Genet. Sel. Evol. 39 (2007) 159-179
DOI: 10.1051/gse:2006040

Haplotype kinship for three populations of the Goettingen minipig

Christine Flury^a, Steffen Weigend^b, Xiangdong Ding^a, Helge Täubert^a and Henner Simianer<sup>a

a</sup>  Institute of Animal Breeding and Genetics, Georg-August-University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany
^b  Institute for Animal Breeding, Federal Agricultural Research Centre (FAL), Hoeltystrasse 10, 31535 Neustadt-Mariensee, Germany

(Received 17 May 2006; accepted 9 November 2006; published online 17 February 2007)

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 sub-populations 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.

Key words: genetic diversity / short term phylogeny / kinship / haplotype kinship / identity by descent

Correspondence and reprints: cflury@gwdg.de

© INRA, EDP Sciences 2007