Domestication over Speciation in Allopolyploid Cotton Species: A Stronger Transcriptomic Pull

Area of Science:

• Genomics
• Plant Biology
• Molecular Evolution

Background:

• Cotton (genus Gossypium) has undergone multiple independent domestications for fiber production.
• The genomic underpinnings of these independent domestication events and their impact on fiber development are largely unknown.
• Understanding these processes can reveal how distinct evolutionary paths lead to similar crop phenotypes.

Purpose of the Study:

• To compare the transcriptomic effects of speciation and domestication in upland (G. hirsutum) and Pima (G. barbadense) cotton.
• To identify genomic targets and gene expression patterns shaped by independent domestication events.
• To investigate whether similar or distinct molecular mechanisms underlie the convergent evolution of cotton fiber.

Main Methods:

• Comparative transcriptome analysis of wild and domesticated G. hirsutum and G. barbadense.
• Differential gene expression analysis at four developmental timepoints (5, 10, 15, 20 days after flowering).
• Coexpression network analysis to assess gene interaction patterns and module functions.

Main Results:

• Extensive differential gene expression was observed between species, timepoints, and domestication states.
• Domestication had a more significant impact on the transcriptome than speciation between G. hirsutum and G. barbadense.
• While species-specific coexpression networks differed, some gene modules showed parallel domestication signatures in both lineages.

Conclusions:

• Independent domestication events in G. hirsutum and G. barbadense resulted in unique transcriptomic trajectories.
• Convergent evolution of similar fiber phenotypes was achieved through the parallel domestication of shared gene coexpression modules.
• These findings highlight the interplay between unique evolutionary paths and conserved molecular mechanisms in crop domestication.