Crop Science 41:6-10 (2001)
© 2001 Crop Science Society of America
REVIEW & INTERPRETATION
The Extent of Use of Plant Genetic Resources in Research—A Literature Survey
N.S. Dudnik,
I. Thormann and
T. Hodgkin
International Plant Genetic Resources Institute, 142 Via delle Sette Chiese, 00145 Rome, Italy
Corresponding author (t.hodgkin{at}cgiar.org)
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ABSTRACT
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Our aim was to assess the level of use of conserved plant genetic resources (PGR) in crop genetic research. To do this, we analyzed in detail the reports from four internationally recognized journals published in 1996. These journals were Crop Science, Euphytica, Plant Breeding, and Theoretical and Applied Genetics. Our results indicate that about 23% of the articles published in these journals reported work conducted with material that originated in an ex situ PGR collection or was collected directly in the field. We also analyzed our results to determine the range of species and research topics involved, the sources of materials used, and the users of PGR for research. Of the material used, 80% was accessed from ex situ germplasm collections housed in genebanks in 27 countries and seven centers of the CGIAR. The rest of the studies utilized material gathered directly in the field. Almost all work was produced at national research centers and universities; very little work from private industry was published in the journals covered. Just under 20% of the institutions represented by authors were located in developing countries. Work published involved 112 species and included assessments of genetic diversity among accessions (42% of the studies), studies of the inheritance of biotic stress resistance (29%), taxonomic and phylogenetic analyses (16%), as well as cytologic, molecular and conservation research. Our research demonstrates a significant use of conserved material in research.
Abbreviations: CGIAR, Consultative Group on International Agricultural Research • FAO, Food and Agriculture Organization of the United Nations • PGR, plant genetic resources
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INTRODUCTION
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THE ESTABLISHMENT of ex situ germplasm collections has been the result of several decades of global efforts to conserve plant biodiversity. The centers of the CGIAR alone maintain over 600 000 accessions of plant species, and over six million more are kept in institutions around the world (FAO, 1998). While these vast collections may hold benefits for society even if they are used only rarely, increasing their use today clearly enhances their value. The genotypic and phenotypic diversity maintained in the collections can be invaluable for breeding programs but also for basic research into evolution, gene expression, resistance, and other areas. Obstacles to use of PGR have been identified (FAO, 1998), and include lack of information on material, difficulty in accessing collections, underproduction of seed and the difficulty in moving specific genes into "good genetic backgrounds." As well as identifying obstacles to the use of PGR, it is important to quantify the level of use more accurately and to obtain better information on current patterns of use. In this paper, we describe the results of a survey of published literature to estimate the extent and frequency of use of plant genetic resources in applied plant genetic research.
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METHODOLOGY
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Four journals were chosen for inclusion in the survey: Crop Science, Euphytica, Plant Breeding, and Theoretical and Applied Genetics. These were chosen as being among the foremost international journals publishing research in agricultural genetics. Moreover, they were felt to provide a comprehensive overview across multiple disciplines and in both theoretical and practical work. Many other international journals publish work that involves the use of PGR but some of these have additional areas of research focus (e.g., animal genetics, botanical studies etc.) beyond crop plant genetics. Two journals, Genetic Resources and Crop Evolution and Plant Genetic Resources Newsletter, devoted specifically to publishing plant genetic resources research, were omitted from our study to maintain the focus on a broader research community. Journals with a primarily national focus which also publish work involving PGR were not included in this survey where the objective was to concentrate on the international dimension.
For this study, we focused on one year's worth of the four journals, and analyzed all issues published in 1996. All articles from these issues (a total of 859) were examined for evidence of the use of PGR. We defined PGR as material falling into one of three categories: 1, from an institute with a known ex situ collection; 2, material collected directly in the field; 3, more than 20 lines, source not specified, which could be presumed to originate in a genebank.
The species, source and type of material, authors, and research topic of these articles were stored and analyzed by an Excel database, which allowed for scrutiny of such aspects as author affiliation, species involved, and source of material. Details of the analytical procedures are presented in the Results and Discussion section of this paper.
Sources of material were verified by means of the IPGRI online Directory of Germplasm Collections (http://www.ipgri.cgiar.org/system/page.asp?theme=1; verified July 31, 2000). In addition, the SINGER database of CGIAR Center genebanks was used for comparative statistics on use of the material in these collections.
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RESULTS AND DISCUSSION
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Frequency of Use of PGR
The results of the survey indicated a high rate of use of conserved germplasm. Of the 859 articles, 191, or 22%, involved use of PGR. The highest frequency of PGR use was found in Euphytica, but the value was very similar for all four journals (see Table 1).
The amount of PGR use in Euphytica may reflect the scope of the journal; the list of research topics acceptable for submission explicitly includes genetic resources. Neither Theoretical and Applied Genetics nor Plant Breeding explicitly mentions genetic resources as a focus. Crop Science classifies articles according to subject matter in eight categories ranging from Crop Breeding, Genetics & Cytology to Crop Physiology & Metabolism, and including a section on Plant Genetic Resources. However, it was found that more than half of the articles identified in Crop Science as using PGR were not published under this specific section, and 33% of the articles in the section did not use materials which met our definition of PGR. We thus felt that this section did not skew the survey results which gave a broad overview of the use of PGR in four nonspecialist journals concerned with publishing work on crop plant improvement. A very different picture would have been obtained from specialist journals such as Genetic Resources and Crop Evolution and Plant Genetic Resources Newsletter. During 1996, these two journals published 68 and 40 articles, respectively. Nearly all of the articles (92%) used plant genetic resources in the sense of our definition, and the remaining 10 articles were largely reviews or treatments of the methodological aspects of conservation.
From the range of articles, two main approaches were evident in the use of genetic resources. One involved studies of large sets of accessions, providing data on agronomic and morphological characters, resistance phenotypes or taxonomic relatedness. These were often carried out by centers holding large collections that they wished to characterize (Ferguson and Robertson, 1996) or by those concerned with identifying sources of rare traits such as new sources of disease resistance (Badenes et al., 1996). The other main use is more investigative and was driven by the need to find specific quantitative phenotypes or genes or to understand the genetic control or a specific trait.
Where is PGR Being Used?
The institutional addresses of the authors of the articles were broken down geographically and by public or private sector affiliation, to determine where most of the research involving PGR was being conducted. Multiple authors on the same paper from one institution were not scored individually, since the aim was understanding the geographic distribution. The authors of the papers collected represented 249 different institutions in 41 countries and seven CGIAR centers. The majority of these institutions, almost 74%, were located in developed countries, and just under 20% in developing countries. CGIAR centers made up the remainder, 6.4% (see Table 2 for details).
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Table 2. Distribution of authors of PGR articles by geographic location of home institution. Numbers refer to number of articles involving at least one author from the country
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Over half (57%) of the institutions in developed countries were universities; 40% were national research centers and only 3% represented private industry organizations. In developing countries, 65% of the institutions were national or other research institutes and 30% were universities; three private corporations (5% of the total) were all located in Brazil.
The choice of journals used in this study is likely to have had a significant effect on the geographic distribution of the authors. Crop Science is seen as a primarily U.S. journal and the other three journals are also English-language publications. Researchers working in the public sector may prefer to publish in their countries' national agricultural and botanical journals. Japan, China, Brazil, and India, for example, publish notable journals in applied plant sciences.
A large number of these studies are the result of collaborations between authors at different institutions and in different countries. Of the 46 Crop Science articles scored as PGR-use, 31 (67.4%) were authored entirely by researchers at U.S. institutions, and 11 involved collaborations between authors from the U.S. and other countries. Non-U.S. authors submitted only four of the articles (2%).
The majority of the authors across the four journals are located at institutions in the USA. This partly reflects the dominance of USA-based authors in Crop Science articles. Excluding this journal, the percentage of U.S. institutions drops from 33 to 16%. Institutions in the UK, Germany, France, Italy, Spain, and Australia were almost equally represented; together they constituted 60% of the authoring institutions. The number of PGR articles authored entirely by researchers in developing-country institutions was only 9%, while another 12% were the result of collaborations with scientists in developed countries.
What Sources of PGR Are Being Tapped?
The world's ex situ germplasm collections are estimated to contain over 6 million accessions. The majority (79.2%) of the studies found in our survey used material explicitly obtained from ex situ collections and an additional 1.5% did not give a source but were assumed to be genebank accessions (see Table 3). There is a fair level of use of material collected directly in the field—31 cases or just over 15%. Table 4 shows a breakdown of the sources of this material by country or international center.
According to the FAO (1998), 12 countries hold more than 45% of the germplasm accessions kept in national collections. These countries are Brazil, Canada, China, France, Germany, India, Japan, Republic of Korea, Russian Federation, Ukraine, UK, and USA. In our study, germplasm from these countries was used in just under 60% of the studies, and 40% of the studies used material obtained from U.S. sources (either the USDA genebank system, or universities and botanical gardens). This last figure is in keeping with the large number of U.S.-authored papers.
It was difficult to quantify the total number of accessions or genotypes used by the research observed in our study, since numbers were not always stated in the papers. An underestimate, based on 177 of the 193 articles, would be 36 851 samples of accessions and material collected in the field. This includes several examples in which entire collections (Greene and Pederson, 1996) or very large samples ( Takeda and Chang, 1996; Tillman et al., 1996) were used. In the majority of the studies (77.5%), material was provided by a center in the same country as at least one of the author institutions. Looked at from the other direction, however, 22.5% of the material was used entirely by researchers outside the country in which it was stored. It is interesting to note that there were more studies contributed by developing-country authors than studies using material from developing country genebanks, and that of the 49 studies presented by authors from developing countries, less than half (22) used material collected or stored in a genebank in their respective countries. These figures indicate that a fair amount of ex situ material is moving across national borders, and not exclusively from developing country to developed country. Of course, the material stored in a national genebank will have been collected in many other countries, and many different factors (knowledge of the material's source, convenience in obtaining all accessions from a single source) will determine the most appropriate supplier of material for an investigation.
The 16 centers of the CGIAR hold in trust accessions of over 3000 species, including major crops such as maize (Zea spp.), rice (Oryza spp.), and wheat (Triticum spp.), which are freely available to researchers (CGIAR, 1999). In this survey, 28 studies involved material from CGIAR collections, amounting to 1242 accessions used. Of these, however, only 108 accessions, 9%, were used in studies not conducted by CGIAR researchers. To see how this figure compares to the material transferred out of CGIAR centers, the SINGER database of all center material was queried to determine the recipients of germplasm transferred each year. Unfortunately, direct comparison is not possible as final figures for transfers from CGIAR genebanks in 1996 are not available; however, between 1975 and 1995, the percentage of total transfers which sent germplasm to non-CGIAR centers ranged from a minimum of 44% to a maximum of 91% with an average value of 64% (The System-Wide Information Network for Genetic Resources, 1999). Material is transferred out of the CGIAR system for many reasons, including direct use in breeding programs or duplication; however, the figure of 9% transfer for research seems low.
Which Species Are Being Used?
Just as important as the degree of use of PGR is the range of species being tapped for research. Certain crops and species predominate in world collections, either because of their high levels of variation, or because of their importance in agricultural production. Their use in research, however, may reflect other factors as well as conservation priority and agricultural importance. According to FAO estimates, 48% of the world's collections consist of cereals, 16% are food legumes, and 8% are vegetable species (The Food and Agriculture Organization of the United Nations, 1998). The material used in the articles found in our study represented 112 different species, with a slightly different distribution into the various categories (see Fig. 1)
. The majority of studies did involve cereals but at a lower level (28% rather than 48%), while there was nearly equal use of vegetable species and food legumes. The major vegetable crops studied were Brassica, Lycopersicon, and Beta species. While these are not the subjects of very large collections worldwide, the especial predominance of Brassica and Lycopersicon may reflect that they have become model crops for plant genetic research. Soybeans [Glycine max (L.) Merr.] were the most commonly studied legumes, with the use of numerous cultivars and wild species. The level of use of forage species in the research studies was equal to the FAO estimate of their predominance in world collections. Research involving tuber species was very low. The "other" category included industrial crops such as sugarcane (Saccharum spp. and Erianthus spp.), coffee (Coffea spp.) and tobacco (Nicotiana spp.), as well as a few aromatic and parasitic species.
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Fig. 1. Species used in PGR research published in four journals in 1996 categorized by major crop group
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What Are Plant Genetic Resources Being Used to Study?
We categorized the research in the articles according to what we interpreted as their primary objectives. Some of the categories used, such as breeding or cytology, are more thematic while others, agromorphology or biotic resistances, are more concerned with areas of agricultural performance. This classification was used because often the scope of an article had a thematic relevance broader than the involvement of a particular technique or character.
Not surprisingly, the largest single category was the measurement of genetic diversity, typically studied by means of a broad group of accessions (see Fig. 2)
. This usually involves comparison of diversity within and between different groups of accessions using morphological, electrophoretic, or molecular markers (Ahmad and McNeil, 1996; Tohme et al., 1996). Work on biotic stress resistance (pest and disease resistance) constitutes the next largest category with many studies on the detection of new useful resistance and its inheritance. Work on breeding included studies of crossability, interspecific hybridization and production of somatic hybrids, and responses to selection for agronomic properties in breeding programs (Demurin et al, 1996; Diaz et al, 1996; Ravel and Charmet, 1996). Other important areas of work were taxonomic studies where large amounts of diverse material are required and cytological studies. Work on abiotic stress resistance was surprisingly low with only six studies in the year investigated. Topics such as QTL identification, molecular mapping, and technology applications tended to be carried out with research lines and other types of elite cultivars rather than the accessions that fit our definition of PGR.
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Fig. 2. Research involving PGR material (published in four journals in 1996) categorized by primary research objective
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CONCLUSIONS
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The results of the survey show clearly that during 1996 a significant body of applied plant genetic research reported in the four international journals surveyed involved the use of PGR according to the narrow definition used here.
The initial focus of the plant conservation community was conservation of biodiversity in the face of its threatened disappearance. More recently, the importance of using the material stored in genebank collections has been increasingly emphasized. "Use" is often thought of solely as the incorporation of a few accessions into breeding programs, but genebank accessions are the ideal material for scientific research—agricultural but also cellular and molecular. The results of our study show that germplasm has begun to make its way into research. The journals we surveyed focus on crop plant genetic research, and it was hypothesized that a majority of work in this area would be carried out with advanced breeding lines, recombinant lines, and commercially-obtained cultivars. That over 20% of these articles, on average, did use PGR, demonstrates the extent to which such material is recognized as valuable for study. Often, the object of study was the material itself, its history and variation, but it was also used to answer molecular and phenotypic questions, as well as a basis for agronomic and trait-based research. It is also encouraging to note the wide range of species used; though most of these have a commercial market, they represented more than the largest cash crops (such as maize) or the traditional research organisms (Lycopersicon or Brassica).
One of the most interesting results of our survey was the range of sources of genebank material used and the locations of the users. As mentioned before, the choice of journals was intended to give a broad overview of the research field, and only some of the most relevant journals, both international and national, were included in this survey. The relative proportions of authors from developed and developing countries, as well as the amount of genebank material accessed from these countries, may have been skewed as a result. Still, it is important to note the amount of collaboration between authors from different countries, because these collaborations almost always include sharing of conserved material.
Further studies of the use of PGR in research are merited. There is undoubtedly a very large body of research reported in nationally focused journals that are published in a variety of different languages. Information from these would give a much more comprehensive view of the global use of PGR. A study focusing on journals covering specific areas of plant research such as physiology or pathology would provide a more complete view of the different ways in which PGR are used in research. Finally, expanding the study to include literature published over succeeding years would indicate whether there is a growing trend towards the use of PGR. This study, however, provides a clear indication of the importance of PGR in developing the knowledge base for improved agricultural production through internationally recognized research.
Received for publication March 3, 2000.
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REFERENCES
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- Ahmad, M., and D.L. McNeil. 1996. Comparison of crossability, RAPD, SDS-PAGE and morphological markers for revealing genetic relationships among Lens species. Theor. Appl. Gen. 93:788–793.
- Badenes, M.L., M.J. Asins, E.A. Carbonell, and G. Glacer. 1996. Genetic diversity in apricot, Prunus armeniaca, aimed at improving resistance to plum pox virus. Plant Breed. 115:133–139.
- The Consultative Group on International Agricultural Research. 1999. http://www.cgiar.org; verified July 27, 2000.
- Diaz, J., P. Schmiediche, and D.F. Austin. 1996. Polygon of crossability between eleven species of Ipomoea: Section Batatas (Convolvulaceae). Euphytica 88:189–200.
- Demurin, Y., D. Skoric, and D. Karlovic. 1996. Genetic variability of tocopherol composition in sunflower seeds as a basis of breeding for improved oil quality. Plant Breed. 115:33–36.
- The Food and Agriculture Organization of the United Nations. 1998. The state of the world's plant genetic resources for food and agriculture. FAO, Rome.
- Ferguson, M.E., and L.D. Robertson. 1996. Genetic diversity and taxonomic relationships within the genus Lens as revealed by allozyme polymorphism. Euphytica. 91:163–172.
- Greene, S.L., and G.A. Pederson. 1996. Eliminating duplicates in germplasm collections: A white clover example. Crop Sci. 36:1398–1400.[Abstract/Free Full Text]
- Jha, P.K., K.K. Shrestha, M.P. Upadhyay, D.P. Stimart, and D.M. Spooner. 1996. Plant genetic resources of Nepal: A guide for plant breeders of agricultural, horticultural and forestry crops. Euphytica 87:189–210.
- Ravel, C., and G. Charmet. 1996. A comprehensive multisite recurrent selection strategy in perennial ryegrass. Euphytica 88:215–226.
- The System-Wide Information Network for Genetic Resources. 1999. http://www.singer.cgiar.org; verified July 27, 2000.
- Takeda, K., and C.L. Chang. 1996. Inheritance and geographical distribution of phenol reactionless varieties of barley. Euphytica 90:217–221.
- Tillman, B.L., S.A. Harrison, C.A. Clark, E.A. Milus, and J.S. Russin. 1996. Evaluation of bread wheat germplasm for resistance to bacterial streak. Crop Sci. 36:1063–1068.[Abstract/Free Full Text]
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TOP
ABSTRACT
INTRODUCTION
