Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain
Mouresan, Elena F (Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal.)
González-Rodríguez, Aldemar (Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal.)
Cañas Álvarez, Jhon Jacobo (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Munilla, S. (Universidad de Buenos Aires. Departamento de Producción Animal)
Altarriba, Juan (Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal.)
Díaz, Clara (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (Espanya). Departamento de Mejora Genética Animal)
Baró, J. A. (Instituto Agroalimentario de Aragón)
Molina, A. (Universidad de Valladolid. Departamento de Ciencias Agroforestales)
Lopez-Buesa, P. (Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal.)
Piedrafita Arilla, Jesús (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Varona, L. (Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal.)

Date:	2019
Abstract:	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 gene ontology (GO) terms between the genes located in the genomic regions with estimates of the recombination rate over (or below) the 95 (or 5) percentile throughout the autosomal genome.
Grants:	Ministerio de Ciencia e Innovación BES-2011-045434 European Commission KBBE.2011.1.3-06
Note:	Altres ajuts: We thank the AGL 2010-15903 grant from the Spanish government and the KBBE.2011.1.3-06 project from the European Union's Seventh Framework. We also thank the Breed Societies for their collaboration in collecting samples. The support of FEAGAS is acknowledged. JC-Á acknowledges the COLCIENCIAS support by the Francisco José De Caldas Fellowship 497/2009, and AG-R acknowledges the financial support provided by the BES-2011-045434 fellowship.
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Vaques ; Recombination rate ; Linkage disequilibrium ; Beef cattle ; Multiple populations ; Gene ontology
Published in:	Frontiers in genetics, Vol. 10 (20 2019) , p. 1170, ISSN 1664-8021

DOI: 10.3389/fgene.2019.01170
PMID: 31824571

12 p, 3.0 MB

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