Gene retention, fractionation and subgenome differences in polyploid plants

Area of Science:

• Plant evolutionary biology
• Genomics
• Molecular evolution

Background:

• All plant species originate from ancient polyploids.
• Polyploidization is a significant driver of plant genome evolution, species divergence, and crop domestication.
• The evolutionary history of polyploidy in plants has led to hypotheses about mass extinctions, asexual reproduction epochs, and post-polyploidy lag times.

Purpose of the Study:

• To review the role of polyploidy in plant evolution, speciation, and crop domestication.
• To discuss gene fractionation, neofunctionalization, subfunctionalization, and dosage balance as mechanisms influencing gene content after duplication.
• To explain genome dominance, heterosis, and paralogue interference in allopolyploids, and present a foundational model for gene expression and vigor in wide hybrids.

Main Methods:

• Review of existing literature on plant polyploidy, genome evolution, and domestication.
• Analysis of mechanisms influencing gene retention and expression following polyploidization, including fractionation, neofunctionalization, subfunctionalization, and dosage balance.
• Discussion of epigenetic modifications, genome dominance, heterosis, and paralogue interference in allopolyploids.

Main Results:

• Polyploidization has occurred repeatedly in plant evolution and is vital for crop domestication.
• Fractionation, the loss of duplicate genes and regulatory elements, occurs after duplication, with varying retention rates for different gene categories.
• In allopolyploids, genetic differences lead to immediate subgenome dominance and heterosis, influenced by epigenetic modifications and paralogue interference.

Conclusions:

• Polyploidy is a fundamental process in plant evolution, impacting speciation and domestication.
• Mechanisms like subfunctionalization, neofunctionalization, and dosage balance shape gene content over evolutionary time.
• Genome dominance and heterosis are immediate, entangled phenomena in wide hybrids, with some evolutionary mechanisms acting immediately and others over longer periods.