Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran
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...
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MDPI AG
2020-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/6/599 |
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| author | Morteza Bitaraf Sani Javad Zare Harofte Ahmad Bitaraf Saeid Esmaeilkhanian Mohammad Hossein Banabazi Nader Salim Abbas Teimoori Ali Shafei Naderi Mohammad Ali Faghihi Pamela Anna Burger Mohammad Silawi Afsaneh Taghipour Sheshdeh |
| author_facet | Morteza Bitaraf Sani Javad Zare Harofte Ahmad Bitaraf Saeid Esmaeilkhanian Mohammad Hossein Banabazi Nader Salim Abbas Teimoori Ali Shafei Naderi Mohammad Ali Faghihi Pamela Anna Burger Mohammad Silawi Afsaneh Taghipour Sheshdeh |
| author_sort | Morteza Bitaraf Sani |
| collection | DOAJ |
| description | 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 (<i>r</i><sup>2</sup> = 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. |
| first_indexed | 2024-03-10T19:30:31Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T19:30:31Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-4ac69f2327f84ba7b64f0507bf522e942023-11-20T02:07:47ZengMDPI AGGenes2073-44252020-05-0111659910.3390/genes11060599Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of IranMorteza Bitaraf Sani0Javad Zare Harofte1Ahmad Bitaraf2Saeid Esmaeilkhanian3Mohammad Hossein Banabazi4Nader Salim5Abbas Teimoori6Ali Shafei Naderi7Mohammad Ali Faghihi8Pamela Anna Burger9Mohammad Silawi10Afsaneh Taghipour Sheshdeh11Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, IranAnimal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, IranAnimal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, IranAnimal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, IranDepartment of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), Karaj 3146618361, IranOrganization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, Yazd 8916713449, IranOrganization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, Yazd 8916713449, IranAnimal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, IranPersian BayanGene Research and Training Center, Shiraz, Iran, Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL 33136, USAResearch Institute of Wildlife Ecology, Vetmeduni Vienna,1160 Vienna, AustriaPersian BayanGene Research and Training Center, Shiraz 7134767617, IranPersian BayanGene Research and Training Center, Shiraz 7134767617, IranThe 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 (<i>r</i><sup>2</sup> = 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.https://www.mdpi.com/2073-4425/11/6/599genotyping-by-sequencinglinkage disequilibriumeffective population Size |
| spellingShingle | Morteza Bitaraf Sani Javad Zare Harofte Ahmad Bitaraf Saeid Esmaeilkhanian Mohammad Hossein Banabazi Nader Salim Abbas Teimoori Ali Shafei Naderi Mohammad Ali Faghihi Pamela Anna Burger Mohammad Silawi Afsaneh Taghipour Sheshdeh Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran Genes genotyping-by-sequencing linkage disequilibrium effective population Size |
| title | Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran |
| title_full | Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran |
| title_fullStr | Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran |
| title_full_unstemmed | Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran |
| title_short | Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran |
| title_sort | genome wide diversity population structure and demographic history of dromedaries in the central desert of iran |
| topic | genotyping-by-sequencing linkage disequilibrium effective population Size |
| url | https://www.mdpi.com/2073-4425/11/6/599 |
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