Genebank Holdings Research Articles

Conservation Gaps in Traditional Vegetables Native to Europe and Fennoscandia

Vegetables are rich in vitamins and other micronutrients and are important crops for healthy diets and diversification of the food system, and many traditional (also termed underutilized or indigenous) species may play a role. The current study analyzed 35 vegetables with a European region of diversity with the effort to map the conservation status in Fennoscandia and beyond. We mapped georeferenced occurrences and current genebank holdings based on global databases and conducted conservation gaps analysis based on representativeness scores in situ and ex situ. Out of the 35 target species, 19 got at a high priority score for further conservation initiatives, while another 14 species got a medium priority score. We identified a pattern where traditional vegetables are poorly represented in genebank holdings. This corresponds well to a lack of attention in the scientific community measured in number of published papers. Considering the grand challenges ahead in terms of climate change, population growth and demand for sustainability, traditional vegetables deserve greater attention. Our contribution is to provide a basis for conservation priorities among the identified vegetables species native to Fennoscandia.

Research Gaps and Challenges in the Conservation and Use of North American Wild Lettuce Germplasm

ABSTRACTThe North American crop wild relatives (CWR) of lettuce (Lactuca L.) represent an underexplored pool of genetic diversity of potential value to breeding programs. The 10 species belong to three different groups: a native clade including at least six allotetraploid species [L. biennis (Moench) Fernald, L. canadensis L., L. floridana (L.) Gaertn., L. graminifolia Michx., L. hirsuta Muhl. ex Nutt., and L. ludoviciana (Nutt.) Riddell], a diploid clade with one species [L. tatarica (L.) C. A. Mey. subsp. pulchella (Pursh) Stebbins], and a clade related to the cultivated taxon (L. sativa L.) with three non‐native species (L. saligna L., L. serriola L., and L. virosa L.). In this review, we examine the role of herbarium and genebank holdings in taxonomic and other foundational studies, as well as for germplasm exploration and use. We compile the state of knowledge on the ranges of lettuce CWR in North America, modeling the potential distributions of the species and assessing their ex situ and (for native species) in situ conservation status. We categorize seven of the species as high priority for further conservation and three as medium priority, with none currently considered low priority or sufficiently conserved. Further, we review morphological, phenological, genetic diversity, and pest and disease information with regard to North American species. We conclude by outlining the critical gaps and describing a way forward for addressing challenges in the conservation and use of North American wild lettuce germplasm.

Assessing Sus scrofa diversity among continental United States, and Pacific islands populations using molecular markers from a gene banks collection

Human migration and trade facilitated domesticated livestock movement, gene flow and development of diverse populations upon which agriculture is based. In addition, varying USA ecological conditions has led to a diverse set of livestock populations to utilize. Quantifying genetic diversity of these populations is incomplete. This paper quantifies genetic diversity captured by the National Animal Germplasm Program and explores genetic structure and differences among 19 pig populations (feral populations from Pacific islands, continental US, and Chinese breeds) using 70,231 SNP from 500 animal samples. Among continental US breeds Fis was consistently low suggesting genetic variability is sufficiently available for breeders to use. A unique population structure using principal component analysis illustrated clear distinctions between Duroc, Yorkshire, Hampshire, breeds of Chinese origin, and feral Pacific Island populations were identified. Five Y chromosome haplotypes were evaluated and demonstrated migration patterns from European, central Asia, and potentially Polynesian waves of gene flow. Quantifying diversity and potential origin of Pacific populations provides insight for future uses, and the need for preservation. Viewing gene bank holdings in context of diversity measures we found a lack of inbreeding within breeds, suggesting the collection represents a wide sampling of individual breeds.

Patterns in the conservation and use of traditional vegetables from the New Guinean biodiversity hotspot

ABSTRACTIn this paper, we survey traditional leafy vegetables linked to the New Guinea biodiversity hotspot. More than 30 species were identified, and data on occurrences and global genebank holdings were retrieved. The result revealed that traditional vegetables from this hotspot are highly under-represented in the global conservation system for plant genetic resources. Among targeted perennial tree or shrub species, no single accessions were reported as conserved in genebanks. We argue for the importance of safeguarding crop diversity for future generations and for promoting the traditional knowledge linked to cultivation and use of such nutritional plants.

World Vegetable Center Eggplant Collection: Origin, Composition, Seed Dissemination and Utilization in Breeding.

Eggplant is the fifth most economically important solanaceous crop after potato, tomato, pepper, and tobacco. Apart from the well-known brinjal eggplant (Solanum melongena L.), two other under-utilized eggplant species, the scarlet eggplant (S. aethiopicum L.) and the gboma eggplant (S. macrocarpon L.) are also cultivated. The taxonomy and identification of eggplant wild relatives is challenging for breeders due to the large number of related species, but recent phenotypic and genetic data and classification in primary, secondary, and tertiary genepools, as well as information on the domestication process and wild progenitors, facilitates their utilization in breeding. The World Vegetable Center (WorldVeg) holds a large public germplasm collection of eggplant, which includes the three cultivated species and more than 30 eggplant wild relatives, with more than 3,200 accessions collected from 90 countries. Over the last 15 years, more than 10,000 seed samples from the Center's eggplant collection have been shared with public and private sector entities, including other genebanks. An analysis of the global occurrences and genebank holdings of cultivated eggplants and their wild relatives reveals that the WorldVeg genebank holds the world's largest public collection of the three cultivated eggplant species. The composition, seed dissemination and utilization of germplasm from the Center's collection are highlighted. In recent years more than 1,300 accessions of eggplant have been characterized for yield and fruit quality parameters. Further screening for biotic and abiotic stresses in eggplant wild relatives is a priority, as is the need to amass more comprehensive knowledge regarding wild relatives' potential for use in breeding. However, as is the case for many other crops, wild relatives are highly under-represented in the global conservation system of eggplant genetic resources.

Digitization of collecting mission data to enhance plant genetic resource management in maize (Zea mays) in India

The data gathered on germplasm collection of maize evidently showed is a preliminary attempt on digitization of collecting mission data of maize genetic resources to enhance its use in plant genetic resource management in maize in India through quality passport data, eco-geographic location, availability of germplasm site description, geographic coordinates for crop improvement programme. Identification of collection sites located in distribution maps would allow: pinpointing of directed collection plans in under represented and identified sites that are rich in landraces/ trait-specific diversity. Since these sites are highly vulnerable to genetic erosion due to spread of hybrids/ genetically modified crops (GM), such areas need to be given special attention in genetic resource management. Broadly all maize growing areas have been surveyed in the past and diversity augmented from different parts of the country. However, based on gaps identified in the genebank holdings of trait specific germplasm and unique material needs to be augmented. Grouping of local cultivars/ landraces of maize based on geographical distribution, morphology, field and molecular characterization is a major challenge that needs special address by the maize breeders and users.

A Case for Crop Wild Relative Preservation and Use in Potato

ABSTRACTCrop wild relatives (CWR) offer a critical resource to address food security needs by providing genetic diversity for crop improvement, leading to increased plasticity and productivity of farming systems. However, plant breeders typically have not developed systematic or comprehensive strategies for the characterization and use of CWR for cultivar improvement. Potato (Solanum tuberosum L.) provides an excellent case study for the use of CWR germplasm in addressing global food security needs. International cooperation and collaboration are critical to collect, characterize, and use CWR in anticipation of future production needs. Both ex situ and in situ preservation of wild potato species are essential to assure a comprehensive conservation plan. Top priorities include a coordinated inventory of gene bank holdings followed by re‐collection of CWR and new collection where gaps exist. Access to CWR genetic diversity will continue to be critical as breeders face the challenge of developing cultivars that fit into new production systems, especially in response to climate change. With the advent of the genomics era, new visions of germplasm use strategies are emerging. In addition to filling gaps in collections, it will be important to expand efforts to characterize and use potato CWR. A systematic and integrated strategy is needed to evaluate CWR in gene banks for traits to continue breeding progress.

ОПЫТ СОХРАНЕНИЯ РАСТИТЕЛЬНЫХ ГЕНЕТИЧЕСКИХ РЕСУРСОВ В ГЕРМАНИИ: РОЛЬ НИКОЛАЯ ИВАНОВИЧА ВАВИЛОВА

This article is dedicated to the 125 th birthday of N.I. Vavilov, with a special emphasis on his interaction during the early years of the 20 th century with German scientists concerned with the conservation of cultivated plants and their wild relatives. The German genebank was established with the foundation of the Institute of Crop Plant Research (at present time the Leibniz Institute of Plant Genetics and Crop Plant Research — IPК) in April 1943, and today, this genebank maintains about 150,000 accessions. Here, we present a review of its characterization and evaluation activity, as well as a description of some research highlights based on the genebank's holdings. The research element focuses particularly on the genetic integrity of genebank accessions subjected to long term storage, the genetic diversity retained in situ over time, and the genetics of seed longevity.

Genetic Selection and Conservation of Genetic Diversity*

For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development.

Genomics of gene banks: A case study in rice

Only a small fraction of the naturally occurring genetic diversity available in the world's germplasm repositories has been explored to date, but this is expected to change with the advent of affordable, high-throughput genotyping and sequencing technology. It is now possible to examine genome-wide patterns of natural variation and link sequence polymorphisms with downstream phenotypic consequences. In this paper, we discuss how dramatic changes in the cost and efficiency of sequencing and genotyping are revolutionizing the way gene bank scientists approach the responsibilities of their job. Sequencing technology provides a set of tools that can be used to enhance the quality, efficiency, and cost-effectiveness of gene bank operations, the depth of scientific knowledge of gene bank holdings, and the level of public interest in natural variation. As a result, gene banks have the chance to take on new life. Previously seen as "warehouses" where seeds were diligently maintained, but evolutionarily frozen in time, gene banks could transform into vibrant research centers that actively investigate the genetic potential of their holdings. In this paper, we will discuss how genotyping and sequencing can be integrated into the activities of a modern gene bank to revolutionize the way scientists document the genetic identity of their accessions; track seed lots, varieties, and alleles; identify duplicates; and rationalize active collections, and how the availability of genomics data are likely to motivate innovative collaborations with the larger research and breeding communities to engage in systematic and rigorous phenotyping and multilocation evaluation of the genetic resources in gene banks around the world. The objective is to understand and eventually predict how variation at the DNA level helps determine the phenotypic potential of an individual or population. Leadership and vision are needed to coordinate the characterization of collections and to integrate genotypic and phenotypic information in ways that will illuminate the value of these resources. Genotyping of collections represents a powerful starting point that will enable gene banks to become more effective as stewards of crop biodiversity.

The economic costs of conserving genetic resources at the CGIAR centers⋆

AbstractThe 11 genebanks of the Consultative Group on International Agriculture (CGIAR) have grown considerably in size over the past few decades, currently holding about 666,000 accessions of germplasm. Conserving germplasm is a very long run, if not in perpetuity, proposition. The mismatch between the mainly annual funding support for this conservation effort and its very long‐term nature and intent is a serious concern. Using the results of five CGIAR genebank case studies (accounting for 87% of the total CGIAR genebank holdings), we estimate the size of an endowment or trust fund that would be required to assure a funding stream to conserve this genetic material for future generations. The annual cost (in year 2000 US$) of conserving and distributing the genetic material presently held in all 11 CGIAR genebanks is estimated to be 5.7 million US$ (mUS$), which could be maintained for all future generations by setting aside a fund of 149 mUS$ (invested at a real rate of interest of 4% per annum). This would be sufficient to underwrite the costs for the CGIAR's current conservation activities in perpetuity (estimated to be 61 mUS$), as well as the cost of maintaining the distribution activities (88 mUS$) that provide germplasm to breeders, scientists, farmers and others world wide.

The economic costs of conserving genetic resources at the CGIAR centres

The 11 genebanks of the Consultative Group on International Agriculture (CGIAR) have grown considerably in size over the past few decades, currently holding about 666,000 accessions of germplasm. Conserving germplasm is a very long run, if not in perpetuity, proposition. The mismatch between the mainly annual funding support for this conservation effort and its very long-term nature and intent is a serious concern. Using the results of five CGIAR genebank case studies (accounting for 87% of the total CGIAR genebank holdings), we estimate the size of an endowment or trust fund that would be required to assure a funding stream to conserve this genetic material for future generations. The annual cost (in year 2000 US$) of conserving and distributing the genetic material presently held in all 11 CGIAR genebanks is estimated to be 5.7 million US$ (mUS$), which could be maintained for all future generations by setting aside a fund of 149 mUS$ (invested at a real rate of interest of 4% per annum). This would be sufficient to underwrite the costs for the CGIAR’s current conservation activities in perpetuity (estimated to be 61 mUS$), as well as the cost of maintaining the distribution activities (88 mUS$) that provide germplasm to breeders, scientists, farmers and others world wide.

Molecular characterization can quantify and partition variation among genebank holdings: a case study with phenotypically similar accessions of Brassica oleracea var. capitata L. (cabbage) `Golden Acre'

To better characterize and conserve crop genetic resources, the assessment of genetic identity, relatedness, and structure among entries and collections becomes a priority. In the present study, a random amplified polymorphic DNA (RAPD) assay was applied as a quick, cost-effective, and preliminary screen to quantify and partition the molecular variation among accessions. Fourteen phenotypically uniform accessions of Brassica oleracea var. capitata L. (cabbage) similarly designated as `Golden Acre' were tested with nine decamer oligonucleotide primers. These amplifications generated 110 fragments, of which 80 were polymorphic ranging in size from 370 to 1720 bp. The 80 polymorphic fragments were sufficient to distinguish between all 14 accessions. Data based on the partitioning of variation among accessions indicated that `Golden Acre' entries could be reduced to as few as four groups, with the potential loss of variation being only 4.6% of the absolute current genetic variation in those holdings as estimated from RAPD analysis. This proposed grouping would concurrently save approximately 70% [$750–1000 (US) per accession] for each cycle of regeneration (approximately 20–25 years at most) which alternatively could then be used for other priorities in B. oleracea conservation and use. This case represents but one example where targeted use of a molecular-marker assay linked with rigorous statistical analysis will be useful for plant genebank management, particularly for questions at the intraspecific level. Molecular markers will provide genebank curators with additional sources of information to better plan and organize collection holdings and use finite financial support in a more effective manner.

Genetic resources of temperate native and low‐input grasses in New Zealand and Australian collections

Abstract Genebank holdings of seed of the temperate native grasses of New Zealand and Australia are very small. For example, seed of only 10 of the 160 grass species native to New Zealand is held in the Margot Forde Forage Germplasm Centre. The Australian situation is only slightly better. Introductions of temperate grasses other than Lolium perenne, Dactylis glomerata, Festuca arundinacea, and Phalaris aquatica into Australia and New Zealand have included over 400 species but, on average, fewer than 10 samples per species. Very few introduced grass species have therefore been adequately sampled for the full range of genetic diversity within the species. This paper lists the accessions of grasses into genebanks in Australia and New Zealand and discusses the strengths and limitations of the collections.