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

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.

Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing

“…TYR is another basic gene that regulates pigmentation [47] and disorders in this gene cause the albino phenotype in mammals and chickens [48]. Genetic diversity of indigenous dromedaries is at risk in Iran [49], their genetic diversity needs to be conserved. One of approaches to prediction of animal breed is coat color, so that morphological selection in domestic animals based on color determines the breed and attribution [17].…”

Long-range linkage disequilibrium events on the genome of dromedary camels as a signal of epistatic and directional positive selection

“…This statistic, which ranges between 0 (no-disequilibrium) to 1 (complete disequilibrium) is preferred in animal populations LD analyses due to its low sensitivity to small sample sizes and low allele frequency markers [ 2 ]. Using these different estimators, the LD level and extent of LD decay have been widely investigated in different animal species, e.g., sheep [ 3 , 4 ], horse [ 5 , 6 ], cattle [ 7 , 8 ], and in Bactrian and dromedary camels [ 9 , 10 ]. The estimation of such LD pattern can be used to infer different evolutionary events, such as effective population size, level of genetic drift, and footprints of selection [ 1 ].…”

Microsatellite-Based Genetic Diversity and Population Structure of Huacaya Alpacas (Vicugna pacos) in Southern Peru

“…There are some previous studies focused on the genetic diversity and population structures of various south American camelids, such as alpacas, llamas, guanacos, and vicuñas [11][12][13][14][15][16][17], mainly in the regions of Peru and Bolivia. In addition, other members of the Camelidae family have been studied [18][19][20][21]. In the vast majority, low-density microsatellite markers or mitochondrial markers were used.…”