## 3 Discussion  
### Identification of DEGs and DEPs  
RNA-Seq and iTRAQ methods have extensively been used to identify DEGs and DEPs involved in plant development and secondary metabolism. In recent years, many RNA-Seq studies have been widely conducted to investigate the transcriptional regulation in the resin yield of masson pine [36, 37, 38, 39, 40]. However, the application of iTRAQ-based proteomic analysis was relatively rare, so far, no report was available to explore the molecular regulatory mechanisms in resin yield of masson pine using these two approaches simultaneously. To better understand the molecular regulatory mechanisms of resin yield and to identify the key genes and pathways at the transcriptomic and proteomic levels, in this study, Iso-Seq, RNA-Seq, and iTRAQ were performed in parallel to investigate the DEGs and DEPs from needles of masson pine with the high and common resin yield. In total, 17,266 genes and 4566 proteins were quantified. However, a poor correlation (R < 0.40) was revealed between these quantified proteins and their corresponding mRNAs, consistent with the results of previous studies comparing protein and mRNA expression levels [41, 42, 43]. Notably, the correlation coefficient was higher between the expression levels of DEGs and DEPs (Figure 5), suggesting the involvement of consistency changes of DEGs and DEPs in resin yield in masson pine. Comparative analysis of DEGs and DEP revealed that a few genes were commonly regulated both at the transcriptomic and proteomic levels, indicating that the proteins showed significant expression changes and did not always have a corresponding change at the transcriptional level. The poor overlap between DEGs and DEPs also demonstrated that post-transcriptional regulation plays an important role in the resin yield of masson pine. Among these overlapped DEGs and DEPs, the functional categories were related to secondary metabolism biosynthesis, then followed by carbon metabolism, Calvin cycle, glycolysis, JA biosynthesis, and glutathione metabolism, indicating their involvement in the resin yield of masson pine.  
Many genes involved in carbohydrate metabolism among these overlapping DEGs and DEPs exhibited the same trend at the transcriptomic, proteomic and biochemical levels, indicating their contribution to the resin yield of masson pine. Previous studies on rubber trees showed that carbohydrate metabolism has a close relationship with rubber yield [44]. In masson pine, studies revealed that the resin-producing capacity reached highly significant levels in relation to soluble sugar content [45]. The results of sugar detection showed that sucrose was the most abundant sugar in the needles of masson pine, then followed by glucose and fructose, and these three soluble sugars accounted for 90% of all sugars. Compared with the common resin yield, the accumulation of more sucrose and glucose could provide more raw materials for resin biosynthesis in the high resin yield. Several key genes involved in carbohydrate metabolism, including _SUS_, referred to sucrose synthesis, _HXK_ and _PGK_ referred to glycolysis, and _PDH_ as well as _DLST_ referred to the TCA cycle, were significantly up-regulated at the transcriptomic and proteomic levels, indicating that the improvement of the expression levels of these key genes was beneficial to enhance the resin biosynthesis and increase the resin yield in masson pine.