Chapter 7: Classifications of infraspecific variation in crop plants

K. Hammer
University of Kassel, Agrobiodiversity, Witzenhausen, Germany
E-mail: khammer.gat(at)t-online.de
Y. Morimoto
Bioversity International, Regional Office for Sub-Saharan Africa, Nairobi, Kenya
E-mail: y.morimoto(at)cgiar.org

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This chapter is a synthesis of new knowledge, procedures, best practices and references for collecting plant diversity since the publication of the 1995 volume Collecting Plant Diversity; Technical Guidelines, edited by Luigi Guarino, V. Ramanatha Rao and Robert Reid, and published by CAB International on behalf of the International Plant Genetic Resources Institute (IPGRI) (now Bioversity International), the Food and Agriculture Organization of the United Nations (FAO), the World Conservation Union (IUCN) and the United Nations Environment Programme (UNEP). The original text for Chapter 7: Classifications of Intraspecific Variation in Crop Plants, authored by P. Hanelt and K. Hammer, has been made available online courtesy of CABI. The 2011 update of the Technical Guidelines, edited by L. Guarino, V. Ramanatha Rao and E. Goldberg, has been made available courtesy of Bioversity International.

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	Considerable intra-specific morphological variation in bottle gourd (Lagenaria siceraria) can be seen in fruit and seed size, shape, degree of development of the handle and shell thickness. The species was possibly the earliest crop to be domesticated by humans for use as a container that is light yet strong. (Photo: Y. Morimoto/Bioversity International)

Abstract

Infraspecific classifications are discussed as useful tools for the plant collector. Whereas formerly many different types of such classifications have been proposed and used, today we have relatively few modern examples. The reasons for this are discussed. In light of the general development in biodiversity, we should expect classification to take on greater importance, which would correspond to the often demanded increase in the importance of taxonomy.

 

Introduction

Germplasm collectors must be thoroughly familiar with what is known about the variation present within their target taxa if they are to sample them efficiently. In crops, this variation can be many times greater than in wild plants, especially for species that were domesticated early and have been widely spread around the world. Such variation is the result of both natural and artificial selection pressures. The latter may be conscious or unconscious and result from the application of diverse agricultural practices and from the disparate and changing demands of growers for specific agronomic and other properties. Variation may be in morphological, anatomical, karyological, ecological, physiological, biochemical and molecular characteristics. Explanatory surveys of genetic diversity can be useful preliminaries to germplasm collecting (von Bothmer and Seberg 1995). Most relevant for the collector in the field, however, is variation in morphological traits and ecological adaptation. Making use of a scheme for the classification of the morphological traits can help collectors to keep track of what they find and to compare the diversity of different areas (Moss and Guarino 1995).

The term “infraspecific” is used here to refer to variation within a cultivated taxon, but it should be pointed out that the crop in a wild-weedy-crop complex is often given subspecific rank, following the proposal of Harlan and De Wet (1971). Morphological infraspecific variation has been studied in many crops, though often for only a limited part of their geographic range or for a restricted set of characters. Formerly there were regular literature reviews on the taxonomy of cultivated plants, but these tasks have been taken over by the Plant Genetic Resources Abstracts (see Dearing and Guarino 1995).Traditional Floras sometimes consider variation within crop plants, though never in much detail. However, there are also specialized Floras dealing only with cultivated plants (see below). A recent encyclopaedia on cultivated plants (excluding ornamentals and forest trees), which also discusses the taxonomic framework of crop taxonomy and evolution, is provided by Hanelt and IPK (2001).

There is general agreement about the necessity and importance of such studies in cultivated plants (Andrews et al. 1999; Baum 1981; Diederichsen 2004; Hanelt 1988, 2001; Hetterscheid et al. 1996; Knüpffer and Ochsmann 2003; Mansfeld 1953; Ochsmann 2004; Styles 1986) in both applied and theoretical applications, ranging from the investigation of the history of domestication of plants and their subsequent evolution to the characterization of germplasm. However, the procedures used to develop the classifications and the resulting schemes themselves are extremely diverse, and a generally agreed-upon approach has not yet emerged (Hanelt 2001). Two extreme types of schemes may be recognized:

• complex hierarchical taxonomic subdivisions of a cultivated plant taxon, with many infraspecific taxa at several taxonomic ranks between the species and cultivar level (e.g., Dorofeev and Korovina 1979; Nechanský and Jirásek 1967)

• relatively simple, non-structured, special-purpose schemes with a few main groups (e.g., De Wet 1978) (The proposed culton concept [Hetterscheid and Brandenburg 1995] can be considered as a special-purpose scheme.)

Because selfing results in the variation within a crop being split into distinct homozygous lines, autogamous species tend to be relatively easier to classify in detail into many groups than allogamous species. In the past, this has led to over-splitting, a trend that has been somewhat reversed by genetic studies.

The different methods of approaching the infraspecific taxonomy of crops are discussed in this chapter insofar as they may be relevant to the needs of collectors. For further details, see Hanelt (1986) and Hanelt et al. (1993). Many classification proposals are written in languages other than English, but these somewhat overlooked approaches are also included in the focus of this paper.

 

Classifications

A classification scheme for classifying the infraspecific variation of crop plants has been proposed by Hanelt (1986; see also the 1995 version of this chapter):

1. Formal taxonomic classifications under the International Code of Botanical Nomenclature (ICBN) (http://ibot.sav.sk/icbn/main.htm):

a) Diagnostic-morphological
b) Phenetic-numerical
c) Ecogeographic

2. Informal classifications:

a) Diagnostic-morphological
b) Phenetic-numerical
c) Genetic

3. Mixed classifications

Two principle types of approaches are distinguished: formal taxonomic and informal classifications. Whereas in the former, formally recognized categories are used (more or less) according to the rules of the ICBN (McNeill et al. 2006), informal classifications use non-standard categories or categories as proposed in the International Code of Nomenclature of Cultivated Plants (ICNCP) (www.ishs.org/sci/icracpco.htm) (Brickell et al. 2009). In informal classifications, therefore, problems with nomenclature that result from the use of the ICBN are avoided, although there are other formal preconditions deriving from the ICNCP. Moreover, the two codes are not always compatible (Brandenburg and Schneider 1988; Ochsmann 2004) and a broadly accepted designation of a group is not guaranteed in informal classifications; therefore, communication of information on the material under study is more difficult.

Formal taxonomic classifications under ICBN

Diagnostic morphological classifications

Usually these classifications are based on a few, easily recognizable morphological characteristics and allow a rapid overview of variation within a crop. Several major publication projects have been based on this type of infraspecific classification, e.g., the Flora of Cultivated Plants of the Soviet Union (Dorofeev and Korovina 1979) and the Cultivated Plants of Hungary (Máthé and Priszter 1982). R. Mansfeld, the founder of the Gatersleben school of taxonomy, which has studied the infraspecific classification of several important cereal, legume and vegetable crops, provides a typical example with his morphological system of Triticum aestivum (Mansfeld 1951). He considers 12 characteristics and organizes infraspecific variation into more than 400 varieties, each differing from related ones in only one character. Mansfeld’s (1950) scheme for Hordeum vulgare can serve as another example. Below the species level, he applied the category of “convariety” (as defined by Alefeld 1866; see also Helm 1964) and accepted five convarieties, defined by major spike characters: convar. vulgare (convar. hexastichon), convar. intermedium, convar. distichon, convar. deficiens and convar. labile. Formerly, some of these convarieties were even described as separate species (not least, by Linnaeus). There are some differences in geographic distribution and even some crossing barriers among them, which might indicate that this category has some biological significance. “Varieties”, of which 191 are described, are purely artificial entities, however. In fact, such classifications are, as a rule, rather artificial, especially at lower taxonomic levels.

The same principles have been applied to Papaver somniferum. Based on the classification of Danert (1958), Hammer (1981) developed a system containing three subspecies: ssp. setigerum is the wild ancestor; ssp. somniferum and ssp. songaricum are both cultivated. The cultivated subspecies differ in having sulcate lobes of the stigmatic disc with dentate margins versus flat lobes with entire margins. These characters have been considered as important by some Papaver taxonomists and also show clear geographic differentiation. The convariety level is defined by indehiscent versus dehiscent capsules, another important character indicating different stages of domestication (Hanelt and Hammer 1987). The variety level is based on seed colour (resulting from selection pressures under domestication) and other characteristics. This system was recently rejected (Dittbrenner 2009; Dittbrenner et al. 2008), mainly using arguments from the culton-concept (Hetterscheid and Brandenburg 1995). After this, the Gatersleben genebank started to follow the Western approach in respect to infraspecific classifications.

Diagnostic-morphological classifications have proven to be very useful for keeping and elaborating large collections of cultivated plants (e.g., in genebanks), as well as for to the plant collector. Since the morphological entities that define these classifications can be recognized relatively easily, they can be used as the basis of field checklists. Rapid comparison of different areas with regard to the variation found there is possible and gaps in collections can be identified. Assessments of variation at different times based on such classifications have been used to estimate genetic erosion, for example in Sicily (Perrino and Hammer 1983; Prestianni 1926) and other parts of Italy (Hammer and Laghetti 2005).

The controversy between the proponents of diagnostic-morphological classification is yet to be resolved. It can best be demonstrated in wheat: Dorofeev and Korovina (1979) subdivide Triticum aestivum into two subspecies, three convarieties and 194 varieties. And whereas Mansfeld (1951) included T. compactum in T. aestivum, Dorofeev and Korovina classified it as a separate species with three convarieties and an additional 93 varieties.

While many interesting conclusions can be drawn on the basis of this system, as recently demonstrated by Filatenko et al. (2010), geneticists and plant breeders like Mac Key (1988), however, resist any further detailed subdivision between the levels of subspecies and cultivar. They do not see the necessity to describe entities that are not genetically meaningful, are characterized by a few common monofactorially inherited character states, and do not indicate properties that are important for the plant breeder (Hanelt 1988). Breeders are inclined to use more open, less formalized classifications, into which their material can be incorporated without difficulty (i.e., in the sense of the ICNCP) (Brickell et al. 2009). The polemics against diagnostic classifications have a long-standing history. Hawkes (1980) observed an East-West division with regard to the preference of such detailed diagnostic classifications (see also Hanelt 1988). Large collections of cultivated plants have been created in the eastern parts of Europe, for which diagnostic classifications have proved to be useful. Some exceptions are Percival (1921) and Mansfeld (1951), but they had considerably large collections at their disposal. At any rate, Mac Key’s (1966) system does not have detailed infraspecific treatment. A tool for the mutual understanding and use of both systems is now available (Hammer et al. 2011). But for the international use of Dorofeev and Korovina’s (1979) Russian wheat monograph, an English translation is necessary; there is one in preparation (Knüpffer et al. 2004).

In some cases, the classifications are of restricted applicability because they deal with the cultivated flora of a rather restricted area (e.g., Máthé and Priszter 1982). However, even country Floras of cultivated flora may employ a comprehensive concept of taxa, even allowing them to be used for a worldwide survey. The Flora of the Cultivated Plants of the Soviet Union is perhaps the best example. Some important contributions, in addition to the Triticum volume mentioned above, are Fursa and Filov (1982), Girenko and Korovina (1988), Kazakova (1978), Kobyljanskij (1989), Kobyljanskij and Lukjanova (1990), Kobyljanskij and Soldatov (1994), Makaševa (1979), Mukhina and Stankevič (1993), Pyženkov (1994), Šmaraev and Korovina (1982), Stankevič and Rep’ev (1999). In the last few years no new infraspecific classifications have appeared in this series. A recent monograph from the Vavilov Institute (Loskutov 2007), but not in the series cited above, has appeared without a detailed infraspecific treatment (which can be found in Kobyljanskij and Soldatov 1994). This could possibly be seen as a new trend.

The old morphological classifications of the Gatersleben school are listed by Hammer (1981). In addition to the species already mentioned, there are treatments of Beta vulgaris, Brassica oleracea, Glycine max, Linum usitatissimum, Lycopersicon esculentum, Nicotiana rustica, N. tabacum, Pisum sativum and many other crops. More recent treatments include Raphanus (Pistrick 1987), Brassica oleracea (Gladis and Hammer 2003), Brassica spp. (Gladis and Hammer 1992), Coriandrum (Diederichsen and Hammer 2003) and Ocimum (Eckelmann 2003). For a recent compilation of diagnostic-morphological classifications, see Landsrath and Hammer (2007).

Obviously, there has been a certain decline in the last few years. A potential problem with diagnostic-morphological classifications is still the difficulty in comprehension and their limited availability – many are not available in English and might be difficult to obtain. As a result, some older classifications, such as that of Percival (1921) on Triticum, are sometimes used even today. The forthcoming edition of Dorofeev and Korovina (1979) in English could improve the situation, at least with respect to Triticum.

Most of the available diagnostic morphological classifications for Central European crop plants are, as already mentioned, included in a modern treatment of Alefeld’s “Agricultural Flora” (Landsrath and Hammer 2007). Alefeld and Körnicke (Hammer 2005) can be considered as the founders of intensive work with those classifications.

Phenetic-numerical classifications

These classifications consider a large number of characters. Various multivariate mathematical methods are used to calculate similarities among infraspecific taxa and to identify groupings. There are several examples (reviewed by Schultze-Motel 1987; see also Baum et al. 1984) but none is particularly convincing in the context of formal taxonomy. They cannot be recommended for the practical use of the plant collector.

Ecogeographic classifications

Such classifications have been developed by the Vavilov Institute, based on the hypothesis that, in an area where selection pressure from environmental factors, cultivation practices, propagation methods, etc., is relatively homogeneous, a crop will tend to have a certain genetic integrity (Vavilov 1940). An example of ecogeographic classification is that proposed by Flaksberger (1935) for Triticum aestivum, which includes two subspecies, 15 proles and six subproles.

New taxonomic categories have often been introduced. Groups are largely defined by their geographic origin and by characteristics that reflect the agricultural and ecological conditions to which they are adapted (e.g., reproductive phenology, pest and disease resistance, growth characteristics, etc.). In general, field experiments are necessary to verify the categories and to incorporate new accessions into such a classification. Therefore, a collector might not be able to apply them directly during fieldwork. However, they might be very useful for the characterization of collections, facilitating the use of the material by breeders. There is still no bridge between formal ecogeographical classifications and the use of an ecogeographic approach in fieldwork (Maxted et al. 1995).

Informal taxonomic classifications

Diagnostic-morphological classifications

There are some regional studies of this type. The classification of French bush bean cultivars is one. They have been arranged into three categories: groups, sections and classes (Anon. 1983). Pod characteristics (11 character states) are used to differentiate groups and sections; and leaf colour, pod length, colour of unripe pods and length of bracts (12 character states) for differentiating classes. The resulting system comprises five groups, 14 sections and many classes. Another example, also from Phaseolus vulgaris, shows that the input of biochemical methods (in this case, phaseoline types) can lead to phytogenetically more relevant groupings within an informal diagnostic-morphological classification (Krell and Hammer 2008, Singh et al. 1991).

The extremely reduced possibilities for infraspecific classifications of cultivated plants under the ICNCP (Brickell et al. 2009), largely following the proposal of the culton concept (Hetterscheid and Brandenburg 1995), which is still heavily disputed (Hanelt 2001, Pickersgill and Karamura 1999), have to be considered here. Many new approaches are of this type, e.g., in Cruciferae, Cucurbitaceae and also Gramineae. They are formally dependent on the ICNCP and thus they lack the flexibility of informal classifications. This is one of the disadvantages of this code, which became user driven (by the flower and seed industry) under the forceful argumentation of the cultonomists.

Phenetic-numerical classifications

One of the best examples of this type of classification is the study of the South American cultivars of cassava (Manihot esculenta) by Rogers and Fleming (1973). They used 55 character states and defined 19 groups of cultivars. Within these groups, there is a high degree of phenotypic similarity, and evidently also considerable genetic similarity. New material can be easily incorporated into the proposed classification scheme; however, the evaluation of the basic data for this type of study is very time consuming.

The range of potentially relevant morphological characteristics for a species, which can be measured in morphological analysis, is summarized in descriptor lists. Some of the crop descriptors and monographs have been published and are available online on the Bioversity International website (www.bioversityinternational.org/publications.html).

Genetic classifications

This type of classification is only possible in crops with well-studied genetics, such as Pisum sativum (Blixt 1979), where the genes responsible for the expression of many different characteristics are known. In peas, there has also been an attempt to combine a formal diagnostic and a genetic classification (Lehmann and Blixt 1984). It is difficult to incorporate new material into such classifications. Test crosses are necessary and multifactoral characteristics cannot be included at all.

Classifications based on genomic composition are somewhat different. An example is that of Simmonds for the edible fruit-bearing bananas (Simmonds 1966; Simmonds and Weatherup 1990). These are classified by references to ploidy (2×, 3×, 4×) and the genomic contribution made by two diploid wild species (AA Musa acuminata and BB Musa balbisiana). Some 15 characteristics are used to distinguish among cultivar groups. Infraspecific items are not involved in this example. Problems with species designations (and also with infraspecific ones) arise when dealing with hybrid genera, as, e.g., × Triticosecale, according to the ICBN (Hammer et al. 2011).

In the last decade, increased attention has been devoted to molecular marker technologies, including DNA sequences. These have provided a wealth of data, which, together with phenotypic and ecological data, have significantly increased our understanding of the intra-specific dynamics of these genetic resources. The study findings provide not only information for classification but also a geographic framework of references to elucidate patterns of genetic diversity and domestication, constituting a source of diversity for a wide range of traits (Gepts et al. 1999). Combined with phenotypic data and multivariate statistical analysis, the recent progress in molecular mapping also provides opportunities to identify and transfer genes (geneflow) for quantitative traits and processes of domestication (Tanksely and McCouch 1997). Molecular marker technologies are useful tools for measuring lineages and comparative relationships between individuals, populations and species, obtaining evidence of recent bottlenecks in populations in size, as well as documenting geneflow, recombination and seed supply and identifying varieties (Brown et al. 1996).

In the genus Vigna, family of Fabaceae, for instance, Tomooka et al. (2002) described the subgenus of Vigna ceratotropis and suggested revising the nomenclature of the group, based on past taxonomic treatments and their biosystematics results, including diversity distributions, species relationships and cross-compatibility studies. Saravanakumar et al. (2004) conducted a random amplified polymorphic DNA (RAPD) analysis to enhance understanding of the diversity of Vigna species from Palney Hills in India, to determine (1) the taxonomic relationship between V. trinervia var. trinervia and V. trinervia var. bourneae, (2) the distinction between V. trinervia collected at a high altitude of about 1000m and at a low altitude, (3) the relationship among V. radiate var. sublobata from different geographic locations and (4) relationships between V. dalzelliana and other species.

In the genus Oryza, the taxonomy of the three diploid CC genome of Oryza species (O. eichingeri, O. officinalis and O. rhizomatis) has been confused and several different names have been used in the literature and herbaria (e.g., Dally and Second 1990; Duistermaat 1987; Harriman 1994; Katayama and Ogawa 1974; Sharma and Shastry 1965; Tateoka and Pancho 1963). This was because two major useful characteristics (chromosome number and rhizome formation) are not readily visible for some species in the complex. Later molecular-based diversity studies helped to find the relationships within the diploid CC genome species complex, thus showing their evolutionally history (e.g., AFLP: Aggarwal et al. 1999; isozymes: Second 1984; RFLP: Wang et al. 1992; ISSR: Joshi et al. 2000; chloroplast SSR: Ishii and McCouch 2000; 5SDNA sequences: McIntyre et al. 1992; RAPDs Xie et al. 1998).

In the common bean, genus Phaseolus, Debouck (1999) has indicated generic limitations in the taxonomic classification. He comments that over 400 species of Phaseolus have been named over the past two centuries, often with poor description or lacking good type specimens. He also indicates that “we do not know yet exactly how many Phaseolus species are existing, 50–60 species would be a reasonable estimate” on the basis of species cross-compatibility, several molecular marker studies (Fofana et al. 1997, 1999; Jaaska 1996; Jacob et al. 1995) and extensive herbarium field exploration surveys, including his own (Debouck 1991, 1999).

Gepts et al. (1999) look at the genetic diversity and domestication of the common bean (Phaseolus vulgaris). For the faba bean (Vicia faba L.), RAPD and restriction fragment length polymorphism (RFLP) techniques were employed to analyse the same faba bean populations described by Muratova (1931), to find possible relationships within the V. faba genepool from different geographic regions and to try to elucidate the routes of dispersal of the faba bean as a crop (Potokina et al. 1999).

Most recently, molecular classification techniques have grown in importance to crop improvement. Arai-Kichise et al. (2011) used single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes, and performed whole-genome sequencing of a landrace of japonica rice. They identified 132,462 SNPs between the genomes of Omachi and Nipponbare, which are closely related cultivars. They also validated InDels on a part of chromosome 2 as DNA markers and successfully genotyped five japonica rice cultivars. This provides a methodology and extensive data on SNPs and InDels available for whole-genome genotyping and marker-assisted breeding.

However, these techniques have been applied so far mostly to “model species” such as humans, yeasts and some of the major crops such as rice, maize and wheat, as well as beans. The technology is still expensive, and a positive return on investment in this technology has not yet been recognized.

Nevertheless, classifications based on genetic data (including molecular markers) are probably the best guides for germplasm collectors when collecting plant genetic resources – better than mostly morphological/botanical traits. Since the genetics of a species need to be well understood for this, the value of such genetic analyses is greater for collectors when gap-filling collections are made.

Mixed classifications

There is no single classification approach suitable for all possible demands; different aims can be achieved with different types of classifications. Hanelt (1972) proposed a combination of classifications for Vicia faba: a formal diagnostic classification into two subspecies, three varieties and six subvarieties (based mainly on seed size, form and structure of pods) was combined with an informal classification into 14 races, based mainly on ecogeographic data. A similar approach has been used for Citrullus lanatus (Fursa 1981).

In a number of cases, Jeffrey (e.g., in the “Compositae” [Jeffrey 2001]) preferred the informal classification according to the ICNCP (open classification, according to Brandenburg 1999). For Cynara cardunculus, Jeffrey considers a cardoon group and a globe artichoke group, with broad synonymy from the formal classifications (closed classification, according to Brandenburg 1999). This can be considered as an extreme case of a mixed classification. Hammer (2001), in treating the Chenopodiaceae, classified Beta according to a formal system and provided the informal groups after the synonymy, e.g., sugar beet: Beta vulgaris var. altissima (the sugar beet group).

At any rate, with the new development of the ICNCP, more synonymy-like indications will be necessary for exact agrobotanical work, especially in the group of cultivated plants within Mansfeld’s definition (Hanelt and IPK 2001).

	Landraces are named according to specific morphological characteristics of the fruit, or sometimes after the village where they were obtained. This homestead is at “Mutha” village in Kitui District, Kenya, where local people classified 242 gourds into 33 landraces. (Photo: Y. Morimoto/Bioversity International)
	Diversity in uses - associated with diverse fruit traits - is the most important driving force for strong selection. Farmers carefully choose several different types from their previous harvest depending on their needs. Varieties used for oil (right) have distinctly larger seeds than varieties used for containers and food (left row). (Photo: Y. Morimoto/Bioversity International)

Farmers’ classifications

Farmers’ classification is considered to be the most uncertain classification system; however, it is the most useful guide in narrowing the range of agro-morphological criteria, which are usually linked to the genetic diversity of a crop. They are used by farmers to distinguish and name crop varieties and are commonly the basis for farmers’ selection of varieties, which is important in shaping the population over time (Jarvis et al. 2000). It is therefore of direct relevance to farmers and plant breeders in their use of germplasm. Berlin (1999) states that while folk or ethnobotanical classifications are not comprehensive, he gives an example of the naming behaviour of the Tzeltal Maya community in Chiapas, Mexico, which is to conceptually relate an unknown plant to a prototype that has been encountered before. Berlin refers to this as “exemplar comparison” (from Medin 1989) and describes it as the basis of the “perceptual affinities” of the new target species to the original prototype.

Many studies have pointed out how farmers recognize and name the crops they grow according to agromorphological, ecological-adaptive, quality and use characteristics (Bellon and Brush 1994; Boster 1985; Quiros et al. 1990; Schneider 1999; Soleri and Cleveland 2001; Teshome et al. 1997). The names of farmers’ varieties, for instance, are often related to the original source of the material, the morphology of the plant, agronomic performance, adaptation to particular environmental factors, and the use of the material, including its role in religious ceremonies. When collecting information from farmers, it is important to note down the exact name of each variety as given by the farmer, without modifying it, using the local alphabet if possible (Jarvis et al. 2000). However, farmers might not be consistent in naming and describing landraces. Studies have indicated that sometimes there is consistency between variety names and genetic distinctiveness (Karamura 2004; Mar and Holly 2000), but other times there is not. For example, a study in Ethiopia has shown different names for the same variety, reflecting an emphasis on different qualities by different farmers or communities. Another example is durum wheat in Ethiopia. In some villages, a variety is called “white”, whereas in the others, the same variety is called “early” (Tanto 2001). Tesfaye and Ludders (2003) found similar evidence in Ethiopia for enset, a clonally propagated crop, for which a few landraces assumed different names at different locations. Sawadogo et al. (2005) indicate that differences in variety names in the same village or community reflect differences in the languages used to name the variety. Farmers’ names also vary with the gender, age or ethnic group of the individual (Canh et al. 2003; Hue et al. 2003; Karamura et al. 2004; Mulumbo et al. 2004). Fujimoto (1997) mentions that farmers also categorize enset landraces based on their reminiscences, such as which offspring are derived from which mother plant, a classification he describes as “genealogical classification”. Sigeta (1995) indicates that farmers’ names are described differently depending on individual recognition. In order to enhance better understanding of this classification, he emphasizes that researchers need to focus more on farmers’ actions and recognition rather than the morphological characteristics and performance of the plants.

In addition to consistency in variety names, it is important to find different degrees of adaptive and quality traits and to develop a level of consensus between farmers on their selection criteria for planting seeds. The structure of genetic variability between and within farmer-named varieties has also been described using biochemical and molecular markers. Teshome et al. (1999) assessed farmers’ knowledge of the resistance of sorghum landraces to the rice weevil in storage and revealed that, according to biochemical and molecular markers, the level of landrace susceptibility to the weevil was highly correlated with farmers’ classifications.

These research approaches require intensive investigation with farmers, visits to the field and participatory measurement during all stages of crop development. Clarification of what constitutes a landrace at each level (individual, family, community, village and region) is the first step toward defining the amount and distribution of crop diversity maintained by farmers.

 

Conclusions

 It is well known that most of the more important and widespread crop species are characterized by an enormous amount of infraspecific variation. Familiarity with this is essential for the effective collecting of plant genetic resources. There are many publications on the infraspecific taxonomy of crop plants, but many have been written in languages other than English (particularly the most important papers of the Vavilov school).

A variety of methods have been proposed for the classification of crop plants. Those most appropriate for collectors seem to be the ones based on easily recognizable characteristics of gross morphology. Variation in such characteristics can be used to establish taxonomically formal or informal diagnostic classifications, which will be no less useful for the later management of collections than for the collector in the field.

As discussed here, there has been a reduction in the use of infraspecific classifications, which is connected with a reduction in knowledge about the functions and usefulness of such classifications. Infraspecific classifications are of limited use for plant breeding, but they are of great use to the plant collector and to genebank management. Together with a six-fold paradigm shift in the area of plant genetic resources (Hammer 2003), we are losing the methods and means that are helpful for their collection, maintenance and characterization. The abandonment of infraspecific classifications, which has been strongly advocated for many crops, leads to a loss of information (quantity and quality).

The momentum that has been lost depends on the crop, the kind of research being done and the research community. In barley, for example, infraspecific classification has been largely abandoned, whereas in wheat, many publications still use infraspecific classifications, especially when reporting about landraces. Moreover, recent developments in the Cultivated Plant Code (Brickell et al. 2009) and its application have exclusively concerned plants grown in developed countries, “with well-organised trades in harvested products, planting material or both, and often with International Registration Authorities to regulate the application of cultivar names” (Pickersgill and Karamura 1999). Landraces with their characteristic and rich morphological structure are today neglected in this respect by the Code.

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References and further reading

Aggarwal AK, Brar DS, Nandi S, Huang N, Khush GS. 1999. Phylogenetic relationships among Oryza species revealed by AFLP markers. Theoretical and Applied Genetics 98:1320–1328.

Alefeld F. 1866. Landwirthschaftliche Flora. Wiegandt & Hempel, Berlin.

Anon. 1983. Description et essai de classification de variétés de Haricot Nain. National Institute for Agricultural Research (INRA), Versailles.

Andrews S, Leslie AC, Alexander C, editors. 1999. Taxonomy of Cultivated Plants: Third International Symposium. Royal Botanic Gardens, Kew, UK.

Arai-Kichise Y, Shiwa Y, Nagasaki H, Ebana K, Yoshikawa H, Yano M, Wakasa K. 2011. Discovery of genome-wide DNA polymorphisms in a landrace cultivar of japonica rice by whole-genome sequencing. Plant Cell Physiology 52(2):274–282.

Baum BR. 1981 Taxonomy of the infraspecific variability of cultivated plants. Kulturpflanze 29:209–239.

Baum BR, Duncan T, Phillips RB. 1984. A bibliography of numerical phenetic studies in systematic botany. Annals of the Missouri Botanical Garden 71:1044–1060.

Bellon MR, Brush SB. 1994. Keepers of the maize in Chiapas, Mexico. Economic Botany 48:196û209.

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Chapter 21: Collecting vegetatively propagated crops (especially roots and tubers)

Alexandre Dansi
Laboratory of Agricultural Biodiversity and Tropical Plant Breeding (LAAPT),
Faculty of Sciences and Technology (FAST), University of Abomey-Calavi (UAC), Benin
E-mail: adansi2001(at)gmail.com

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This chapter is a synthesis of new knowledge, procedures, best practices and references for collecting plant diversity since the publication of the 1995 volume Collecting Plant Diversity; Technical Guidelines, edited by Luigi Guarino, V. Ramanatha Rao and Robert Reid, and published by CAB International on behalf of the International Plant Genetic Resources Institute (IPGRI) (now Bioversity International), the Food and Agriculture Organization of the United Nations (FAO), the World Conservation Union (IUCN) and the United Nations Environment Programme (UNEP). The original text for Chapter 21: Collecting Vegetatively Propagated Crops (Especially Roots and Tubers), authored by Z. Huaman, F. de la Puente and C. Arbizu, has been made available online courtesy of CABI. The 2011 update of the Technical Guidelines, edited by L. Guarino, V. Ramanatha Rao and E. Goldberg, has been made available courtesy of Bioversity International.

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	Farmers and researchers using four-square analysis to collect information about yam diversity at Igboloudja, Togo (Photo: A. Dansi)

Abstract

Many of the developing world's poorest farmers and food-insecure people are highly dependent on root and tuber crops (RTCs) as a supplementary, if not principal, source of food, nutrition and cash income. Hence, the development and utilization of genotypes that can withstand abiotic and biotic pressures are the keys for sustainable production. Genes for such traits are often available in wild species and landraces; therefore, their genetic resources need to be collected, documented, characterized, evaluated and preserved. This paper supplements the original 1995 chapter by summarizing recent technical guidelines for collecting both wild and cultivated roots and tubers. The sampling procedures are discussed with particular attention given to the involvement of local communities in the case of cultivated species. To be of value, accessions should be well documented, an issue that is discussed, and guidelines are provided. Techniques of handling vegetative material in the field are summarized and the concept of in vitro collecting presented. Future challenges and needs in the areas of report preparation, germplasm conservation, research (characterization and evaluation) and information exchange are briefly discussed.

 

Introduction

Root and tuber crops are plants that are grown for their modified, thickened roots or stems, which generally develop underground (Bradshaw 2010). These organs are rich in carbohydrates and are commonly used as a dietary staple, livestock feed, raw material for the production of industrial products such as starch and alcohol, or processed into various food products.

The 1995 version of this chapter lists the most important root and tuber crops. This list has not changed. Those cultivated on a global scale include potato (Solanum tuberosum), cassava (Manihot esculenta), sweet potato (Ipomoea batatas), yams (Dioscorea spp.) and taro (Colocasia esculenta). Others that are of regional, national or local importance include, in total, over a dozen dicot and monocot families, most of which originated in tropical or subtropical areas. While they are mainly used as sources of carbohydrates, many minor root and tuber crops, such as turmeric (Curcuma longa) and arrowroot (Maranta arundinacea, Tacca leontopedaloides), are used in folk medicine and as spices (Sastrapradja et al. 1981).

All these crops are vegetatively propagated. There are many different types of plant material that can be used to propagate crops vegetatively, definitions and examples of which are given in the 1995 version of this chapter.

 

Collecting material

Site selection

In addition to the plant material used for propagation, the selection of the site where the plants are to be collected is very important. Selecting sites only along roads should be avoided. Selected sites should be well spread throughout the occurring (wild species) or the production (cultivated species) zones of the species. Some collecting sites should be also selected in the marginal production areas where rare varieties may be found, following Bressan et al. (2005), Clausen et al. (2005) and Pillai et al. (2000). With yam, for example, marginal areas include arid zones affected by drought, lowland rich regions and mountainous zones with gravelly soils normally not suitable for the production of this crop but where particular varieties adapted to these abiotic constraints are cultivated.

Documentation

To be of value, collected accessions should be well documented. For this, it is important to prepare a documentation sheet adapted to the species considered. Bioversity International has developed such collecting sheets for many crops (including roots and tubers). These sheets included in the crop descriptors, can be used as models. Multi-crop passport descriptors (Alercia et al. 2001) also exist and can be used. Descriptors for farmers’ knowledge of plants have also been recently developed by Bioversity International to provide a standard format for the gathering, storage, retrieval and exchange of farmers’ knowledge (Bioversity and The Christensen Fund 2009). Labelling (markers, plastic labels, etc.) and field handling materials (bags made with net, for example, for better airing) should also be prepared. Collecting sites should be georeferenced (latitude, longitude, altitude) using GPS.

Sampling

In a traditional farmer's field of a root or tuber crop, there will be a mixture of many different genotypes (e.g., Jackson et al. 1980), each being the result of intensive selection by farmers over many generations. Random sampling of such a field, the usual method for sexually reproducing species, is not appropriate, as it will over-represent abundant clones at the expense of rare ones. In regions such as West Africa, where there is a good association between names and diversity for some crops (yam, taro, cassava, etc.), a two-step procedure involving farmers at both the community and individual level is recommended.

First, an exhaustive inventory of the farmer-named varieties or morphotypes is made at village level and in groups of 40 to 60 farmers (depending on the size of the community) of different ages as older farmers have a better knowledge of the ancient varieties, while young farmers will be more knowledgeable about the novel varieties and uses. To carry out a correct inventory, an understanding of the folk nomenclature is sometime a prerequisite. A typical example is related to yam with the sociolinguistic group Yom in northern Benin. In that ethnic area, where single-harvest and double-harvest varieties of guinea yam (D. cayenensis and D. rotundata) and varieties of water yam (D. alata) are known under the generic names of “assina”, “noudouosse” and “kpatanga”, respectively (Dansi et al. 1997), a diversity inventory generally erroneously yields three varieties (instead of 20 to 60), which are nothing more than these three types of yam, if a detailed listing under each category is not requested from farmers.

Second, collect three to four propagules of each listed variety per site (e.g., village). Generally, at tuber-collecting time for some crops, such as potatoes and yam, there will be no above-ground parts visible to identify the variety or look for any morphological variation. Moreover, when farmers harvest the tubers, they gather them (mixed or separated) in barns. It is recommended that the propagules be collected from different farmers, and when possible, experienced farmers should be asked, in groups, to confirm the identities of the propagules before numbering them (e.g. collector number) and recording data on them. With species like yam, where two harvests are possible, the use of the terms “early-maturing” and “late-maturing” to distinguish single-harvest and double-harvest varieties should be avoided as it creates confusion: farmers differentiate early-maturing and late-maturing cultivars within the single-harvest and the double-harvest classes of yam. This process should be repeated at each sampling site.

Farmer’s knowledge

Local knowledge is crucial to the sampling process, just as it is crucial in deciding when and where to sample in the first place. Most farmers are aware of the extent of variation in their field, village and district, i.e., the number of distinct cultivars available in a given area, their names, appearance and characteristics. Documentation of varieties by individual farmers is good, but for accurate data collection, it is recommended that the documentation exercise be carried out with farmers in groups in order to avoid incorrect information. At each collecting site, the distribution and extent of each listed variety are among the crucial information to be documented; its compilation at the national level will indicate where and how common each farmer-named variety is across the country. This can easily be assessed using the Four Squares Analysis (FSA) approach described by Brush (2000), Tuan et al. (2003) and Dansi et al. (2008; 2010). At the community level, and based on two parameters (number of households and cultivated area), this method of participatory analysis helps to classify existing varieties into four groups: varieties cultivated by many households on large areas (++), varieties cultivated by many households on small areas (+ -), varieties cultivated by few households on large areas (- +) and varieties cultivated by few households on small areas (- -) (see table 21.1). To do this, varieties are individually taken and evaluated by farmers (in groups) using the first parameter (number of households). For this parameter, farmers are asked to indicate for each variety whether it is produced by many or few households. The same evaluation process is repeated for all the varieties for the second parameter (cultivated area). By combining the results of the two parameters, varieties can be classified into the different quadrants, and the results can immediately be presented to the farmers for comments and validation. Table 21.1 and figure 21.1 present, as examples, the results recently obtained on yam (Dioscorea rotundata) at Igboloudja (District of Ogou, Department of Plateau), a village of southern Togo (Dansi, unpublished).

Four-cell/square analysis is a powerful participatory tool to understand the amount (richness) and distribution (evenness) of crop diversity at the community level and socioeconomic rationale of them for community-based conservation actions. At the same time, this can be used to make decision as to which varieties to collect on priority basis. In the above example, the collector may assign higher priority to collect the varieties that are rare (occurring in the right hand bottom quadrant) as these are cultivated by few households and in small areas and hence are greatly threatened with genetic erosion. It is important to note that the time required to do the FSA depends on the number of varieties. Generally, the time available to collectors in any given location or site is relatively short, so to avoid wasting time, the process should be well understood by the collectors (some level of training in using the methodology is therefore required) and well explained to the local community.

In vitro collecting

Chapter 24 of the Technical Guidelines describes the concept of in vitro collecting, gives general guidelines and provides some examples. Two further examples are worth mentioning here, specifically that focus on root and tuber crops. The in vitro collecting method developed at the International Center for Tropical Agricultural (CIAT) for cassava consists in taking actively growing vegetative buds or terminal stem cuttings from branches without flowering buds. Explants of 1.0cm to 1.5cm are immersed in 70% ethanol for 5–15 minutes and then surface-sterilized by immersion in a 0.5% solution of calcium hypochlorite for 5 minutes. Finally, they are rinsed with cool boiled water. Explants are inoculated into semisolid culture medium (MS or 4E) containing an antibiotic such as rifampicin in a small wick of filter paper. In contrast, the in vitro methods tested at the International Potato Center (CIP) for sweet potatoes have so far not produced high rates of survival of the cultures. A simple method that has been partially successful consists of taking cuttings containing one node with axillary buds; they are surface-sterilized and introduced into a test tube containing 1ml of antibiotic solution (100ml distilled water + 0.025 g streptomycin). Particularly high losses due to contamination have been noticed in sweet potatoes with thin or very pubescent stems.

Table 21.1: List, Distribution and Extent of Yam (Dioscorea rotundata) Landraces Recorded at Igboloudja (South of Togo)

Double-harvest varieties	Households	Cultivated Areas	Single-harvest varieties	Households	Cultivated Areas
Afo Akoko Amoula Awonté Dendi Digbiri Dôdô Ewourou Fananan Gnidou Kangni Kodjéwé Laassiri Labôkô Lafia Lèkè Loumon Modji Oboti Ôkpè Sotouboua Tédji Yobèrè	+ – – – – – – – + + – – – + + – – + – – + – –	– – – – – – – – + + – – + – + – + + – + + – –	Arèkpè Bodé Gnarabo Karatchi Kôlor Korodjo Koukou Koukou foulani Kpakata Tchabigara Tchakatchaka Tchôkôyôkôtô	– – – + – – + – – – + –	– – – + – – + – – – + –

 

COMMON VARIETIES Varieties cultivated by many households on large areas (++)		COMMON BUT THREATENED VARIETIES Varieties cultivated by many households on small areas (+ –)
Fananan Gnidou Karatchi Koukou Lafia Modji Tchakatchaka Sotouboua		Afo Labôkô
RARE BUT NOT THREATENED VARIETIES Varieties cultivated by few households on large areas (– +)		RARE VARIETIES Varieties cultivated by few households on small areas (– –)
Laassiri Loumon Ôkpè		Akoko * Amoula* Arèkpè Awonté Bodé Dendi* Digbiri Dôdô Ewourou* Gnaranbo Kangni Kodjéwé	Kôlor Korodjo Koukou foulani Kpakata Lèkè Oboti Tchabigara Tchôkôyôkôtô* Tédji Yobèrè

Note: Newly introduced varieties are marked with an asterisk.

Figure 21.1: Diagrammatic representation of the classification of yam varieties into the four quadrants after the participatory evaluation at Igboloudja (south of Togo)

 

Future challenges/needs/gaps

Conservation of collected germplasm in the field

Various approaches exist for the conservation of the collected germplasm, among which is the field genebank. In field genebanks, the plant genetic resources (PGR) are kept as live plants that undergo continuous growth and require continuous maintenance. Field genebanks provide an easy and ready access to the PGR for characterization, evaluation or utilization (Saad and Ramanatha Rao 2001). However, a field genebank is generally expensive to maintain and has high levels of risk from natural disasters and adverse environmental conditions like drought, floods or attacks from pests and diseases (Engels and Visser 2003). When field genebank conservation is the only feasible option, careful planning and field management can help to mitigate the risks.

For cultivated species like cassava, taro and yam, in which synonymies are frequent, accessions of the same vernacular name may be planted side by side to facilitate observations. Before planting, some collected materials may be cleaned through treatment with a complex of insecticide, nematicide and fungicide to avoid attack by and /or propagation of pests and diseases. It is recommended that a minimum of five plants be maintained for each accession, as well as duplicate field genebanks in more than one site or an in vitro genebank as a safety backup (Reed et al. 2004). Best practices for establishing and managing a field genebank are described by Reed et al. (2004). Recently, the Global Crop Diversity Trust assisted many countries in regenerating and safely duplicating their root and tuber crop germplasm in another genebank, such as the one at the International Institute of Tropical Agriculture (IITA).

Information exchange

Effective sharing of information about the collected germplasm is important. For this, Bioversity and its partners have published several descriptor lists (www.bioversityinternational.org) to standardize the way plant resources should be documented. For Allium, banana, carrot, potato, sweet potato, taro, Xanthosoma and yam, such descriptors exist free of charge and should be used. Recently, FAO has developed a database named HORTIVAR (www.fao.org/hortivar/index.jsp) in which information on the performance of cultivars can be compiled for public use. Writing and publishing a comprehensive report on a collection mission – as Pillai et al. (2000) have done on taro, Adair et al. (2006) have done on Allium, and Nair and Sekharan (2009) have done with Saccharum – is recommended.

Morphological and genetic characterization

Morphological characterization should be carried out to identify morphotypes and cultivar groups. For the cultivated species in which synonymy exists, complementary participatory characterization and classification is recommended for correct establishment of the equivalence between vernacular names.
Some species, like yam, that are polyploid, require cytogenetic characterization by chromosome count and flow cytometry (Dansi et al. 2000, 2001, 2005).
When possible, molecular characterization should be also done for diversity assessment and duplicate identification. Details on the use of molecular markers in the management of PGR can be found in Karp et al. (1997) and Spooner et al. (2005), as well as for some species, such as cassava (Raji et al. 2009, yam (Siqueira et al. 2011) and taro (Mace et al. 2006). There are numerous specific publications in the literature that can serve as guides.

Conclusions

There are not many countries that have perfect germplasm collections of their root and tuber crops. Many root and tuber crop species are neglected, underutilized, absent or poorly represented in both national and international genebanks. Apart from the commonly cultivated species, the genetic variability of many root and tuber crops is seriously endangered, mainly due to environmental degradation and changes in agricultural practices. Their diversity can be preserved and used only if it is collected in time.

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References and further reading

Adair R, Johnson RC, Hellier B, Kaiser W. 2006. Collecting tapertip onion (Allium acuminatum Hook.) in the great basin using traditional and GIS methods. Native Plant Journal 7(2):141–148.

Alercia A, Diulgheroff S, Metz T. 2001. FAO/IPGRI multi-crop passport descriptors. International Plant Genetic Resources Institute (IPGRI), Rome. Available online (accessed 8 October 2011): www.bioversityinternational.org/nc/publications/publication/issue/faoipgri_multi_crop_passport_descriptors.html.

Bell AD. 1991. Plant Form: An Illustrated Guide to Flowering Plant Morphology. Oxford University Press, Oxford, UK.

Bioversity and The Christensen Fund. 2009. Descriptors for Farmers’ Knowledge of Plants. Bioversity International, Rome, and The Christensen Fund, Palo Alto, California. Available online (accessed 8 October 2011): www.bioversityinternational.org/nc/publications/publication/issue/descriptors_for_farmers_knowledge_of_plants.html.

Bradshaw JE, editor. 2010. Root and Tuber Crops. Handbook of Plant Breeding, Vol. 7. Springer Verlag, London.

Bressan EA, Veasey EA, Peroni N, Felipim AP, Santos KMP. 2005. Collecting yam (Dioscorea spp.) and sweet potato (Ipomoea batatas) germplasm in traditional agriculture small-holdings in the Vale do Ribeira, São Paulo, Brazil. Plant Genetic Resources Newsletter 144:8–13.

Brush SB, editor. 2000. Genes in the field: on-farm conservation of crop diversity. Boca Raton, Lewis Publishers, p 288

Clausen AM, Colavita M, Butzonitch I, Carranza AV. 2005. A potato collecting expedition in the province of Jujuy, Argentina and disease indexing of virus and fungus pathogens in Andean cultivars. Genetic Resources and Crop Evolution. 52(8):1099–1109. Available online (accessed 8 October 2011): www.springerlink.com/content/p2q2101253288938.

Dansi A, Zoundjihékpon J, Mignouna HD, Quin M. 1997. Collecte d'ignames cultivées du complexe Dioscorea cayenensis - rotundata au Bénin. Plant Genetic Resources Newsletter: 112, 81- 85

Dansi A, Pillay M, Mignouna HD, Daïnou O, Mondeil F, Moutaïrou K. 2000. Ploidy level of the cultivated yams (Dioscorea cayenensis / D. rotundata complex) from Benin Republic as determined by chromosome counting and flow cytometry. African Crop Science Journal 8(4):355–364.

Dansi A, Mignouna HD, Pillay M, Zok S. 2001. Ploidy variation in the cultivated yams (Dioscorea cayenensis-Dioscorea rotundata complex) from Cameroon as determined by flow cytometry. Euphytica 119:301–307.

Dansi A, Daïnou O, Agbangla, Ahanhanzo C, Brown S, Adoukonou-Sagbadja H. 2005. Ploidy level and nuclear DNA content of some accessions of water yam (Dioscorea alata) collected at Savè, a district of central Benin. Plant Genetic Resources Newsletter 144:20–23.

Dansi A, Adjatin A, Adoukonou-Sagbadja H, Faladé V, Yedomonhan H, Odou D, Dossou B. 2008. Traditional leafy vegetables and their use in the Benin Republic. Genetic Resources and Crop Evolution 55(8):1239–1256.

Dansi A, Adoukonou-Sagbadja H, Vodouhe R. 2010. Diversity, conservation and related wild species of Fonio millet (Digitaria spp.) in the northwest of Benin. Genetic Resources and Crop Evolution 57(6):827–839.

Engels JMM, Visser L, editors. 2003. A guide to effective management of germplasm collections. IPGRI Handbooks for Genebanks No. 6. International Plant Genetic Resources Institute (IPGRI), Rome. Click here to download this publication. (1.3 MB)

Jackson MT, Hawkes JG, Rowe PR. 1980. An ethnobotanical field study of primitive potato varieties in Peru. Euphytica 29:107–113.

Karp A, Kresovich S, Bhat KV, Ayad WG, Hodgkin T. 1997 Molecular Tools in Plant Genetic Resources Conservation: A Guide to the Technologies. IPGRI Technical Bulletin No. 2. International Plant Genetic Resources Institute (IPGRI), Rome. Available online (accessed 8 October 2011): http://pdf.usaid.gov/pdf_docs/PNACB166.pdf.

Mace ES, Mathur PN, Izquierdo L, Hunter D, Taylor MB, Singh D, DeLacy IH, Jackson GVH, Godwin ID. 2006. Rationalisation of taro germplasm collections in the Pacific Island region using SSR markers. Plant Genetic Resources 4:210–220

Nair NV, Sekharan S. 2009. Saccharum germplasm collection in Mizoram, India. SUGAR TECH 11(3):288–291. Available online (accessed 8 October 2011): www.springerlink.com/content/q54rq7784u846455.

Pillai SV, Nair PG, Thankamma PK, Hore DK. 2000. Collecting taro and other tuber crops from North Eastern Hill region of India. Indian Journal of Plant Genetic Resources 13(2): 159–162.

Raji AAJ, Anderson JV, Kolade OA, Ugwu CD, Dixon AGO, Ingelbrecht IL. 2009. Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC Plant Biology 2009, 9:118 . Available online (accessed 8 October2011): www.biomedcentral.com/1471-2229/9/118.

Reed BM, Engelmann F, Dulloo ME, Engels JMM. 2004. Technical guidelines for the management of field and in vitro germplasm collections. IPGRI Handbook for Genebanks No.7. International Plant Genetic Resources Institute (IPGRI), Rome. Click here to download this publication. (0.5 MB)

Saad MS, Ramanatha Rao V, editors. 2001 Establishment and management of field genebank: a training manual. IPGRI-APO, Serdang, Malaysia.

Sastrapradja S, Wilijarmi-Soetjipjo N, Donimihardja S, Soejono R. 1981. Root and Tuber Crops. International Board for Plant Genetic Resources (IBPGR), Rome.

Siqueira MVBM, Marconi TG, Bonatelli ML, Zucchi MI, Veasey EA. 2011. New microsatellite loci for water yam (Dioscorea alata, Dioscoreaceae) and cross-amplification for other Dioscorea species. American Journal of Botany 98(6):144–146.

Spooner DM, Van Treuren R, De Vicente MC. 2005. Molecular Markers for Genebank Management. IPGRI Technical Bulletin No. 10. International Plant Genetic Resources Institute (IPGRI), Rome.

Tootill E, editor. 1984. Dictionary of Botany. Penguin, London.

Tuan HD, Hue NN, Sthapit BR, Jarvis DI, editors. 2003. On-farm management of agricultural biodiversity in Vietnam. Proceedings of a symposium 6–12 December 2001, Hanoi, Vietnam. International Plant Genetic Resources Institute (IPGRI), Rome.

 

Internet resources

Descriptors for farmers’ knowledge: www.bioversityinternational.org/nc/publications/publication/issue/descriptors_for_farmers_knowledge_of_plants.html

HORTIVAR (Horticulture Cultivars Performance Database): www.fao.org/hortivar/index.jsp

Multi-crop passport descriptors: www.bioversityinternational.org/nc/publications/publication/issue/faoipgri_multi_crop_passport_descriptors.html.

 

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Chapter 40: Collecting DNA for conservation

M. C. de Vicente
Consultant Es Mercadal, Spain
E-mail: cdevicente(at)gmail.com

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This chapter is a synthesis of new knowledge, procedures, best practices and references for collecting plant diversity since the publication of the 1995 volume Collecting Plant Diversity: Technical Guidelines, edited by Luigi Guarino, V. Ramanatha Rao and Robert Reid, and published by CAB International on behalf of the International Plant Genetic Resources Institute (IPGRI) (now Bioversity International), the Food and Agriculture Organization of the United Nations (FAO), the World Conservation Union (IUCN) and the United Nations Environment Programme (UNEP). The 2011 update of the Technical Guidelines, edited by L. Guarino, V. Ramanatha Rao and E. Goldberg, has been made available courtesy of Bioversity International.

Please send any comments on this chapter using the Comments feature at the bottom of this page. If you wish to contribute new content or references on the subject please do so here.

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References for this chapter

Internet resources for this chapter

 

Abstract

	Preparing samples prior to storage in the tissue collection. Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Cali, Colombia. (Photo: Carlos Andres Tovar/Bioversity.)

There are increasing initiatives to collect DNA for conservation, either as a "back-up" to traditional ex situ collections, such as seed and tissue genebanks, or as samples generated from the application of genetic and genomic tools. A few concerted efforts have been made and nowadays DNA banks are not just in-house initiatives: some are open to hosting samples from different origins. Conservation of DNA is still a new way of collecting genetic resources, and the development of standard procedures is happening slowly. This chapter annotates key references that summarize the most up-to-date procedures and protocols for collecting DNA for conservation.

 

Introduction

Of all the types of material collected for conservation of diversity, DNA is undoubtedly the latest and likely the last. In the late 1980s molecular studies started an era of expansion, and soon conserving DNA for future research was identified as a sensible undertaking, given the cost and time involved in extracting DNA, no matter the project. Tests of viability of DNA samples kept at different temperatures and in different storage solutions were done routinely to ensure that further research, late verifications and even exchanges with collaborators would be possible. Then, in the early 2000s conserving DNA in general became an activity in itself.

After traditional collections of genetic resources, DNA banks provide a new resource for the ready availability of DNA with great potential for the characterization and utilization of biodiversity. The DNA molecule contains all the information necessary to make up any plant, but conserved DNA is not a direct resource for conservation, as DNA alone cannot contribute to the regeneration of biodiversity as seeds and other tissues can. The objectives of DNA collections are diverse. DNA is kept as a by-product of ongoing research and as the foundation of future research. DNA serves the study of the origin and evolution of species (including the effects of environmental factors). It helps in understanding biodiversity and analysing phylogenetic relationships. It complements taxonomic studies and helps define biodiversity conservation strategies. And it contributes to the investigation of population dynamics, and acts as a resource for biotechnological applications, among other things.

The scope of the Technical Guidelines, as published in 1995, was restricted to collecting material, but the conservation of DNA for banking, in addition to collection, involves operations such as extracting, storing, documenting, analysing and exchanging. Also, a DNA collection may include much more than just raw DNA: a DNA collection may store tissues, and DNA in the form of genetic and genomic resources, which are "identified" DNA sequences.

Similar to conventional collections, all DNA collections require the establishment of good practices and methods. However, because setting up DNA banks is a recent phenomenon in the conservation of genetic resources, collecting procedures for the development and maintenance of DNA banks are only slowly being documented and improved.

 

Current status

Generic advice for collecting plant material for DNA extraction and conservation is basically similar to that for plant tissues in general. Distinctive and essential advice for collecting material for DNA conservation is that the material must be high quality to guarantee good extraction, and the associated information must be correct and adequate. For a very recent and complete publication on collecting for DNA banking, see Gemeinholzer et al. (2010). This paper gives guidelines for all the tasks required for pre-DNA isolation of samples, from both plants and animals. It includes information about sampling strategies, methodological considerations for collecting different types of plant tissues, strategies for tissue preservation and DNA isolation in the field, relevant logistics and safety considerations in the field, labelling of samples and recording essential information, transportation practices from the field to the laboratory and necessary equipment. Preserving DNA samples both in the field and in the DNA bank, standardization of DNA quality and characterization, and hosting sample information is thoroughly covered by Walters and Hanner (2006).

A complementary publication on collecting DNA for conservation is the comprehensive review by Hodkinson et al. (2007). This paper contains information on collecting material – including the preparation of associated vouchers or maintenance of living collections, tissue banking as DNA-rich material, a compilation of DNA extraction methods, assessment of DNA quality and quantity, DNA storage conditions, documenting DNA banks, and considerations for DNA exchange. In view of the delay observed in the development of procedures for DNA collection, the authors claim that DNA banks should be integrated with other collection initiatives, such as botanic gardens and seed and genetic resources in general, which have developed appropriate protocols for curation and documentation. With this in mind, they review and illustrate DNA curation and management practices, following the different steps of bank operation.

Simple recommendations are summarized on the web page of the Department of Molecular Biodiversity and DNA Bank of the Botanic Garden "Viera y Clavijo" of the Canary Islands (www.bioclimac.com/mbdna/index.php?option=com_content&view=article&id=128&Itemid=220). It contains tips to set up a DNA bank, which cover the entire DNA banking operation: collecting and organizing samples, extracting and storing DNA and sample-exchange procedures, including a link to an example of sample-management policy.

 

Future challenges/needs/gaps

No matter the advances in DNA conservation, there are challenges – technical, infrastructural and legal – to be resolved for this conservation approach to become widespread and to benefit the genetic resources community from north to south.

From a technical point of view, the cost of DNA extraction and the consistency in obtaining high-quality material continue to be important limitations. While problems of consistency can largely be solved by the use of commercial kits amenable to different types of species and tissues, the cost of the extraction per sample remains the highest among collecting operations.

DNA extraction protocols that allow preservation at room temperature are extremely important, as they remove the necessity of equipment for cold storage. In developing countries, an added challenge is not only the availability of the appropriate infrastructure – including bioinformatics – but also the maintenance of that infrastructure, which is often the main obstacle to setting up a DNA bank. Perhaps it is because of the costs related to the infrastructure that developing countries lag behind in DNA conservation; however, regional collaborative initiatives could overcome some of these difficulties (Ebert et al. 2006). Therefore, an effort to communicate with the scientific communities in these countries could help to close the gap.

DNA storage has advanced in the private sector, where infrastructure and capacity – including funds – are optimal (Andersson et al. 2006). This could also be an indirect result of the legalities involved in DNA exchange, with issues pending in the public sector being much less relevant in the private sector.

Legal issues related to collecting, conserving and exchanging DNA are complex, perhaps even more complex than those that affect genetic resources in general. Graner et al. (2006) provide a simple account of ownership and intellectual property issues, both for DNA held in trust in a collection and for its products, following the International Treaty for Plant Genetic Resources for Food and Agriculture and the Trade Related Aspects of Intellectual Property Rights agreement of the World Trade Organization. In spite of several areas of confusion, current DNA banks are routinely exchanging DNA, taking care to observe the legal issues by using material transfer agreements.

Last, but not least, issues related to data standards, data curation and information retrieval and exchange are also pending. In the end, it is not the DNA, per se, that counts, but the access to the information it contains that will assure the use of genetic resources like DNA to the fullest – realizing the maximum benefit of DNA banks and their resources.

DNA banking may be considered to be in a beginning phase as compared with traditional methods of collecting and storing plant genetic resources, but in order to work towards a standardized set of procedures and best practices, it would be very helpful to compile a list of world DNA collections, to which one could refer for information and comparison. The task would require first defining what a "DNA collection" is and a "DNA bank", considering whether functions include DNA storage only or also hosting and sharing DNA. A DNA collection could exist in many modern laboratories that engage in genetic and genomic research, and they could exchange material samples among collaborators in similar projects. Other DNA collections might consider exchanging resources outside a close circle of collaborators. A DNA bank might host DNA samples from other laboratories and organizations, and it should offer to share samples with clients at large. Starting a list of collections should take these considerations into account. Once the criteria are clear, this list could focus first on official DNA collections linked to national collections of plant genetic resources (for example, those belonging to a national genebank, or those adjunct to botanical gardens and herbaria) and it could then be expanded to accommodate DNA collections of genomic resources.

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References and further reading

Andersson MS, Fuquen EM, de Vicente MC. 2006. State of the art of DNA storage: results of a worldwide survey. In: de Vicente MC, Andersson MS, editors. DNA Banks—Providing Novel Options for Genebanks? Topical Reviews in Agricultural Biodiversity. International Plant Genetic Resources Institute, Rome. pp.6–10. Available online (accessed 31 October 2011): http://cropgenebank.sgrp.cgiar.org/images/file/learning_space/dna_banks.pdf.

de Vicente MC, Andersson MS, editors. 2006. DNA Banks—Providing Novel Options for Genebanks? Topical Reviews in Agricultural Biodiversity. International Plant Genetic Resources Institute, Rome. Available online (accessed 31 October 2011): http://cropgenebank.sgrp.cgiar.org/images/file/learning_space/dna_banks.pdf.

Ebert AW, Karihaloo JL, Ferreira ME. 2006. Opportunities, limitations and needs for DNA banks. In: de Vicente MC, Andersson MS, editors. DNA Banks—Providing Novel Options for Genebanks? Topical Reviews in Agricultural Biodiversity. International Plant Genetic Resources Institute, Rome. pp.61–68. Available online (accessed 31 October 2011):  http://cropgenebank.sgrp.cgiar.org/images/file/learning_space/dna_banks.pdf.

Gemeinholzer B, Rey I, Weising K, Grundmann M, Muellner AN, Zetzsche H, Droege G, Seberg O, Petersen G, Rawson DM, Weigt LA. 2010. Organizing specimen and tissue preservation in the field for subsequent molecular analyses. In: Eymann J, Degreef J, Häuser C, Monje JC, Samyn Y, VandenSpiegel D, editors. ABC-Taxa, Volume 8. Manual on Field Recording Techniques and Protocols for All Taxa Biodiversity Inventories, Chapter 7. pp.129–157.

Graner A, Andersson MS, de Vicente MC. 2006. A model for DNA banking to enhance the management, distribution and use of ex situ stored PGR. In: de Vicente MC, Andersson MS, editors. DNA Banks—Providing Novel Options for Genebanks? Topical Reviews in Agricultural Biodiversity. International Plant Genetic Resources Institute, Rome. pp.69–76. Available online (accessed 31 October 2011):  http://cropgenebank.sgrp.cgiar.org/images/file/learning_space/dna_banks.pdf.

Hodkinson TR, Waldren S, Parnell JAN, Kelleher CT, Salamin K, Salamin N. 2007. DNA banking for plant breeding, biotechnology and biodiversity evaluation. Journal of Plant Research 120:17–29. Available online (accessed 31 October 2011): www.scribd.com/doc/45316957/DNA-Banking-for-Plant-Breeding.

Walters C, Hanner R. 2006. Platforms for DNA banking. In: de Vicente MC, Andersson MS, editors. DNA Banks—Providing Novel Options for Genebanks? Topical Reviews in Agricultural Biodiversity. International Plant Genetic Resources Institute, Rome. pp.25–35. Available online (accessed 31 October 2011):  http://cropgenebank.sgrp.cgiar.org/images/file/learning_space/dna_banks.pdf.

 

Internet resources

Australian Plant DNA Bank: www.dnabank.com.au

Berlin-Dahlem DNA Bank and its Database: www.bgbm.org/bgbm/research/dna

Department of Molecular Biodiversity & DNA Bank of the Canarian Flora: www.bioclimac.com/mbdna/index.php?option=com_content&view=article&id=128&Itemid=220

DNA Bank, Brazilian Flora Species: www.jbrj.gov.br/pesquisa/div_molecular/bancodna/sobre_ing.htm

DNA Bank Network: www.dnabank-network.org

Kew Royal Botanic Gardens, DNA Bank Database: http://data.kew.org/dnabank/homepage.html

NIAS DNA Bank, National Institute of Agrobiological Sciences: www.dna.affrc.go.jp

William L. Brown Center, Missouri Botanical Garden: www.wlbcenter.org/dna_banking.htm

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Chapter 42: Gap analysis: A tool for genetic conservation

N. Casteneda
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N. Maxted
School of Biological Sciences, University of Birmingham, UK
E-mail: nigel.maxted(at)dial.pipex.com

 

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