Graph-based pangenome reveals structural variation dynamics during cucumber breeding.

Area of Science:

• Plant genomics
• Population genetics
• Bioinformatics

Background:

• Structural variants (SVs) are a key but understudied aspect of plant genome diversity.
• Understanding SVs is crucial for crop improvement and breeding strategies.

Purpose of the Study:

• To construct a graph-based cucumber pangenome to analyze structural variant diversity.
• To investigate the dynamics of SVs during cucumber domestication and geographical expansion.
• To assess the impact of SVs on agronomically important traits and genomic prediction.

Main Methods:

• Construction of a graph-based pangenome using 39 high-quality cucumber genomes.
• Identification and genotyping of 171,892 high-confidence structural variants across 447 accessions.
• Comparative analysis of SVs and single nucleotide polymorphisms (SNPs) during domestication and expansion.
• Integration of SV burden into genomic prediction models.

Main Results:

• The cucumber pangenome captured extensive SV diversity.
• SVs were purged during domestication, unlike mildly deleterious SNPs, indicating their highly deleterious nature.
• Geographical expansion showed reduced SV burden and younger SVs, suggesting strong purifying selection.
• Introgressions from wild relatives increased SV burden.
• Incorporating SV burden improved prediction accuracy for agronomically important traits.

Conclusions:

• Structural variants play a significant role in cucumber genome evolution and domestication.
• Purifying selection strongly acts on SVs during population expansion.
• SV burden is a valuable factor for improving genomic prediction models in cucumber breeding.