Haplotype kinship for three populations of the Goettingen minipig

Abstract

-To overcome limitations of diversity measures applied to livestock breeds marker based estimations of kinship within and between populations were proposed. This concept was extended from the single locus consideration to chromosomal segments of a given length in Morgan. Algorithms for the derivation of haplotype kinship were suggested and the behaviour of marker based haplotype kinship was investigated theoretically. In the present study the results of the first practical application of this concept are presented. Full sib pairs of three subpopulations of the Goettingen minipig were genotyped for six chromosome segments. After haplotype reconstruction the haplotypes were compared and mean haplotype kinships were estimated within and between populations. Based on haplotype kinships a distance measure is proposed which is approximatively linear with the number of generations since fission. The haplotype kinship distances, the respective standard errors and the pedigree-based expected values are presented and are shown to reflect the true population history better than distances based on single-locus kinships. However the marker estimated haplotype kinship reveals variable among segments. This leads to high standard errors of the respective distances. Possible reasons for this phenomenon are discussed and a pedigree-based approach to correct for identical haplotypes which are not identical by descent is proposed. genetic diversity / short term phylogeny / kinship / haplotype kinship / identity by descent

Genetic diversity in an indigenous horse breed - implications for mating strategies and the control of future inbreeding

“…2006), no correlation between microsatellite‐based homozygosity and pedigree‐based inbreeding coefficients was found for FM horses. A very low accuracy was found for the regression of microsatellite marker‐based kinship on pedigree‐based kinship coefficients for a sample of the Göttingen minipig (Flury et al. 2007).…”