and microsatellite analyses of genetic variation to test whether high levels of crop-wild gene flow and/or unfavorable phenotypic correlations have hindered noug domestication. With the exception of one population, analyses of microsatellite variation failed to detect substantial recent admixture between noug and its wild progenitor. Likewise, only very weak correlations were found between seed mass and the number or size of flowering heads. Thus, noug's 'atypical' domestication syndrome does not seem to be a consequence of recent introgression or unfavorable phenotypic correlations. Nonetheless, our data do reveal evidence of local adaptation of noug cultivars to different precipitation regimes, as well as high levels of phenotypic plasticity, which may permit reasonable yields under diverse environmental conditions. Why noug has not been fully domesticated remains a mystery, but perhaps early farmers selected for resilience to episodic drought or untended environments rather than larger seeds. Domestication may also have been slowed by noug's outcrossing mating system.

Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome

We present an EST library, chloroplast genome sequence, and nuclear microsatellite markers that were developed for the semi-domesticated oilseed crop noug (Guizotia abyssinica) from Ethiopia. The EST library consists of 25 711 Sanger reads, assembled into 17 538 contigs and singletons, of which 4781 were functionally annotated using the Arabidopsis Information Resource (TAIR). The age distribution of duplicated genes in the EST library shows evidence of two paleopolyploidizations-a pattern that noug shares with several other species in the Heliantheae tribe (Compositae family). From the EST library, we selected 43 microsatellites and then designed and tested primers for their amplification. The number of microsatellite alleles varied between 2 and 10 (average 4.67), and the average observed and expected heterozygosities were 0.49 and 0.54, respectively. The chloroplast genome was sequenced de novo using Illumina's sequencing technology and completed with traditional Sanger sequencing. No large re-arrangements were found between the noug and sunflower chloroplast genomes, but 1.4% of sites have indels and 1.8% show sequence divergence between the two species. We identified 34 tRNAs, 4 rRNA sequences, and 80 coding sequences, including one region (trnH-psbA) with 15% sequence divergence between noug and sunflower that may be particularly useful for phylogeographic studies in noug and its wild relatives.

Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

PREMISE OF STUDY

To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA-barcoding using next-generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions of the traditional DNA-barcoding loci in the plastid and ribosomal DNA, we call our approach ultra-barcoding (UBC).

METHODS

We used high-throughput next-generation sequencing to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an individual of the related species T. grandiflorum, as well as an additional publicly available whole plastid genome of T. cacao.

KEY RESULTS

All individuals of T. cacao examined were uniquely distinguished, and evidence of reticulation and gene flow was observed. Sequence variation was observed in some of the canonical barcoding regions between species, but other regions of the chloroplast were more variable both within species and between species, as were ribosomal spacers. Furthermore, no single region provides the level of data available using the complete plastid genome and rDNA.

CONCLUSIONS

Our data demonstrate that UBC is a viable, increasingly cost-effective approach for reliably distinguishing varieties and even individual genotypes of T. cacao. This approach shows great promise for applications where very closely related or interbreeding taxa must be distinguished.