Profiling of Key Hub Genes Using a Two-State Weighted Gene Co-Expression Network of 'Jao Khao' Rice under Soil...

Area of Science:

• Plant Biology
• Molecular Biology
• Genomics

Background:

• Soil salinization threatens global agriculture, necessitating the development of salt-tolerant crops.
• Identifying molecular mechanisms of salt tolerance in rice is crucial for breeding resilient varieties.
• Understanding early stress responses can reveal key genetic targets for improving crop survival in saline conditions.

Purpose of the Study:

• To investigate the time-course transcriptome of a salt-tolerant Thai rice variety ('Jao Khao') under salinity stress.
• To identify key genes and molecular pathways involved in the early salt stress response using RNA-sequencing and co-expression network analysis.
• To provide candidate genes for enhancing salt tolerance in rice breeding programs.

Main Methods:

• RNA-sequencing (RNA-Seq) was performed on 'Jao Khao' rice leaves sampled over 48 hours under normal and saline (160 mM NaCl) conditions.
• Time-series transcriptome analysis, differential gene expression analysis, and weighted gene co-expression network analysis (WGCNA) were employed.
• Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to validate the expression of key genes.

Main Results:

• 'Jao Khao' demonstrated high salt tolerance with stable physiological parameters under saline conditions.
• 111 key hub genes were identified from 1,950 highly variable genes, enriched in pathways related to ATP-driven transport, light reactions, ATP synthesis, and carbon fixation.
• Early upregulation of energy metabolism genes, including RuBisCo and ATP synthase, was observed during the initial salt stress response.
• Differential gene expression analysis revealed significant changes in gene activity within the first 48 hours of salt exposure.

Conclusions:

• The study highlights the critical role of energy metabolism management in the early stages of plant salt stress response.
• Key genes involved in energy production and utilization are crucial for conferring salt tolerance in rice.
• The identified hub genes represent promising targets for genetic engineering and breeding strategies to enhance rice salt tolerance.