# Transcriptome Profiling of Powdery Mildew-Stressed ‘Yeniang No. 2’ Grapevine Reveals Differential Expression, Alternative Splicing, and the Identification of 1232 Annotated Novel Genes

## TL;DR

This study identifies genes and splicing events in grapevines infected with powdery mildew, revealing how the plant defends itself and offering tools for breeding resistant cultivars.

## Contribution

The study identifies 1232 novel genes and reveals transcriptomic changes in grapevines under powdery mildew stress, including alternative splicing and defense-related pathways.

## Key findings

- 1219 differentially expressed genes were identified, with 790 upregulated and 429 downregulated in response to powdery mildew.
- 1883 novel genes and 22,210 alternative splicing events were discovered, primarily involving skipped exons and intron retention.
- Key defense pathways activated include plant-pathogen interaction, phenylpropanoid biosynthesis, glutathione metabolism, and oxidative phosphorylation.

## Abstract

Background: The global transcriptome reprogramming in grapevines in response to powdery mildew remains poorly understood, despite its economic implications, especially the new cultivars. Methods: Thus, this study aimed to elucidate these changes through RNA sequencing in ‘Yeniang No. 2’ grapevine leaves infected with powdery mildew compared to healthy ones. Results: A total of six samples were subjected to transcriptome sequencing, resulting in 36.85 Gb of clean data. A minimum of 5.89 Gb of clean data was generated for each sample, with at least 92.24% of the clean data attaining a quality score of Q30. Clean reads from each sample were aligned to the designated reference genome. The mapping ratio varied between 88.77% and 89.66%. The high-quality sequencing data revealed 1219 differentially expressed genes (DEGs), of which the infection upregulated 790 and downregulated 429. Functional enrichment analyses revealed a significant activation of key defense-related pathways. These included plant–pathogen interaction, phenylpropanoid and flavonoid biosynthesis for creating antimicrobial compounds, glutathione metabolism for reducing oxidative stress, and oxidative phosphorylation for enhanced energy production. This indicates a coordinated, multi-faceted defense strategy. The study also uncovered a complex layer of post-transcriptional regulation, identifying 1883 novel genes and 22,210 alternative splicing events, primarily skipped exons and intron retention. Key hub proteins identified within interaction networks, along with these splicing changes, underscore a sophisticated defense involving transcriptional reprogramming and metabolic shifts. Conclusions: The genes and molecular markers discovered are valuable resources for marker-assisted breeding. Leveraging these findings, particularly hub genes and favorable splice variants, can accelerate the development of new grapevine cultivars with durable resistance to powdery mildew.