Volume 13, Issue 38 (12-2022)
rap 2022, 13(38): 155-161 |
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Khalkhali R, Hedayat N. (2022). Detection of Selection Signatures on the X Chromosome in Iranian Dromedary Camels using Whole Genome Sequencing Data. rap. 13(38), 155-161. doi:10.52547/rap.13.38.155
URL: http://rap.sanru.ac.ir/article-1-1310-en.html
URL: http://rap.sanru.ac.ir/article-1-1310-en.html
Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
Abstract: (1152 Views)
Extended Abstract
Introduction and Objective: Although, unlike many livestock, no intense artificial selection has been made on dromedary camels, traces of natural selection along with selection by the human can still be found as selection signatures in the camel genome. Due to the development of new technologies as well as bioinformatics tools, the detection of these genomic regions can be done with high accuracy. This study aimed to identify the selection signatures on the X chromosome in Iranian dromedary camels using whole genome sequencing data.
Material and Methods: For the present study, the genomic data from six Iranian dromedary camels were used as the target population and also eight samples of dromedary camels from the Arabian Peninsula as the reference population. Signatures of selection were identified using two methods, including Fst and XP-EHH. A window size of 50kb and a step size of 25kb were used for this analysis, and genomic windows with scores higher than the 99th percentile of ZFst and XP-EHH distribution were considered as putative selection signatures. BEDtools program was used to extract genes located in these regions. Gene ontology analysis was performed on mentioned genes using g:profiler program.
Results: Based on the results, 13 and 27 genes identified using Fst and XP-EHH approaches as positively selected genes on the X chromosome in Iranian dromedary camels, respectively. The results of gene ontology (GO) analysis showed that terms related to fat metabolism have a significant contribution among the significant GO terms. Among the important identified genes, the genes of DGAT2L6 and AWAT2 may involve in the camel's resistance to high levels of ultraviolet radiation in desert conditions. Also, the NSDHL gene, which is involved in cholesterol biosynthesis, play a role in male fertility. The only significant KEGG pathway in this study was related to vitamin A metabolism.
Conclusion: It seems that the positive selection of genes related to fat metabolism, behavior and resistance to ultraviolet radiation in Iranian dromedary camels has been for interaction with humans and harsh desert conditions. Due to the lack of breeding programs on camels, it seems that knowing the genomic features of this species can be considered as a prerequisite for designing breeding strategies.
Introduction and Objective: Although, unlike many livestock, no intense artificial selection has been made on dromedary camels, traces of natural selection along with selection by the human can still be found as selection signatures in the camel genome. Due to the development of new technologies as well as bioinformatics tools, the detection of these genomic regions can be done with high accuracy. This study aimed to identify the selection signatures on the X chromosome in Iranian dromedary camels using whole genome sequencing data.
Material and Methods: For the present study, the genomic data from six Iranian dromedary camels were used as the target population and also eight samples of dromedary camels from the Arabian Peninsula as the reference population. Signatures of selection were identified using two methods, including Fst and XP-EHH. A window size of 50kb and a step size of 25kb were used for this analysis, and genomic windows with scores higher than the 99th percentile of ZFst and XP-EHH distribution were considered as putative selection signatures. BEDtools program was used to extract genes located in these regions. Gene ontology analysis was performed on mentioned genes using g:profiler program.
Results: Based on the results, 13 and 27 genes identified using Fst and XP-EHH approaches as positively selected genes on the X chromosome in Iranian dromedary camels, respectively. The results of gene ontology (GO) analysis showed that terms related to fat metabolism have a significant contribution among the significant GO terms. Among the important identified genes, the genes of DGAT2L6 and AWAT2 may involve in the camel's resistance to high levels of ultraviolet radiation in desert conditions. Also, the NSDHL gene, which is involved in cholesterol biosynthesis, play a role in male fertility. The only significant KEGG pathway in this study was related to vitamin A metabolism.
Conclusion: It seems that the positive selection of genes related to fat metabolism, behavior and resistance to ultraviolet radiation in Iranian dromedary camels has been for interaction with humans and harsh desert conditions. Due to the lack of breeding programs on camels, it seems that knowing the genomic features of this species can be considered as a prerequisite for designing breeding strategies.
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2022/06/14 | Revised: 2023/01/8 | Accepted: 2022/07/16 | Published: 2022/12/1
Received: 2022/06/14 | Revised: 2023/01/8 | Accepted: 2022/07/16 | Published: 2022/12/1
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