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Haplotype kinship for three populations of the Goettingen minipig

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...

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Autores principales: Flury, Christine, Weigend, Steffen, Ding, Xiangdong, Täubert, Helge, Simianer, Henner
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682835/
https://www.ncbi.nlm.nih.gov/pubmed/17306199
http://dx.doi.org/10.1186/1297-9686-39-2-159
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author Flury, Christine
Weigend, Steffen
Ding, Xiangdong
Täubert, Helge
Simianer, Henner
author_facet Flury, Christine
Weigend, Steffen
Ding, Xiangdong
Täubert, Helge
Simianer, Henner
author_sort Flury, Christine
collection PubMed
description 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.
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spelling pubmed-26828352009-05-16 Haplotype kinship for three populations of the Goettingen minipig Flury, Christine Weigend, Steffen Ding, Xiangdong Täubert, Helge Simianer, Henner Genet Sel Evol Research 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. BioMed Central 2007-02-17 /pmc/articles/PMC2682835/ /pubmed/17306199 http://dx.doi.org/10.1186/1297-9686-39-2-159 Text en Copyright © 2007 INRA, EDP Sciences
spellingShingle Research
Flury, Christine
Weigend, Steffen
Ding, Xiangdong
Täubert, Helge
Simianer, Henner
Haplotype kinship for three populations of the Goettingen minipig
title Haplotype kinship for three populations of the Goettingen minipig
title_full Haplotype kinship for three populations of the Goettingen minipig
title_fullStr Haplotype kinship for three populations of the Goettingen minipig
title_full_unstemmed Haplotype kinship for three populations of the Goettingen minipig
title_short Haplotype kinship for three populations of the Goettingen minipig
title_sort haplotype kinship for three populations of the goettingen minipig
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682835/
https://www.ncbi.nlm.nih.gov/pubmed/17306199
http://dx.doi.org/10.1186/1297-9686-39-2-159
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