Structural Variation and 3D Genome-Driven DNA/RNA Methylation Divergence Contributing to Cotton Fiber Domestication

Area of Science:

• Genomics
• Epigenetics
• Plant Biology

Background:

• Cotton domestication enhanced fiber quality through unknown mechanisms.
• The roles of structural variations (SVs), 3D genome architecture, and epigenetic regulation in cotton domestication are poorly understood.

Purpose of the Study:

• To investigate the integrative roles of SVs, 3D genome architecture, and epigenetic regulation in cotton fiber domestication.
• To elucidate the regulatory network connecting SVs, genome architecture, epigenetics, and gene expression in cotton.

Main Methods:

• Genome assembly of wild (yucatanense) and cultivated (Xinluzao 61) cotton.
• Identification of structural variations (InDels, inversions) and differential methylation regions (DNA and RNA).
• Construction of an ultra-dense genetic map and quantitative trait loci (QTL) mapping.

Main Results:

• 86.6% of SVs were found in differential topologically associating domain regions, indicating SVs remodel 3D genome architecture.
• Millions of differential DNA and RNA methylation loci were identified, affecting nearly half of differentially expressed genes.
• SV-associated methylation changes had a stronger impact on gene expression than epigenetic modifications alone.
• SVs and 3D genome remodeling-driven methylation divergence contribute to increased fiber length in domesticated cotton.

Conclusions:

• The study elucidates a crucial "SVs-3D genome remodeling-epigenetic modifications-gene expression" cascade regulatory network in cotton fiber domestication.
• Findings provide a theoretical foundation and genetic resources for molecular design breeding in fiber crops.
• Structural variations play a pivotal role in reshaping trait variation during crop domestication.