DOI: 10.5061/dryad.37pvmcvff
title: Population structure and genetic diversity of sheep breeds in the Kyrgyzstan

description: 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&gt;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.
description: <strong>Data collection.</strong>
 This study does not involve any endangered or protected
 species. The animal tissue samples were
 collected by trained personnel under strict veterinary rules. Sampling was
 performed in accordance with the ethical guidelines of the L.K. Ernst
 Federal Science Center for Animal Husbandry. The protocol was approved by
 the Commission on the Ethics of Animal Experiments of the L.K. Ernst
 Federal Science Center for Animal Husbandry. 
   Methods
 <b>Preparation of the genomic DNA </b>
 DNA was extracted from ear tissue samples using Nexttec columns
 (Nexttec Biotechnology GmbH, Germany) according to the manufacturer's
 instructions. DNA quality was checked by 1% agarose gel
 electrophoresis.The concentrations of the dsDNA solutions were measured
 with a Qubit 3.0 fluorimeter (Life Technologies, USA). The OD260/OD280
 ratio of DNA solutions was determined with a NanoDrop-2000 (Thermo Fisher
 Scientific, Wilmington, DE, USA). <b>SNP
 genotyping and Quality control </b> SNP genotyping was performed using
 the OvineSNP50 BeadChip (Illumina, San Diego, CA, United States) or the
 Ovine Infinium HD BeadChip (Illumina, San Diego, CA, United
 States) (Kijas et al., 2014). Genotype
 quality control (QC) procedures were performed using PLINK
 v1.90 (Chang et al., 2015). To consider the accuracy and efficiency of SNP
 genotyping, valid genotypes for each SNP were determined by setting a
 cut-off of 0.5 for the GenCall (GC) and GenTrain (GT) scores (Fan et al.,
 2003). Samples that did not pass the
 quality criteria (missing genotype call rate 0.1) were excluded from the
 analysis. After merging the
 genotypic data from the 600K and 50K arrays, a total of 42 230 autosomal
 SNPs that overlapped between the two arrays were left in the analysis.
 SNPs with a call rate below 0.90, a minor allele frequency (MAF) lower
 than 0.05, or that were located on sex chromosomes were discarded.
 <b>Genetic
 diversity</b> The observed
 heterozygosity (Ho), unbiased expected heterozygosity
 (H<sub>E(u)</sub>) (Nei, 1978), rarefied allelic richness
 (A<sub>R</sub>) and the inbreeding coefficient
 (<i>F<sub>IS</sub></i>) based on the unbiased
 expected heterozygosity were calculated using the R package “diveRsity”
 (Keenan et al., 2013). <b>Runs of
 homozygosity (ROH) and genomic inbreeding (F<sub>ROH</sub>)
 </b> A window-free
 method for consecutive SNP-based detection
 (consecutive runs method (Marras et al., 2015))
 implemented in the R package “detectRUNS” (Biscarini et al., 2018) was
 used. One SNP with missing genotype and
 up to one possible heterozygous genotype was allowed in the run. The
 minimum ROH length was 1000 kb. 
 The genomic inbreeding coefficient based on ROH
 (F<sub>ROH</sub>) was computed as the sum of the length of all
 ROH per animal as a proportion of the total autosomal SNP coverage (2.44
 Gb). <b>Effective population sizes
 </b> Trends of effective population size
 (<i>Ne</i>) were estimated from linkage disequilibrium (LD) as
 implemented in <i>SNeP</i> (Barbato et al., 2015).
 <b>Genetic
 relationships and population structure</b>
 Pairwise genetic
 differentiation (fixation index,
 <i>F</i><sub>ST</sub>) (Weir and Cockerham, 1984)
 between all pairs of sheep breeds were calculated using the R package
 “diversity” (Keenan et al., 2013). Neighbor-Net graphs based on the matrix
 of pairwise <i>F</i><sub>ST</sub> values were
 constructed using SplitsTree 4.14.5 software (Huson and Bryant, 2006).
 A multidimensional scaling analysis (MDS)
 based on pairwise identical-by-state (IBS) distances and Principal
 Component Analysis (PCA) were performed with PLINK v1.90 and visualized
 with the R package “ggplot2” (Wickham, 2009). Genetic
 admixture was inferred using Admixture v1.3 software (Alexander et al.,
 2009) and plotted with the R package “pophelper” (Francis,
 2017). Inference of population splits and
 mixtures was performed using the TreeMix program
 (Pickrell and Pritchard, 2012). R version
 3.3.2 was used to create the input files (R Core Team, 2018).
description: The uploaded data included the data set of 129 animals
 representing five sheep breeds of the Kyrgyzstan, including 
 Alai (n=32), Aykol (n=31), Gissar (n=30), Kyrgyz coarse wool (n=13), and
 Tien-Shan (n=24). The SNP array data .bed, .bim and .map files include
 a total of 42 230 autosomal SNPs that overlapped between the
 the 600K and 50K Illumina arrays.