Whole-Genome Sequencing-Based Population Genetic Analysis of Wild and Domestic Rabbit Breeds

Area of Science:

• Genomics
• Population Genetics
• Animal Science

Background:

• The European rabbit (Oryctolagus cuniculus) encompasses wild populations and diverse domesticated breeds.
• Intensive selective breeding has led to distinct forms and uses of domestic rabbits.
• Understanding the genetic interplay between wild and domestic European rabbits is crucial for conservation and breeding programs.

Purpose of the Study:

• To conduct an extensive whole-genome sequencing (WGS)-based population genomics study on wild European rabbit populations and select domestic breeds.
• To investigate genetic diversity, population structure, inbreeding, and signatures of selection.
• To identify genetic variants and regulatory elements associated with domestication.

Main Methods:

• Whole-genome sequencing (WGS) of multiple wild and domestic European rabbit populations.
• Application of various population genomics analytical methods.
• Analysis of genetic admixture, inbreeding levels (runs of homozygosity), fixed variants, and selection signatures.

Main Results:

• Wild and domestic European rabbit populations are genetically distinct, with evidence of admixture in French and Hungarian populations.
• Inbreeding was detected across populations, with one Hungarian subpopulation exhibiting excess runs of homozygosity.
• Numerous fixed variants were identified between domestic and wild groups, including two fixed at different alleles. Putatively selected regions, some intergenic, were enriched for transcription factor binding sites.

Conclusions:

• Domestic and wild European rabbits maintain distinct genetic identities, but gene flow occurs.
• Inbreeding and selection have shaped the genomes of different populations.
• Intergenic regions and regulatory elements, particularly transcription factor binding sites, may have played a significant role in rabbit domestication.
• The generated high-coverage genome sequences offer valuable resources for future population genetics research.