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Genome-wide population structure and evolutionary history of the Frizarta dairy sheep1

Published online by Cambridge University Press:  09 March 2017

A. Kominakis ,
A. L. Hager-Theodorides ,
A. Saridaki ,
G. Antonakos  and
G. Tsiamis
A. Kominakis
Affiliation:
Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
A. L. Hager-Theodorides*
Affiliation:
Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
A. Saridaki
Affiliation:
Department of Environmental and Natural Resources Management, University of Patras, Seferi 2, 30100 Agrinio, Greece
G. Antonakos
Affiliation:
Agricultural and Livestock Union of Western Greece, 13rd Km N.R. Agrinio-Ioannina, 30100 Lepenou, Greece
G. Tsiamis
Affiliation:
Department of Environmental and Natural Resources Management, University of Patras, Seferi 2, 30100 Agrinio, Greece
*
†E-mail: [email protected]
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Abstract

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals’ genomic relationships. The Wright’s fixation FST index was also employed to assess herds’ genetic homogeneity and to indirectly estimate past migration rates. The Wright’s fixation FIS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r2 and |Dʹ| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed’s formation was as high as 549, was then reduced to 463 in 1981 (end of the breed’s formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, FST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals’ genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.

Keywords

Livestocksingle nucleotide polymorphismlinkage disequilibriumeffective population sizegenomics
Type
Research Article
Information
animal , Volume 11 , Issue 10 , October 2017 , pp. 1680 - 1688
Copyright
© The Animal Consortium 2017 

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Footnotes

1

In memory of Associate Professor Zafeiris Abas.

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