title: Genetic diversity comparison of the DQA gene in European rabbit (Oryctolagus cuniculus) populations.
abstract: The European rabbit (Oryctolagus cuniculus) natural populations within the species native region, the Iberian Peninsula, are considered a reservoir of genetic diversity. Indeed, the Iberia was a Pleistocene refuge to the species and currently two subspecies are found in the peninsula (Oryctolagus cuniculus cuniculus and Oryctolagus cuniculus algirus). The genes of the major histocompatibility complex (MHC) have been substantially studied in wild populations due to their exceptional variability, believed to be pathogen driven. They play an important function as part of the adaptive immune system affecting the individual fitness and population viability. In this study, the MHC variability was assessed by analysing the exon 2 of the DQA gene in several European rabbit populations from Portugal, Spain and France and in domestic breeds. Twenty-eight DQA alleles were detected, among which 18 are described for the first time. The Iberian rabbit populations are well differentiated from the French population and domestic breeds. The Iberian populations retained the higher allelic diversity with the domestic breeds harbouring the lowest; in contrast, the DQA nucleotide diversity was higher in the French population. Signatures of positive selection were detected in four codons which are putative peptide-binding sites and have been previously detected in other mammals. The evolutionary relationships showed instances of trans-species polymorphism. Overall, our results suggest that the DQA in European rabbits is evolving under selection and genetic drift.
authors: CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
authors: Vanessa
authors: V
authors: Magalhães
authors: CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
authors: Joana
authors: J
authors: Abrantes
authors: CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
authors: Antonio Jesús
authors: AJ
authors: Munõz-Pajares
authors: CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal. pjesteves@cibio.up.pt.|Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal. pjesteves@cibio.up.pt.|Centro de Investigação em Tecnologias da Saúde (CITS), ISPN, CESPU, Gandra, Portugal. pjesteves@cibio.up.pt.
authors: Pedro J
authors: PJ
authors: Esteves
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D000818:Animals; D005060:Europe; D005091:Exons / Q000235:genetics*; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D000949:Histocompatibility Antigens Class II / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011817:Rabbits / Q000235:genetics*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods; D017386:Sequence Homology, Amino Acid
chemical_list: D000949:Histocompatibility Antigens Class II
keywords: European rabbit (Oryctolagus cuniculus); Genetic diversity; MHC-DQA; Population genetics