Comparative transcriptome provides insights into the selection adaptation between wild and farmed foxes

Area of Science:

• Genomics
• Animal Science
• Evolutionary Biology

Background:

• Farmed foxes (silver and blue) exhibit distinct physiological traits compared to their wild ancestors (arctic and red foxes).
• The molecular basis for these domestication-driven differences remains largely unknown.

Purpose of the Study:

• To identify genes influenced by human domestication in farmed foxes using transcriptomic data.
• To analyze selective pressures and sequence variations in genes related to fox domestication.

Main Methods:

• RNA sequencing (RNA-seq) was performed on pooled tissues from farmed arctic foxes (AF), blue foxes (BF), red foxes (RF), and silver foxes (SF).
• Comparative transcriptome analysis, including selection analysis and sequence-level examination of orthologous genes, was conducted.
• Functional enrichment analysis was used to identify biological processes associated with identified genes.

Main Results:

• High-quality transcriptome datasets were generated, yielding millions of clean reads and numerous unigenes for each fox species.
• Positive selection analysis identified 11 and 14 genes in AF vs. BF and RF vs. SF groups, respectively, including genes related to immunity (CFI, LRRIP1) and metabolism (ACO1, ACAD10).
• Sequence analysis of shared orthologous genes revealed potential artificial selection signatures in LEMD2, RRBP1, and IGBP1.

Conclusions:

• This study provides a valuable transcriptomic resource for understanding fox domestication.
• Identified genes offer insights into the genetic underpinnings of physiological changes during fox domestication.
• Findings can aid in future genetic studies and assisted breeding programs for foxes and other farmed animals.