Copy Number Variation Shapes Structural Genomic Diversity Associated With Ecological Adaptation in the Wild Tomato...

Area of Science:

• Plant genomics
• Evolutionary biology
• Population genetics

Background:

• Copy Number Variation (CNV) significantly impacts plant genetic diversity and adaptation.
• Understanding CNVs in wild relatives is crucial for crop improvement.
• The role of CNVs in adaptation of wild tomato species remains largely unexplored.

Purpose of the Study:

• To characterize the CNV landscape in Solanum chilense, a wild tomato species.
• To identify genes associated with adaptation through CNVs at the population level.
• To investigate the evolutionary dynamics and environmental associations of CNVs in S. chilense.

Main Methods:

• Whole-genome short-read sequencing of 35 S. chilense individuals from 7 populations.
• Identification and analysis of Copy Number Variations (deletions and duplications).
• Integration of CNV data with single-nucleotide polymorphism (SNP) analysis and environmental variables.

Main Results:

• Discovery of 212,207 CNVs (160,926 deletions, 51,281 duplications) in S. chilense.
• Higher CNV frequency observed in populations from stressful habitats.
• Identification of 3,539 candidate genes with divergent CNV profiles, associated with abiotic stress response and flowering time.

Conclusions:

• CNVs in S. chilense reflect historical demographic events and recent colonization.
• Gene copy number changes are linked to adaptation to contrasting habitats and climatic variables.
• Natural selection has likely shaped CNV patterns in stress-response genes, facilitating adaptation and range expansion.