Identification of genomic runs of homozygosity and investigation of related genes in the dromedary camels using whole-genome sequencing data

Document Type : Research Paper

Authors

Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran.

Abstract

essential, as well as, the first step for designing breeding programs in this species. In this regard, powerful tools such as next-generation sequencing technology have made it possible to decode the genome information in this species. Based on this research motive, the aim of the current study was to identify the genomic runs of homozygosity (ROH) and investigate related genes in dromedary camels using whole genome sequencing data. For this purpose, a total of 12 sequenced genomic data related to Iranian and non-Iranian dromedary camels were used. After bioinformatics analysis including quality assessment, data pre-preprocessing, alignment in the reference genome, and identification of variants, qualitative filter of variants, finally, ROH regions were identified. Based on the obtained results, 549 (137.3 regions per sample) and 1356 (169.5 regions per sample) ROH were identified in the genomes of Iranian dromedary camels and dromedaries from the Arabian Peninsula, respectively. The results of the annotation revealed that some important fertility-related genes such as FSHR and LHCGR are located in the ROH regions of Iranian dromedary camels. Also, investigation of gene ontology results revealed that some important genes including CXCL9, CXCL10 and CXCL11 (immune-related), STBD1 (related to energy metabolism), SCARB2 (related to lipid metabolism and fertility) and SHROOM3 (related to kidney function) are shared between Iranian and non-Iranian camels. Finally, as a summary, it seems that the controlling factor and the reason for the creation of ROHs in the genome of dromedary camels is natural selection to adapt to the desert environment.

Keywords

Main Subjects

Extended Abstract

Introduction

Due to the specific ability of camels to survive in harsh desert conditions, they can be one of the main options for food supply in these areas. Despite this special feature and its importance for a country like Iran, as well as its potential role in becoming a farm species, no major effort has been made in the field of breeding this species. Studies of different aspects of genomic characteristics can be the key to solving the backwardness problem in camel studies. This study aimed to identify the genomic runs of homozygosity (ROH) and investigate related genes in dromedary camels using whole genome sequencing data.

 

Material and methods

In the present study, we used a total of 12 sequenced genomic data related to Iranian and non-Iranian dromedary camels for the identification of genome-wide ROHs. Prior to ROH identification, quality assessment, data pre-preprocessing, mapping to reference genome, identification of variants, and qualitative filter of variants were implemented, respectively. Also, the following criteria were used to define a genomic region as ROH: genomic regions with at least 40 SNPs (homozyg-snp) and two heterozygous SNPs (homozyg-window-het), also, the minimum number of SNP with missing genotype (homozyg-window-missing) was set to four. In addition, the minimum distance between SNPs to be in two separate ROHs is equal to one million base pairs (homozyg-gap) and the minimum SNP density within an ROH is equal to one SNP per 50 kb (homozyg-density). In order to annotate the ROHs and identify the genes in these regions, the BEDtools program was used. After identification of the genes located in the ROH regions, g:Profiler was implemented for gene ontology (GO) and KEGG pathway analysis.

 

Results and discussion

Here, we identified 549 (137.3 regions per sample) and 1356 (169.5 regions per sample) ROHs in the genomes of Iranian dromedary camels and dromedaries from the Arabian Peninsula, respectively. Based on the GO analysis results, we detected some important fertility-related genes such as FSHR and LHCGR that are located in the ROH regions of Iranian dromedary camels. Also, several important genes including CXCL9, CXCL10, and CXCL11 (immune-related), STBD1 (related to energy metabolism), SCARB2 (related to lipid metabolism and fertility), and SHROOM3 (related to kidney function) are common between Iranian and non-Iranian camels.

 

Conclusion

Considering that breeding and artificial selection on camel ecotypes have not been done in different regions of the world, including Iran, therefore, it seems that the creation of ROHs in the genome of camels is a product of positive natural selection for adaptation to harsh desert conditions. It seems that the use of genomic data of a larger number of Iranian camels can provide researchers with a profile of these regions to be used for purposes such as designing appropriate breeding strategies.

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Iranian Journal of animal Science
Volume 54, Issue 2
June 2023
Pages 105-116

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History

  • Receive Date: 25 March 2022
  • Revise Date: 02 August 2022
  • Accept Date: 05 August 2022

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