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Integrated Differential Expression Analysis and WGCNA Identify Hub Genes Underlying Cotton Plant Height Development.

Ruiqiang Qi¹, Juwu Gong^1,2, Yangming Liu²

¹Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China.

International Journal of Molecular Sciences

|June 12, 2026

Summary

This study identifies key genes regulating cotton plant height by analyzing gene expression in two recombinant inbred line populations. Findings reveal molecular pathways controlling stem elongation, offering insights for improving cotton architecture.

Keywords:

WGCNA dynamic development hub genes plant height transcriptome

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Area of Science:

Plant genetics and molecular biology
Agronomy and crop science

Background:

Plant height is a crucial trait for cotton architecture and harvestability.
The molecular basis of dynamic plant height development in cotton is not well understood.

Purpose of the Study:

To identify molecular mechanisms and hub genes regulating cotton plant height.
To characterize pathways governing stem elongation across different growth stages.

Main Methods:

Developed two recombinant inbred line (RIL) populations for genetic analysis.
Performed transcriptome sequencing on tall and short extreme lines.
Integrated differential gene expression analysis with weighted gene co-expression network analysis (WGCNA).

Main Results:

Identified 15,052 differentially expressed genes (DEGs) with stage- and population-specific patterns.
WGCNA revealed 25 gene modules, with green and yellow modules positively correlated with plant height.
Seven hub genes were identified, potentially crucial for plant height development, enriched in hormone regulation and transport pathways.

Conclusions:

This research provides valuable genetic resources and a theoretical foundation for cotton plant height gene functional validation.
The identified hub genes and pathways offer targets for improving cotton plant architecture and agronomic traits.