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Area of Science:

  • Agricultural Science
  • Plant Molecular Biology
  • Genomics

Background:

  • Cotton is a crucial oilseed crop, but its oil-related biosynthetic and regulatory pathways are understudied.
  • Upland cotton (Gossypium hirsutum L.) is an allopolyploid with two genomes (A/D), complicating gene expression analysis.

Purpose of the Study:

  • To conduct a global transcriptome analysis of cotton seed development.
  • To investigate genic and subgenomic patterns of expression, including homeologous gene contributions.
  • To identify key genes and pathways involved in oil and flavonoid biosynthesis during seed development.

Main Methods:

  • RNA sequencing (RNA-seq) was employed to analyze gene expression across four developmental time-points.
  • Expression data were partitioned to differentiate contributions from homeologous gene copies within the A and D genomes.
  • Co-expression network analysis and functional enrichment tests were performed to identify biological pathways.

Main Results:

  • The period between 20-30 days postanthesis (DPA) showed the most dynamic transcriptome changes, with approximately 20% of genes exhibiting homeolog expression bias.
  • Co-expression analysis revealed largely congruent homeolog networks, alongside instances of homeolog-specific divergence.
  • Flavonoid biosynthesis genes were enriched early in development, while lipid-related genes were prominent later. DGAT3 (diacylglycerol acyltransferase) was identified as a novel contributor to triglyceride synthesis.

Conclusions:

  • This study provides the first temporal analysis of duplicated gene expression in cotton seed development.
  • It offers a valuable resource for understanding novel aspects of oil and flavonoid biosynthetic processes in cotton.
  • The findings highlight the complex interplay of homeologous gene regulation in shaping seed composition.