Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation...

Area of Science:

• Evolutionary genetics
• Molecular evolution
• Population genetics

Background:

• Parallel evolution, where similar traits arise independently in different populations adapting to similar environments, is a key indicator of natural selection.
• Understanding the molecular basis of adaptive evolution, particularly the genetic variants driving trait divergence, remains a significant challenge.

Purpose of the Study:

• To investigate the roles of copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) in gene expression differences between lake and river populations of the three-spined stickleback (Gasterosteus aculeatus).
• To identify specific genetic mechanisms, such as CNVs and cis-regulatory SNPs, that contribute to parallel adaptation to distinct habitats.

Main Methods:

• Genome-wide analysis of CNVs and SNPs in four pairs of lake and river stickleback populations.
• Correlation of gene copy number with gene expression levels to identify dosage effects of CNVs.
• Identification of expression quantitative trait SNPs (eSNPs) in cis-regulatory regions associated with gene expression variation.

Main Results:

• 135 gene CNVs were significantly associated with gene expression, indicating their role in dosage-dependent phenotypic variation and adaptation.
• CNV differentiation between lake and river populations influenced the expression of immune genes (cathepsin A, GIMAP7).
• 1,865 genes showed expression associations with SNPs in cis-regulatory regions (eSNPs), including a carboxypeptidase gene with differentiated alleles and expression.

Conclusions:

• CNVs and cis-regulatory SNPs are crucial sources of genetic variation that can alter gene expression.
• These genetic mechanisms provide substrates for adaptive evolution, potentially facilitating repeated adaptation to novel environments.