Comparison of diversity parameters from SNP, microsatellites and pedigree records in the Lidia cattle breed

Abstract Genetic drift, loss of heterozygosity and decrease in genetic variability are consequences of high rates of inbreeding over generations.. High density single nucleotide polymorphisms arrays offered new possibilities to estimate inbreeding coefficients more accurately than those from pedigree records or microsatellites genotypes. In the present study different inbreeding coefficients were estimated and compared from SNP data: (1) runs of homozygosity of different length (>1Mb, > 4Mb, > 8Mb and > 16Mb), (2) inbreeding coefficients based on the observed vs . expected number of homozygous genotypes and (3) standardized observed homozygosity, from pedigree records and from three microsatellite derived diverse metrics. SNP inbreeding coefficients ranging from 0.14 to 0.26 and shown correlations ≥ 0.84 among them. The correlation among SNP and pedigree inbreeding coefficients was moderate ranged from 0.37 to 0.5 and low than the expected correlation. The limited pedigree depth of the Lidia cattle breed as revealed the average number of equivalent complete generations (5.5) probably explain that the higher correlation coefficient with pedigree records was with the runs of homozygosity of high length (>16Mb). Also, the absence of identity disequilibrium on our molecular data could explain the moderate correlation values (0.43–0.54 in absolute values) among microsatellite derived metrics and SNP inbreeding coefficients.