Short communicationOn the haplotype diversity along the genome in Spanish beef cattle populations
Introduction
The advent of massive genotyping technology has allowed the use of genomic information for genome-wide association studies –GWAS- (Bush and Moore, 2012) and for prediction of breeding values in Genomic Selection –GS- (Meuwissen et al., 2001). Both procedures make use of the linkage disequilibrium (LD) between causative mutations and neutral SNP markers. However, there is evidence that the structure of linkage disequilibrium is not homogeneous along the genome (Ardlie et al., 2002). In fact, the genome can be parsed into haplotype blocks of variable length, as described in human (Gabriel et al., 2002) and cattle (Mokry et al., 2014), caused by variability in the recombination rate across the genome (Myers et al., 2005). In general, the recombination rate is higher in the telomere regions of the chromosomes and lower near the centromere (Coop and Przeworski, 2007), but there is strong evidence of the presence of well-defined regions with a higher rate of recombination, denoted as recombination hotspots (Paigen and Petkov, 2010).
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Material and methods
The data used in this study comprised the BovineHD Beadchip genotypes of 171 trios (sire-dam-offspring) of seven beef cattle breeds (Asturiana de los Valles – AV-, N=25, Avileña - Negra Ibérica – ANI-, N=24, Bruna dels Pirineus – BP- N=25, Morucha –Mo-, N=25, Pirenaica –Pi-, N=24, Retinta – Re-, N=24 and Rubia Gallega –RG-, N=24). After filtering for mendelian error lower than 0.05 and individual and SNP call rate over 0.95, 707,307 SNP markers were considered.
First, we established the
Results and discussion
In first place, we analyzed the distribution of the number of SNPs present within genomic regions of 500 kb (Fig. 1a). We found that they followed an almost perfect Gaussian distribution with an average of 149.21 (±33.22) SNPs. This indirectly confirms the adequacy of SNP selection when the Bovine HD Beadchip was constructed. Moreover, the distribution of the number of haplotypes within these genomic regions had a mean of 253.94 (±69.34) and presented a positive skewness (0.0596) (Fig. 1b). This
Acknowledgements
The authors want to thank the AGL 2010–15903 grant from the Spanish government; the collaboration of Breed societies in collecting samples and the support of FEAGAS is also acknowledged. J. J. Cañas-Álvarez acknowledges the COLCIENCIAS support by the Francisco José de Caldas fellowship 497/2009 and A. González-Rodríguez acknowledges the financial support by the BES-2011-045434 fellowship.
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