Abstract
Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of FST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.
Highlights
Since ancient times, cattle have been an essential element in the subsistence of humankind because they have provided humans with food, clothing, and draught force
Using the multiple-tube approach, we were able to estimate the consensus genotypes for all forty-nine samples analysed for all nine microsatellite loci (Supplementary Materials, Table S1)
The quality of genotyping based on QI values differed between microsatellite loci, varying from QI = 0.965 in TGLA126 to QI = 0.991 in ETH225
Summary
Cattle have been an essential element in the subsistence of humankind because they have provided humans with food, clothing, and draught force. Most of the local breeds cannot compete with commercial breeds owing to their lower productivity and lack of adaptability to industrial production systems. This has led to a drastic decline in the population census size of the majority of the local breeds or to the extinction of several breeds [2]. Most of the local breeds are carriers of unique forms of variability associated with adaptations to geoclimatic conditions, desired milk composition, disease resistance, and other useful breed-related properties [3], which make them an invaluable source of genetic diversity for livestock management in the future [4,5]. A study of local breeds aimed at the identification of ancestral breed-specific genetic components is important for their conservation, sustainable breeding, and development
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