Comparative metabolite profiling in single and multiple bulb cultivars of shallot (Allium cepa L. Aggregatum group)

Tuk-Tuk and Sanren F1 are two shallot cultivars that exhibit divergent bulb multiplication traits. Tuk-Tuk typically produces one bulb. In contrast, Sanren F1 tends to produce multiple bulbs. This study used metabolomics during bulb development and harvesting. The objective of the study was to identify the metabolites that might affect the bulb multiplication of shallot. The initial samples of both cultivars were collected during the bulbs developmental stage i.e, 11 weeks after sowing (WAS), while the second sample was gathered during harvesting stage (16 WAS). The Proton Nuclear Magnetic Resonance (1H NMR) analysis was applied to freeze-dried shallot bulbs for metabolomics analysis. Multivariate analysis utilizing Principal Component Analysis (PCA) followed by Orthogonal Projections Discriminant Analysis (OPLS-DA) were conducted using MetaboAnalyst 5.0. The 1H NMR spectra revealed 28 putative metabolites. All data, including both cultivars during development and harvesting, was not clearly separated by PCA. However in the development stage, Sanren F1 was observed to have higher histidine than Tuk-Tuk, indicating the involvement of histidine kinase signaling system in the bulb multiplication. Hence, histidine kinase known for its role in the cytokinin signaling which contributing in the cell division regulation and may affect Sanren F1 bulb multiplication. Four metabolites i.e., sucrose, arginine, acetic acid, and myricetin were higher in Tuk-Tuk than Sanren F1, a cultivar tends to produce a single bulb. Valine, phenylalanine, formic acid, and α-linolenic acid were considerably higher in Sanren F1 than Tuk-Tuk during harvesting. There were also several metabolites with greater relative concentrations than the others. Though not all of those metabolites significantly differed amongst the examined cultivars, it was thought that they had an impact on bulb development. It would be of great interest to ascertain whether metabolites detected in Sanren F1 at higher levels have the potential to function as chemical markers for distinguishing shallot cultivars that are capable of producing multiple bulbs.