Selection signatures and population dynamics of transposable elements in lima bean

Area of Science:

• Plant genetics and genomics
• Evolutionary biology
• Crop domestication

Background:

• Lima bean (Phaseolus lunatus L.) domestication occurred independently in Mesoamerican and Andean regions, offering a model for convergent evolution.
• Mechanisms of adaptation in lima bean landraces are not well understood, particularly the role of genetic elements beyond Single Nucleotide Polymorphisms (SNPs).
• Transposable Elements (TEs) have been largely overlooked in previous genetic analyses of lima bean domestication.

Purpose of the Study:

• To characterize genomic variation, including TEs and SNPs, in lima bean.
• To identify selective sweeps associated with variable TEs and predict candidate domestication genes.
• To understand the distinct genetic pathways of domestication in Mesoamerican and Andean gene pools.

Main Methods:

• Analysis of whole-genome sequencing data from 61 lima bean accessions.
• Characterization of a genomic variation database incorporating TEs and SNPs.
• Association of selective sweeps with variable TEs to identify candidate domestication genes.

Main Results:

• A small proportion of selected genes were shared between the Mesoamerican and Andean gene pools, indicating divergent domestication routes.
• Approximately 75% of TEs were found near genes, suggesting a significant role in influencing gene function during domestication.
• Genetic structure inferred from variable TEs correlated with SNP data, linking TE dynamics to lima bean's demographic history and adaptive evolution.

Conclusions:

• Lima bean domestication followed different genetic strategies in its major gene pools.
• Transposable elements are crucial genomic components that likely played a significant role in lima bean adaptation and domestication.
• This study provides a foundation for understanding TE-mediated evolution and identifying genes under selection in crop plants.