Mapping recombination rate on the autosomal chromosomes based on the persistency of linkage disequilibrium phase among autochthonous beef cattle populations in Spain

Autor: A. González-Rodríguez, Pascual López-Buesa, Clara Díaz, J. J. Cañas-Álvarez, Juan Altarriba, Luis Varona, Jesus A. Baro, Jesús Piedrafita, E. F. Mouresan, Antonio Molina, Sebastián Munilla
Rok vydání: 2021
Předmět:
Zdroj: Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
Zaguán. Repositorio Digital de la Universidad de Zaragoza
instname
Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Frontiers in Genetics
Vol.10, no.1170
FAUBA Digital (UBA-FAUBA)
Universidad de Buenos Aires. Facultad de Agronomía
instacron:UBA-FAUBA
no.1170
Vol.10, no.1170 (2019)
Recercat. Dipósit de la Recerca de Catalunya
CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
Frontiers in Genetics, Vol 10 (2019)
Popis: Fil: Mouresan, Elena Flavia. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal. Zaragoza, España. Fil: González Rodríguez, Aldemar. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal. Zaragoza, España. Fil: Cañas Alvarez, Jhon J. Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments. Barcelona, España. Fil: Munilla Leguizamón, Sebastián. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal. Zaragoza, España. Fil: Altarriba, Juan. Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal. Zaragoza, España. Fil: Díaz, Clara. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA). Departamento de Mejora Genética Animal. Madrid, España. Fil: Baro, Jesus A. Instituto Agroalimentario de Aragón (IA2). Zaragoza, España. Fil: Molina, Antonio. Universidad de Valladolid. Departamento de Ciencias Agroforestales. Valladolid, España. In 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. tbls., grafs.
Databáze: OpenAIRE
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