How many Garlics are there?
Gayle Volk, Adam Henk and Christopher Richards
View the complete scientific paper: Genetic Diversity among U.S. Garlic Clones as Detected Using AFLP Methods" (381 KB Adobe Acrobat file)
Garlic is botanically known as Allium sativum. Another described species, A. longicuspis, can be found in the wild in Central Asia and was once thought to be the living progenitor of A. sativum. USDA's National Plant Germplasm System (NPGS) maintains 193 main accessions of garlic at the Western Regional Plant Introduction Station (WRPIS) in Pullman, WA. One hundred eighteen of these accessions were provided by Barbara Hellier (collection curator) and included in our current study. There are many additional named garlic varieties that are available through growers nationwide. We included 75 commercially available varieties that were generously provided by Walt Lyons (www.thegarlicstore.com) and Tom Cloud (www.filareefarms.com).
In our dataset we included some accessions that had the same names but were obtained from different sources. Accessions duplicated in this manner were identified in tables and figures with an appended number on the name, for example 'Siberian-1' and 'Siberian-2'. We included these duplications to test if clones bearing the same name from two sources were genetically similar.
A description of our methods is detailed in our full-length publication. We briefly describe our methods and techniques in this summary. We extracted DNA from two tissue samples from garlic shoot tips within cloves from each of the 211 accessions, which gave us 422 samples. We then followed the standard AFLP protocol as described by Vos et al. (1995). After a series of treatments and digesting the DNA with enzymes that cut it into pieces, we had DNA fragments that we could separate by size on a large, thin gel. In Figure 1, DNA fingerprints of several garlic accessions are shown. One accession is represented by a column of bands. Banding patterns differed among samples. The rows of bands in this gel are all the same length. For some pairs of accessions, the band might be absent (white space), and in others, it may be present (black band). We selected 27 rows of bands (each row is called a locus- a position in the garlic genome) that we scored for all 422 samples. We felt confident scoring 27 rows of bands that were variable between samples, yet unambiguously black or white for all the samples. We determined whether a band was present or absent for each of the 27 loci in all the samples. We then made sure that the fingerprint assigned was identical for both of the two replicate DNA samples for a given garlic cultivar. For 158 samples, the scores were identical between the replicate samples for each cultivar. For the remaining 53 of the 211 cultivars, 26 of the 27 loci scores were in agreement between the two replicates. We considered that one locus to be a "missing data point". We performed a number of statistical analyses on these data to determine differences and similarities across cultivars in our dataset. These results will be presented in a detailed manner in our published paper. Here we concentrate on the results revealed by one of our figures.
We used the technique called a minimum spanning network that uses genetic distance to graphically illustrate genetic diversity among the complete set of 211 accessions (Figure 2). Genetic distance measures how closely related one individual clone is to another. This diagram shows similarity among the 211 accessions in our study. The length of the lines between nodes in Figure 2 reflects genetic distance. In some cases, connections among nodes create loops in the network where there are several "closest" relatives. In fact, the network is better thought of as a mobile in three dimensions that has been laid flat. This would explain why lines connecting nodes that appear far apart are linked in the two dimensional representation. The large ellipse in the center of the network represents accessions with many connections and appears to be the basal or most primitive group of accessions because of its similarity with an unrelated Allium species. The diameter of each node is proportional to the number of accessions in that group. We were able to identify garlic accessions that were unique, and the names of those accessions are written directly on Figure 2. Many of the clones, however, were clustered into genetically identical groups listed as lettered nodes in the network. The names of the clones that were assigned to a lettered node are listed in Table 1.
Overall, 64% of the WRPIS and 41% of the commercial accessions had some degree of duplication according to this method. Cultivars may differ at loci that we did not examine. Therefore, cultivars that we identified as belonging to the same group are genetically very similar (but statistically identical). We certainly DO NOT promote the renaming of known accessions since there could be genetic differences among cultivars that were not identified using our method.
Growers looking to maximize the diversity of accessions they are growing should select a clone from among nodes in the networks. Alternatively, if some growers know that accessions listed under group "F" and "G" grew and sell particularly well in their region, they may want to try other accessions that are assigned to those nodes. Finally, if planting stock for an accession listed under group "I" is unavailable, a grower could try to grow a differently named, yet genetically similar accession listed in the same group.
Our genetic analysis confirms previous observations of Pooler and Simon (1993), Ipek et al. (2003), and Al-Zahim et al. (1997) that A. longicuspis is indistinguishable from A. sativum and may not be an appropriate taxonomic entity. These data also provide some indication of the diversity of garlic lineages. There is substantial structure in the network that indicates the genetic origins of certain plant morphologies. An example of this is the split between hardneck (dark nodes) and softneck (white nodes) clones. These data suggest that the softneck neck type may have arisen out of a much broader hardneck pool of diversity. These kinds of analyses provide a framework for further studies on the domestication process but also for the development of forensic tools that can be used to provide the genetic identity of garlic clones.
Al-Zahim, H.J. Newbury and B.V. Ford-Lloyd. 1997. Classification of genetic variation in garlic (Allium sativum L.) revealed by RAPD. HortScience. 32:1102-1104.
Ipek, M., A. Ipek and P.W. Simon. 2003. Comparison of AFLPs, RAPD markers, and isozymes for diversity assessment of garlic and detection of putative duplicates in germplasm collections. J. Amer. Soc. Hort. Sci. 128:246-252.
Pooler, M.R. and P.W. Simon. 1993. Characterization and classification of isozyme and morphological variation in a diverse collection of garlic clones. Euphytica 68:121-130.
Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van de Lee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper and M. Zabeau. 1995. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407-4414.