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. 2020 May 29;11(6):599.
doi: 10.3390/genes11060599.

Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran

Morteza Bitaraf Sani  1 , Javad Zare Harofte  1 , Ahmad Bitaraf  1 , Saeid Esmaeilkhanian  2 , Mohammad Hossein Banabazi  3 , Nader Salim  4 , Abbas Teimoori  4 , Ali Shafei Naderi  1 , Mohammad Ali Faghihi  5 , Pamela Anna Burger  6 , Mohammad Silawi  7 , Afsaneh Taghipour Sheshdeh  7
Affiliations

Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran

Morteza Bitaraf Sani et al. Genes (Basel). .

Abstract

The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r2 = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran's camels was estimated to be 89. Predicted Tajima's D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran's dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries.

Keywords: effective population Size; genotyping-by-sequencing; linkage disequilibrium.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Yazd province, the central desert of Iran. *: samples collected places.
Figure 2
Figure 2
Minor allele frequency of SNPs.
Figure 3
Figure 3
The linkage disequilibrium (LD) decay plot.
Figure 4
Figure 4
Camels clustered on the basis of principal components analysis using individual genotypes. The highlight box shows five samples (GBS046, GBS047, GBS042, GBS057, and GBS058) which belong to outside of Iran.
Figure 5
Figure 5
ADMIXTURE plots of 5 dromedary camel populations in the Iranian central desert.
Figure 6
Figure 6
SplitsTree network. Phylogenetic network calculated with SplitsTree using Neighbour-net, with a zoom to visualize the split among five regions of Iran’s central desert.
Figure 7
Figure 7
The historical demography of the dromedary camel was examined using SNeP.
See this image and copyright information in PMC

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