Abstract
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 ≤ 4 Mb) were predominant in all breeds. Long ROH segments (ROH > 16 Mb) 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.
Highlights
The Kyrgyz Republic (Kyrgyzstan) is a Central Asian country comprising the Western part of the Tien-Shan and the Northern regions of the high Pamir Mountains and of the Alay Range (Raimzhanov and Lushihina, 2017)
We aimed to address the genetic variability and population structure within five sheep breeds in the Kyrgyzstan on a genome-wide level as well as to infer the phylogeny and to detect expected admixture patterns of these breeds in a worldwide context
Our results showed that the level of genetic variability in the Kyrgyz breeds was comparable to that demonstrated in other worldwide populations (Kijas et al, 2012; Beynon et al, 2015; Ciani et al, 2015; Deniskova et al, 2018)
Summary
The Kyrgyz Republic (Kyrgyzstan) is a Central Asian country comprising the Western part of the Tien-Shan and the Northern regions of the high Pamir Mountains and of the Alay Range (Raimzhanov and Lushihina, 2017). Despite the challenging landscape and shortage of arable land, Kyrgyzstan has great capacities to produce economically cheap and environmentally friendly livestock products using about 9.6 million hectares of natural mountain pastures (Lushihina, 2013). Livestock farming (especially sheep breeding) has been the foundation supporting the livelihoods of local people from nomadic times until the present day. The contribution of the agricultural production to the economy is crucial (about 45% of gross income) (Kadyrkulov and Kalchayev, 2000). During the twentieth century, the sheep breeding industry underwent great changes that were caused by political and economic alterations (Kerven et al, 2011)
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