Population structure and genetic diversity of sheep breeds in the Kyrgyzstan

Sheep are a main livestock species of Kyrgyzstan, a Central Asian country
with predominating mountain terrain. The current gene pool of local sheep
resources has been forming under diverse climate conditions from the era
of the trading caravans of the Great Silk Road, through the Soviet period
of large-scale livestock improvements, which was followed by the deep
crisis at the end of the 20th century, up to now. However, not much is
known about the genetic background and variability of the local sheep
populations. Therefore, our aims were to provide a characterization of the
population structure and genetic relations within the Kyrgyz sheep breeds
and to study their genetic connections with the global sheep breeds using
SNP analysis. Samples of the Alai (n=31), Gissar (n=30), Kyrgyz coarse
wool (n=13), Aykol (n=31), and Tien-Shan (n=24) breeds were genotyped with
the OvineSNP50 BeadChip or the Ovine Infinium HD BeadChip (Illumina Inc.,
USA). The measure of inbreeding based on runs of homozygosity showed a
minimum value in the Aykol breed (FROH = 0.034), while the maximum was
found in the Alai breed (FROH = 0.071). Short ROH segments (ROH≤4Mb) were
predominant in all breeds. Long ROH segments (ROH>16Mb) were absent
in the Gissar breed. The Gissar and Aykol breeds had the highest values of
the effective population sizes estimated for five generations ago (Ne5=660
and 563), whereas the Alai and Kyrgyz coarse wool displayed lower values
(Ne5 =176 and 128, respectively). The synthetic origin of the Aykol breed
was clearly evidenced by all analyses applied. Based on the network and
admixture analyses of the Kyrgyz and global sheep breeds, the Tien-Shan
and the Russian semi-fine wool breeds demonstrated a common ancestry that
most likely is due to a contribution of the Lincoln breed. The Gissar,
Aykol and Kyrgyz coarse wool breeds showed a genetic background
predominating in sheep populations from Iran and China whereas the Alai
demonstrated the different ancestry type. The revealed admixture patterns
probably resulted from the exchange and trade during the era of the Great
Silk Road, which partly overlapped with historical and archeological
findings.