Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust...

Area of Science:

• Plant Biology
• Genomics
• Biotechnology

Background:

• Sorghum bicolor is a vital crop for biofuel and biopolymer production due to its deep-rooted, stress-tolerant nature.
• The sorghum stem is a rich source of lignocellulosic biomass and soluble sugars, making it a prime bioenergy feedstock.
• Limited genome-wide studies exist on functional gene dynamics across sorghum organs and developmental stages, hindering targeted engineering.

Purpose of the Study:

• To identify genes with stem-preferential expression and their regulatory elements in Sorghum bicolor.
• To understand the functional dynamics and regulatory networks governing stem development across different stages and genotypes.
• To discover candidate genes for genetic engineering to enhance sorghum stem biomass and composition.

Main Methods:

• Reanalysis of a published RNA-sequencing dataset to identify organ-preferential gene expression.
• Inference of organ functions based on gene expression patterns across developmental stages.
• Gene regulatory network analysis to identify key transcription factors and their roles in stem development.

Main Results:

• Sorghum stems display distinct temporal functional signatures linked to stem-specific gene dynamics.
• A set of genes with ubiquitous stem-specific expression across genotypes was identified, indicating broad applicability.
• SbTALE03 and SbTALE04 were validated as stem hub transcription factors crucial for stem development regulation.

Conclusions:

• This study provides a genome-wide perspective on sorghum stem gene expression and regulatory networks.
• Identified core stem-specific genes, including validated transcription factors, offer targets for improving sorghum stem biomass.
• The findings support further research into genetic engineering for enhanced bioenergy feedstock development in sorghum.