## 3 Application Examples
### Metabolic Diversity of Hairy Root Exudates and Genetic Diversity in Hyoscyamus niger  
One of the goals of studies of chemical diversity in plants is to assess the relationship between metabolic and genetic diversity. The results of a limited number of studies indicated that patterns of genetic and metabolic similarity may be incongruent [34; 35; 68]. The bioreactor designed in this work will facilitate comparison of root exudates and/or hairy root exudates for plant accessions with known genetic relationships. To demonstrate this approach on hairy root exudates of _Hyoscyamus niger_ (see Section 3.7), we determined pairwise Euclidean distances among normalized metabolic profiles of hairy root exudates of three varieties of \(H\). _niger_. To determine the effect of cultivation system on the composition of the exudates, we also determined the distances between metabolic profiles of each variety grown in bioreactors and in shaking flasks.  
\begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Accession** & **RT \({}^{*}\)** & \multicolumn{2}{c}{**Iran**} & \multicolumn{2}{c}{**Germany**} & \multicolumn{2}{c}{**Iraq**} \\
**Metabolite** & **Bioreactor** & **Flasks** & **Bioreactor** & **Flasks** & **Bioreactor** & **Flasks** \\ \hline Compound **1** & 3.6 & N.d. & \(224\pm 191\) & N.d. & N.d. & N.d. & N.d. \\ Compound **2** & 4.3 & \(41\pm 4\) & N.d. & \(41\pm 4\) & N.d. & N.d. & \(100\pm 125\) \\ Compound **3** & 6.1 & \(128\pm 18\) & \(20\pm 2\) & \(24\pm 1\) & \(32\pm 2\) & \(30\pm 4\) & \(41\pm 2\) \\ Compound **4** & 6.8 & \(12500 The results showed that the differences among accessions were of the same magnitude as differences due to cultivation conditions (Figure 10). To obtain a first insight into the relationship between metabolic profiles and genetic distances among plant accessions from which the hairy roots were derived, the third intron of the Tr2 gene was sequenced. Tr2 encodes tropinone reductase, which is involved in the synthesis of tropane alkaloids. The sequences were deposited in NCBI under Nos. MN017172 (accession Iraq), MN017173 (accession Iran), and MN017174 (accession Germany). The number of nucleotide differences per 1000 bp between the sequences from the accessions Iraq/Iran and Iraq/Germany were 21 and 23, respectively, while the accessions Iran and Germany differed in only 2 nucleotides. Thus the accessions Iran and Germany appeared more closely related than each of them to the accession Iraq. The similarity between sequences of a Tr2 gene of the accessions Iran and Germany was not reflected by the similarities of metabolic profiles of their hairy root exudates (Figure 10). Depending on cultivation conditions, the most similar profiles were Iraq/Germany and Iraq/Iran. The discrepancy between metabolic and genetic similarity is in line with the results of previous studies in other plant species [34; 35; 68]. In contrast, chemical profiles and microsatellite markers in _Citrus aurantium_ were correlated [69]. _Hyoscyamus niger_ is an attractive model to study the relationship between metabolic and genetic diversity in plants because it is a source of medicinally useful tropane alkaloids [70]. Attempts to produce tropane alkaloids in hairy root cultures of _Hyoscyamus niger_ began decades ago [71] yet nothing is known about the genetic variation within the species. The availability of small-scale, inexpensive bioreactors will allow for comprehensive sampling of metabolic diversity in hairy root cultures of _H. niger_, which will facilitate selection of accessions for production purposes and enable studies of the relationship between metabolic and genetic diversity in this medical plant.