# Proteomic Landscape of the Mature Roots in a Rubber-Producing Grass _Taraxacum Kok-saghyz_
## 2 Results  
### Morphological Observation of Rubber Particles in the Main Roots of TKS  
Natural rubber in TKS is produced from the latex system of its enlarged roots, and the biomass of the main roots is important for rubber yield. Therefore, the mature 6-month TKS plants with flowers were selected to perform morphological analysis, and the enlarged main roots are highlighted (Figure 1A). The light microscope results revealed that the concentric rings of laticifers as specialized tubular vessels in roots can be detected, and the total number of laticifer vessels is about \(137\pm 32\) (\(n=20\)) in the main roots of 6M TKS. The brown rubber latex granules, known as the specific cytoplasm of laticifer cells, can be clearly detected in the areas of endodermis and cortex in phloem tissues from both the crosscutting and slitting slices of the main roots. All the laticifer cells were considered to originate from the initial cells of vascular cambium to secondary laticifers in paralleling rings (Figure 1B), and most of these laticifer cells seem to connect into tubular vessels in the main roots (Figure 1C). Ultrastructural investigation of rubber particles in TKS root at 6 months was conducted under a transmission electron microscope (TEM). Many spherical or ovoid-ellipsoid rubber particles, ranging from 50 nm to 2000 nm, were examined in the laticifer cells (Figure 1D). We noticed that most rubber particles have a diameter less than 200 nm; they are termed small rubber particles (SRPs). However, rubber particles with diameter larger than 400 nm are fewer in number; they are traditionally called large rubber particles (LRPs). These particles, including SRPs and LRPs, are surrounded by a monolayer membrane (Figure 1D), in which many enzymes related to NRB are anchored or combined with each other [33]. Establishment of a Visual Two-Dimensional Gel Electrophoresis (2-DE) Proteome Map and Mass Spectrometry (MS) Identification of High Abundance Proteins in Taraxacum Kok-saghyz (TKS) Roots  
To further obtain the protein accumulation profiling, the total proteins from the 6M TKS roots were extracted and performed 2-DE to separate the total proteins. Finally, a high-resolution 2-DE gel was obtained and a visual proteome map was established (Figure 2). In this reference 2-DE gel, \(428\pm 15\) protein spots, ranged from pH 4 to pH 7, were detected from three biological replicates (Figure S1). We manually excised all abundant protein spots from the 2-DE gel, and finally identified 371 protein species by MALDI TOF/TOF MS. These proteins occupied 84.38% volume of all the detected spots in the 2-DE gel and belonged to 231 gene products or named unique proteins (Table S1). We compared the theoretical and experimental ratios of molecular weight (M\(r\)) and isoelectric point (_p_l) of the 371 proteins identified from the 2-DE gel, and presented their ratios as radar axis labels (M\(r\) for radial value; _p_l ratio for annular value) in radial chart (Figure 3A). Most proteins showed similar radial and annular values, and their ratios for theoretical and experimental M\(r\) and _p_l are near line 1.0. However, some proteins demonstrated differentially experimental M\(r\) and _p_l values in the 2-DE gel (Figure 2). In the proteomics study based on 2-DE gel, they are called different protein isoforms or protein species. In this study, 90 unique proteins were identified from at least two different spots, and these proteins contained 229 spots in the 2-DE gel. Among them, 56 proteins were identified from 112 spots, and they contained two protein isoforms in the 2-DE gel. Twenty-two proteins had three isoforms, and nine proteins were determined from 36 spots with four isoforms (Table S2). There are three unique proteins containing five isoforms; they are aldolase (spots 305, 313, 314, 403 and 405),  
Figure 1: Morphological observation of the laticifer cells and rubber particles in the main roots of _Taraxacum Kok-saghyz_ (TKS). A six months old TKS plant and its main roots are highlighted (**A**).