Allium Core collection

Author: E.R. Joachim Keller

General Information

The genus Allium has got an especially high level of consideration in our institute. Intensive studies were performed of all aspects of taxonomy including morphology (e .g. growth forms), anatomy (e. g. seed testa), cytology (e. g. karyograms), phenology and molecular markers (RFLP, AFLP, microsatellites, and ITS sequencing). These studies were done mainly on original material collected in the wild or from the local sites of their cultivation in case of old landraces. Garlic is an important part in IPK’s genebank collection. The material is maintained in two living collections in the field, one is the genebank collection proper containing 1500 accessions of Allium. In 2011, it included 460 garlics and 162 shallots. The other one is a taxonomic Allium reference collection (1750 accessions, 340 wild species). Allium species are stored as seeds in the genebank, when the plants are able to form seeds. This is not the case in garlic. Surveys on these collections can be found in the Genebank Information System [link]GBIS-I. Vouchers of this plant material are deposited in the [link]herbarium of IPK, which contains about 400,000 specimens of cultivated plants and their wild relatives from extra-tropical regions. It is one of the largest herbaria for cultivated plants in the world. In this herbarium, around 7,500 sheets of Allium can be found, amongst them many garlics and shallots.


Garlic and shallot collections in Europe

Europe has a long tradition of garlic and shallot utilization. Because of the cultural and climatic diversity of this continent, various forms of use and, hence, selection in different directions, garlic and shallot diversity is very high in Europe. This is represented by a whole set of garlic and shallot collections in Europe. Europe’s Allium germplasm maintenance is, like that of all the other crops, supervised and coordinated by the European Cooperative Programme for Crop Genetic Resources Networks ECP/GR, which is structured into working groups within thematic networks. The Allium Working Group is one of them. A crop-specific database is coordinated by this group, the European Allium Database EADB. Here all, who are interested in passport data and other information about garlic, shallots and other alliums, can get information.

What are core collections?

In large genebanks, it is not possible to treat all the material with the same intensity. Therefore, a part of the accessions is selected and arranged as a Core Collection.

The strategy to form core collections in order to facilitate the use of genebanks is one of the main actions in the FAO Global Plan of Actions agreed at the Leipzig Conference on June 17-23, 1996. There it is Activity 9: Expanding the characterization, evaluation and number of core collections to facilitate use.

This is not only useful for the internal management but also for a broader external use insofar, as various users are recommended to rely on the same material, which will increase comparability of results in science. There are various aspects and parameters to select a Core Collection. It may be that breeding questions determine the scope of the ensemble or a special character like interesting chemical constituents or disease resistances. It may also be the greatest diversity within a given taxon. This was the determining aspect for the selection of IPK’s Garlic Core collection.

 The following figure shows that it is evident that most of the material was introduced from original places. Some material was cultivated in other regions of the world (USA and southern hemisphere), where it was introduced rather recently. The material from botanic gardens was included in few cases only, when it was interesting for unique characters or as reference material already in use for research.

Germplasm maintenance at IPK genebank

Garlic is a crop which normally does not form seeds. It lost its fertility already long ago in its history. Although there have been some successful attempts to re-store fertility in the last years, and some more or less fertile material was found in Central Asia, the overwhelming part of garlic’s germplasm must be maintained vegetatively.


Similar situation is present in shallot, which is also only partly fertile, and the breeding of which is mainly based on clonal material. Therefore, the maintenance of garlic and shallot was performed in the past by means of cultivation gardens.


The main bulk of garlic accessions is cultivated in field plots, which are replanted every four years (upper pictures). However, the garlic core collection is replanted annually (pictures below). Shallots are planted in spring and harvested in late summer. The bulbs are stored over winter in cool places under the roofs of the buildings.


However, due to abiotic (unfavourable weather, flood etc.) and biotic factors (mainly virus diseases and fungi), the existence of such a field collection is endangered and a certain percentage of more susceptible accessions will disappear year by year.  Therefore, the IPK genebank maintains garlic also by means of modern biotechnological methods such as in vitro storage and cryopreservation. These methods provide the protection of the material against infection, elimination of viruses from the plants and long-term storage of shoot tips without genetic changes.

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Taxonomic affilitation and intraspecific structure of garlic and shallot


One of the most interesting results of the Allium research project is a novel proposal of the taxonomical structure of the genus Allium. In contrast to the formerly accepted four to seven subgenera, the new proposal covers 15 subgenera which belong to three evolutionary lines. This schema represent the phylogenetical interrelationships more clearly as it has been before. Garlic occupies its traditional place in the subgenus Allium [Allium group] section Allium. Also shallot belonging to the botanical species onion (Allium cepa L.) remains at its place in the system.

As a characteristic feature of the living world, diversity does not end at the species level. Infraspecific diversity requires as much attention as the higher taxonomical levels. Garlic and shallot breeding centres use living collections to characterize their material. Thus, there have been several attempts to classify in infraspecific groups.

Due to the large collection in the IPK genebank, garlic’s diversity can be very well documented here. The main approach has been endeavoured by Maaß and Klaas in 1995. They used isozymes and RAPD’s and summarized that in dendrograms. Good correlation was found between the molecular grouping and morphological characters.

the main results of the taxonomical research on garlic are:

1.   One of the main morphological characters of garlic is the gradual reduction of the generative part of the plant, beginning with the loss of fertility within the still existing flowers until to the total reduction of the scape, which corresponds to, spoken in agricultural terms, the loss of bolting.

2.   The garlic diversity consists of 5 main groups.

3.   The most original one, situated in the probable centre of origin, is the Longicuspis group. This group is based on the former separate species Allium longicuspis Regel, which is clearly a part of the garlic germplasm, and the botanical name at species level is, therefore, no longer valid.

4.   The groups can be distinguished by morphological and molecular markers, the correlation of which is sufficiently high.


 IPK’s terminology of the infraspecific taxa follows the approach of informal groups. Thus, the following groups are listed in the database: Longicuspis group, Pekinense group, Ophioscorodon group, Sativum group (here with two subgroups according to the bolting behaviour, which is an important agronomical character), Subtropical group.  

The infraspecific groups of the Isozym/RAPD classification according to Maaß and Klaas (1995) are explained here with respect to their correspondence to the morphological characterization:


The Longicuspis Group (I and IV)

Bolting and coiling scapes, small bulbils, numerous flowers with exserted anthers, inner filaments with two or four lateral teeth. Many accessions produce more or less fertile flowers in dependence on the wheather conditions. Ia and IVe correspond to Pooler & Simon’s ‘fertile, pollen-shedding ophioscorodon types’. Ic correspond to Pooler & Simon’s ‘yellow-anthered pollen sterile ophioscorodon types’. The description is in agreement with that of A. longiscuspis sensu Regel 1875 in Vvedensky (1935), Wendelbo (1971) and Kollmann (1984).


 The Pekinense Group

Not distinguishable with the markers so far used by Maaß & Klaas from the Longicuspis Group and localized in group IV b. Hight 40-75 cm, relatively broad leaves, non-coiling inflorescence stalk, few relatively large bulbils, a very long and often non-opening spathe.


 The Sativum Group (II)

IIa/b: Bolting and coiling (IIa corresponds to group V, IIb corresponds to group I according to Messiaen et al. [1993], bolting later than other groups, flowers do not open under our conditions). IIc/d: Incompletely or non-bolting (correspond to group III after Messiaen et al., [1993] and ‘non-bolting sativum’ type of Pooler & Simon [1993]).


 The Ophioscorodon Group (III)

Corresponds to group IV after Messiaen et al., (1993) and ‘early senescing, non fertile flowering type’ of Pooler & Simon (1993). Bolting and coiling, colour of spathes whitish-green, flowers often deformed, being four-merous instead of three-merous, inner filament usually with two lateral teeth, the outer with four, yellow anthers, sterile pollen, spathe remains closed in some types.


 V - Subtropical group

No bolting observed in our conditions (presumably because of too weak growth).

Morphological characters of garlic


Besides the molecular markers, morphological characters are still the main indicators for the infraspecific diversity. This is also true for garlic. IPK’s garlic specialists took part in the re-formulation of the descriptors of garlic, which are summarized, like for many other crop species, in a descriptor list, which is downloadable from the website of [link]Bioversity International under Descriptors for Allium spp. These descriptors are also the backbone for the characterization of the accessions in this database. Some deviations may, however, occur.

Bolting ability, an example of the morphological diversity

As an example, how the infraspecific grouping of garlic corresponds to its phylogeny, the bolting behaviour of the plants is described here. It is thought that garlic, during the history of its cultivation, lost gradually its generative reproduction strategy by permanent positive selection of the vegetatively most productive plants which are clearly those with smaller or no inflorescence stalk.

The inflorescence itself changed from structures with flowers and many small bulbils to a lower number of larger bulbils accompanied by total loss of flowers. Then, the stalk shortened more and more, ending finally in an inclusion of the inflorescence into the bulb. The bulbils appeared more and more clove-like. The resulting structure is then an irregular compound bulb with no separable inflorescences at all. One of the intermediate types of this evolutionary line is forming even bulbils in several, more than one, levels of the stalk.

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Morphological character of shallot

Morphological classification of shallot is much less documented. The main fact is that shallot forms a part of the genepool of Allium cepa and that fertile shallots may be freely crossed with onion. The mainly differing characters which are, however, not as suitable for sharp distinction are the branching tendency, the concomitant tendency of vegetative multiplication and tendency to lose ability to flower, which are connected with the clonal breeding strategy of shallot. At present, this border is more and more blurred by breeding of true seed shallots. At present, based on the existing slight differences, shallot is divided as Aggregatum Group from the onion proper (termed as Common Onion Group). There is some grouping within shallot into shallot s. st. and potato onion (also called multiplier onion). Some authors describe potato onion as being larger than shallot and possessing round or flat-round bulbs growing together in smaller groups. Shallots s. str., however, have elongated bulbs in dense clumps of higher bulb numbers (Fritsch & Friesen, 2002). Furthermore, there is a tunica formed from remainders of old scales, which remains longer in shallots than in potato onion and even persists during harvest (Gladis, 2002).

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