Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the...

Area of Science:

• Genomics
• Plant Science
• Evolutionary Biology

Background:

• Common bean (Phaseolus vulgaris) domestication involved significant genetic and phenotypic changes.
• Understanding these changes requires analyzing genetic diversity and gene expression patterns.

Purpose of the Study:

• To compare nucleotide diversity and gene expression between wild and domesticated common bean accessions.
• To identify genes under selection during domestication and their functional roles.

Main Methods:

• RNA sequencing and de novo transcriptome assembly were used to analyze gene expression.
• Single nucleotide polymorphisms (SNPs) were identified to assess nucleotide diversity.
• Coexpression network analysis and demographic simulations were employed to study selection.

Main Results:

• Domestication caused a ~60% reduction in nucleotide diversity and altered gene expression by 18%.
• Nearly 50% of polymorphic contigs were fixed, and distinct gene coexpression network structures emerged.
• Selection affected 9% of genes, further reducing gene expression diversity by 26%.

Conclusions:

• Domestication profoundly impacted common bean's genetic makeup and gene expression, with selection playing a key role.
• Selection favored certain genes, although some loci related to stress response and morphology showed increased diversity in domesticated beans.