Prospects for whole genome sequencing of ancient Finnish cattle

Genetic diversity and population structure of prehistorical and historical cattle populations have been typically investigated by analyzing partial D-loop of mitochondrial DNA and Y-chromosomal DNA-markers. However, autosomal nuclear markers would offer more detailed information on ancient animals t...

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Bibliographic Details
Published in:Journal of animal science 2016-09, Vol.94, p.105-105
Main Authors: Weldenegodguad, M B, Sarkissian, C Der, Bläuer, A, Pokharel, K, Taavitsainen, J P, Orlando, L, Kantanen, J
Format: Article
Language:English
Subjects:
Animal populations
Animals
Bones
Bovidae
Cattle
Deoxyribonucleic acid
DNA
DNA damage
DNA sequencing
Excavation
Genetic diversity
Genetics
Genomes
Historical metallurgy
Historical structures
Livestock
Markers
Mitochondrial DNA
Nucleotide sequence
Population genetics
Population structure
Prehistoric era
Y chromosomes
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Summary:Genetic diversity and population structure of prehistorical and historical cattle populations have been typically investigated by analyzing partial D-loop of mitochondrial DNA and Y-chromosomal DNA-markers. However, autosomal nuclear markers would offer more detailed information on ancient animals than uniparentally inherited markers. By comparing ancient animals with modern animals one could also investigate temporal changes in genetic diversity occurred through different time periods. We have applied the next generation sequencing (NGS) technology to decipher for the first time genome sequences of ancient cattle specimens in Finland. Four ancient cattle bones from three different excavation sites were selected for the sequencing study. We successfully extracted the DNA and built indexed Ulumina libraries from ancient DNA extracts from 2 specimens: a sample of Late Iron Age Western Finland (coded as 'Mulli-2r; approximately 1200 y old) and that of Medieval Eastern Finland ('Viipuri-4'; approximately 500 y old). Shallow sequencing revealed minimal proportions of reads aligning uniquely against the cattle reference genome, providing ≤ 0.1X genome coverage. Read alignments showed typical DNA damage signatures, consisting of an excess of "C→T and G→A transitions" toward read termini. This pleads in favor of the sequence authenticity. Further sequencing aimed at recovering the whole genome sequence is ongoing, but the data already available, especially at sites overlapping the OMIA database, revealed for example the presence of disease-related allele in ancient Finnish cattle. As this is absent in contemporary breeds, this suggests possible recent genetic changes in the Finnish livestock.
ISSN:0021-8812
1525-3163