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Published on: May 11, 2020
Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis
Eliana Valencia-Lozano1, Lisset Herrera-Isidrón2, Jorge Abraham Flores-López2
1Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico.
Abstract:
Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein-protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs-MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9-may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging.
Insights
Potato microtuber (MT) development involves complex gene regulation. This study identified key up-regulated genes in ribosomal proteins and cell cycle, alongside down-regulated genes in photosynthesis and hormone response, revealing molecular mechanisms for MT formation.
Area of Science:
- Plant Biotechnology
- Molecular Biology
- Genomics
Background:
- In vitro potato microtuber (MT) development is crucial for high-quality plant propagation.
- MT formation is influenced by environmental and chemical factors like photoperiod, sucrose, hormones, and osmotic stress.
- Previous research established a protocol for MT induction using sucrose, gelrite, and cytokinin (2iP) in darkness.
Purpose of the Study:
- To elucidate the molecular mechanisms underlying potato microtuber development.
- To identify key genes and pathways involved in MT formation through transcriptome-wide analysis.
Main Methods:
- Transcriptome-wide analysis was conducted to identify differentially expressed genes during MT development.
- Protein-protein interaction (PPI) network analyses were performed using the STRING database (v11.5).
- Identification and clustering of up- and down-regulated genes and proteins involved in MT formation.
Main Results:
- A total of 1715 genes were up-regulated and 1624 genes were down-regulated during MT development.
- PPI network analysis revealed 299 genes in 14 clusters, with significant enrichment in ribosomal proteins (RPs) and cell cycle (CC) proteins among up-regulated genes.
- Key up-regulated transcription factors (TFs) potentially involved include MYB43, TSF, bZIP27, bZIP43, HAT4, and WOX9.
- Down-regulated genes were predominantly associated with light and photosynthesis, hormone response, hormone-mediated signaling, and aging pathways.
Conclusions:
- The study reveals significant molecular reprogramming during potato microtuber development, involving coordinated regulation of ribosomal proteins, cell cycle progression, and transcription factors.
- Down-regulation of photosynthesis and hormone-related pathways suggests a shift towards storage and dormancy mechanisms.
- These findings provide insights into the genetic basis of potato microtuberization, aiding in the optimization of propagation protocols.
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