Mapping recombination rate on the autosomal chromosomes based on the persistency of linkage disequilibrium phase among autochthonous beef cattle populations in Spain
Mouresan, Elena Flavia. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal. Zaragoza, España.González Rodríguez, Aldemar. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal. Zaragoza, España.Cañas Alvarez, Jhon J. Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments. Barcelona, España.Munilla Leguizamón, Sebastián. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal. Zaragoza, España.Altarriba, Juan. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal. Zaragoza, España.Díaz, Clara. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA). Departamento de Mejora Genética Animal. Madrid, España.Baro, Jesus A. Instituto Agroalimentario de Aragón (IA2). Zaragoza, España.Molina, Antonio. Universidad de Valladolid. Departamento de Ciencias Agroforestales. Valladolid, España.12In organisms with sexual reproduction, genetic diversity, and genome evolution are governed by meiotic recombination caused by crossing-over, which is known to vary within the genome. In this study, we propose a simple method to estimate the recombination rate that makes use of the persistency of linkage disequilibrium (LD) phase among closely related populations. The biological material comprised 171 triplets (sire/ dam/offspring) from seven populations of autochthonous beef cattle in Spain (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta, and Rubia Gallega), which were genotyped for 777,962 SNPs with the BovineHD BeadChip. After standard quality filtering, we reconstructed the haplotype phases in the parental individuals and calculated the LD by the correlation -r- between each pair of markers that had a genetic distance smaller than 1 Mb. Subsequently, these correlations were used to calculate the persistency of LD phase between each pair of populations along the autosomal genome. Therefore, the distribution of the recombination rate along the genome can be inferred since the effect of the number of generations of divergence should be equivalent throughout the genome. In our study, the recombination rate was highest in the largest chromosomes and at the distal portion of the chromosomes. In addition, the persistency of LD phase was highly heterogeneous throughout the genome, with a ratio of 25.4 times between the estimates of the recombination rates from the genomic regions that had the highest (BTA18-7.1 Mb) and the lowest (BTA12- 42.4 Mb) estimates. Finally, an over representation enrichment analysis (ORA) showed differences in the enriched gene ontology (GO) terms between the genes located in the genomic regions with estimates of the recombination rate over (or below) the 95th (or 5th) percentile throughout the autosomal genome
