TY - JOUR
T1 - Genome-wide diversity, population structure and demographic history of dromedaries in the central desert of Iran
AU - Sani, Morteza Bitaraf
AU - Harofte, Javad Zare
AU - Bitaraf, Ahmad
AU - Esmaeilkhanian, Saeid
AU - Banabazi, Mohammad Hossein
AU - Salim, Nader
AU - Teimoori, Abbas
AU - Naderi, Ali Shafei
AU - Faghihi, Mohammad Ali
AU - Burger, Pamela Anna
AU - Silawi, Mohammad
AU - Sheshdeh, Afsaneh Taghipour
N1 - Funding Information:
Funding: P.B. acknowledges funding from Austrian Science Fund (FWF): Project number P29623-B25. This research was jointly funded by Animal Science Research Institute of Iran (ASRI), Animal Breeding Center of Iran, and Yazd Agricultural and Natural Resources Research and Education Center, grant number 34-64-1357-005-970180.
Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2020/6
Y1 - 2020/6
N2 - 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.
AB - 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.
KW - Effective population Size
KW - Genotyping-by-sequencing
KW - Linkage disequilibrium
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U2 - 10.3390/genes11060599
DO - 10.3390/genes11060599
M3 - Article
C2 - 32485848
AN - SCOPUS:85085909009
VL - 11
JO - Genes
JF - Genes
SN - 2073-4425
IS - 6
M1 - 599
ER -