# Unravelling the Molecular Regulation Mechanisms of Slow Ripening Trait in _Prunus persica_
## 3 Discussion
### Sequencing Results and Differential Expression Analysis  
All developmental stages of the NR and SR phenotypes were compared at the transcriptomic level. Even though significant differences between all developmental stages in NR phenotypes were expected, the transcriptomic results showed that the fruit mesocarp did not display such large differences between T2 and T3 (Figure 2A,B). These results were probably because this period corresponds to a reduction in fruit growth and seed development, and the beginning of lignification [4]. In the case of the transcriptomic information of SR, in T1, T2, and T3 the SR information was similar to that of NR, but in T7 significant differences were observed between NR and SR, where T7 SR samples seemed to be more similar to T2 and T3, respectively. These results suggest a stop in SR development between the T2 and T3 developmental stages (Figure 2A). It is possible that the absence of  
Figure 4: Validation of RNAseq results by qPCR. Comparison between normal and slow ripening expression profiles determined by RNAseq and qPCR of three differentially expressed candidate genes are displayed. The left axis represents the expression profile, in FPKM, of genes measured by RNAseq (bars). The right axis presents the relative expression profiles of genes measured by qPCR (lines). A Pearson correlation was calculated between the RNAseq and qPCR expression data and presented in each graph as the R value.  
_NAC072_ triggers an alteration in seed development or the lignification process; however, a detailed analysis of seed development could help us better understand why the slow ripening fruits stop their growth and how _NAC072_ is involved in this phenotype.  
Considering the differences between NR and SR, a total of 78 genes were differentially expressed in all developmental stages (Figure 2C), among them was _NAC072_. Four of these genes seemed to have a correlation with the slow ripening phenotype either due to their function or the metabolic pathway to which they belong. These genes were described as an \(\alpha\)-farnesene synthase, the transcription factor WRKY, and two auxin-related genes described as small auxin up RNA (SAUR), thus indicating a possible correlation with the _NAC072_ regulation pathway. Even though we expected to find other genes with the same expression pattern as _NAC072_ in this group, none of them presented exactly the same expression pattern.  
On the other hand, it is possible to identify a developmental stagnation of the slow ripening fruits that begins to be noticed in T3 (Figure 2D), when it is not possible to observe the enriched gene ontology terms of the cell wall remodeling enzymes. Neither gene ontology terms are observed for pigmentation or caroten synthesis in T7 for the slow ripening individuals, which agrees with the phenotypes observed in Figure 1A, where the normal ripening phenotype develops a change in pigmentation and fruit size accompanied by the softening process (Figure 1C). In contrast, the SR phenotype seems to be stopped in the middle of fruit development.