Hard versus soft selective sweeps during domestication and improvement in soybean

Area of Science:

• Plant genetics
• Evolutionary biology
• Genomics

Background:

• Genome scans identify genetic adaptations during crop evolution.
• Soft sweeps (multiple allele selection) are under-studied in crop domestication.

Purpose of the Study:

• Systematically scan soybean genomes for both hard and soft selection sweeps.
• Identify genetic loci associated with soybean domestication and adaptation.

Main Methods:

• Utilized genome resequencing data from 302 wild and domesticated soybean accessions.
• Employed five widely used statistics to detect selection candidates under hard and soft sweeps.
• Assessed the detectability of sweeps using six known domestication-related genes as positive controls.

Main Results:

• Inferred hard sweeps were predominant in domesticated soybean, while soft sweeps were more prevalent in wild soybeans.
• Differentiation-based (FST) and LD-based (iHH) methods identified 66 shared candidate loci.
• No tested statistic successfully detected a previously documented soft sweep at the Dt1 gene.

Conclusions:

• The study provides a comprehensive scan for selection sweeps in soybean domestication.
• Identified candidate loci offer insights into the genetic basis of soybean domestication traits.
• Highlights the prevalence of different sweep types in wild versus domesticated soybeans and informs future crop adaptation research.