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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01170

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

 Elena F. Mouresan1,  Aldemar González-Rodríguez1, Jhon J. Cañas-Álvarez2,  SEBASTIAN MUNILLA LEGUIZAMON1, 3, Juan Altarriba1,  Clara Diaz4,  Jesús A. Baro5, Antonio Molina6, Pascual Lopez-Buesa1, Jesús Piedrafita2 and  Luis Varona1*
  • 1University of Zaragoza, Spain
  • 2Autonomous University of Barcelona, Spain
  • 3University of Buenos Aires, Argentina
  • 4Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Spain
  • 5University of Valladolid, Spain
  • 6Universidad de Córdoba, Spain

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 < 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 overrepresentation enrichment analysis (ORA) showed differences in the enriched 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.

Keywords: Linkage Disequilibrium, beef cattle, Recombination rate, Multiple populations, gene ontology

Received: 16 Nov 2018; Accepted: 23 Oct 2019.

Copyright: © 2019 Mouresan, González-Rodríguez, Cañas-Álvarez, MUNILLA LEGUIZAMON, Altarriba, Diaz, Baro, Molina, Lopez-Buesa, Piedrafita and Varona. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Luis Varona, University of Zaragoza, Zaragoza, 50009, Aragon, Spain, lvarona@unizar.es