Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa)

• Published in: Genomics (San Diego, Calif.) Vol. 115; no. 2; p. 110591
• Main Authors: Ros-Freixedes, R., Pena, R.N., Richart, C., Nadal, J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.03.2023
• Subjects: Admixture; Animals; Farms; Galliformes - genetics; Genetic homogenization; Genomics; Hybridisation; Selective sweeps; Skin; Wildlife management; Genetic homogenization; Wildlife management; Admixture; Hybridisation; Selective sweeps
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2023.110591

The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (FIS and FROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations. •Natural and artificial selection in partridges are sources of genome differentiation.•Wild and farm partridges had similar nucleotide diversity although their genomes were distinct.•We found higher heterozygosity and lower inbreeding coefficients in farm partridges.•Selective sweeps were enriched with genes that explain differences between wild and farm partridges.