Linkage disequilibrium, persistence of phase, and effective population size in Spanish local beef cattle breeds assessed through a high-density single nucleotide polymorphism chip

J. J. Cañas-Álvarez, E. F. Mouresan, L. Varona, C. Díaz, A. Molina, J. A. Baro, J. Altarriba, M. J. Carabaño, J. Casellas, J. Piedrafita

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11 Citations (Scopus)

Abstract

© 2016 American Society of Animal Science. All rights reserved. Linkage disequilibrium (LD) and persistence of phase are fundamental approaches for exploring the genetic basis of economically important traits in cattle, including the identification of QTL for genomic selection and the estimation of effective population size (Ne) to determine the size of the training populations. In this study, we have used the Illumina BovineHD chip in 168 trios of 7 Spanish beef cattle breeds to obtain an overview of the magnitude of LD and the persistence of LD phase through the physical distance between markers. Also, we estimated the time of divergence based on the persistence of the LD phase and calculated past Ne from LD estimates using different alternatives to define the recombination rate. Estimates of average r2 (as a measure of LD) for adjacent markers were close to 0.52 in the 7 breeds and decreased with the distance between markers, although in long distances, some LD still remained (0.07 and 0.05 for markers 200 kb and 1 Mb apart, respectively). A panel with a lower boundary of 38,000 SNP would be necessary to launch a successful within-breed genomic selection program. Persistence of phase, measured as the pairwise correlations between estimates of r in 2 breeds at short distances (10 kb), was in the 0.89 to 0.94 range and decreased from 0.33 to 0.52 to a range of 0.01 to 0.08 when marker distance increased from 200 kb to 1 Mb, respectively. The magnitude of the persistence of phase between the Spanish beef breeds was similar to those found in dairy breeds. For across-breed genomic selection, the size of the SNP panels must be in the range of 50,000 to 83,000 SNP. Estimates of past Ne showed values ranging from 26 to 31 for 1 generation ago in all breeds. The divergence among breeds occurred between 129 and 207 generations ago. The results of this study are relevant for the future implementation of within- and across-breed genomic selection programs in the Spanish beef cattle populations. Our results suggest that a reduced subset of the SNP panel would be enough to achieve an adequate precision of the genomic predictions.
Original languageEnglish
Pages (from-to)2779-2788
JournalJournal of Animal Science
Volume94
Issue number7
DOIs
Publication statusPublished - 1 Jul 2016

Keywords

  • Beef breeds
  • Effective population size
  • High-density single nucleotide polymorphism chip
  • Linkage disequilibrium
  • Persistence of phase

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