Detection of genomic regions under positive selection in adapting to high altitude in Iranian sheep

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.

2 Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

3 Department of Animal Science, Faculty of Agriculture, University of Arak, Arak, Iran

Abstract

Selective signatures provide information about the stages of evolution of different species, including sheep, which lead to changes in their genome over many years. The aim of this study was to detect signatures of selection in the genome of Iranian sheep in the highlands. A total of 58 sheep from 4 breeds, two breeds scattered in the highlands and two breeds scattered in the lowlands, were genotyped using Illumina ovine SNP600K BeadChip genomic arrays. Two statistical tests of unbiased FST (Theta) and hapFLK were used to identify the selection signatures. The results of Theta revealed 22 genomic regions and the results of hapFLK revealed 15 genomic regions. Bioinformatics analysis demonstrated that many of genes had important effects on adaptation to hypoxia conditions e.g. rheumatoid arthritis (TXNDC5), hematopoiesis (FANCA), immunity and fighting infection (LEF1, NMUR1, PTMA and COPS7B), regulating blood pressure and responding to pain and inflammation (NMUR1) and suppressing cancer (CD82, GAS8, PRMT1, B3GNT7). For example, TXNDC5 and FANCA functional genes, which are located on chromosome 13 and 14, were related to reacts to hypoxic conditions and hematopoiesis. Also, genes such as LEF1, NMUR1, PTMA and COPS7B are effective in immunogenicity and fighting infection. Study of the reported QTL in these regions of the sheep genome showed that they overlapped with QTL of economically important traits such as corpuscular hemoglobin concentration, hematocrit, traits related to meat, carcass, milk, body weight, bone density, and the total number of lambs born.
 Due to the fact that little research has been done regarding adaptation to altitude in sheep, the results of this research may facilitate the identification of genes affecting adaptation to altitude. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.

Keywords

Main Subjects

Extended Abstract

Introduction

Iran has many breeds of sheep that are distributed in the highlands and lowlands, many of which have evolved over a long period of time. Environmental heterogeneity and differences in climatic factors (temperature, precipitation, altitude, etc.) affect the distribution of phenotypic and genetic diversity of all kinds of organisms. Changes in climate and altitude have many effects on organisms, including sheep. Therefore, understanding the factors affecting the adaptation of sheep breeds to different environments is necessary for the development of breeding programs in future environmental changes. Selective signatures in whole genome can help us to understand the mechanisms of selection and to identify the genomic regions that have been under natural or artificial selection for long years. Since Selective signatures are usually associated with major effect genes and important economic traits, they can provide suitable information sources to improve the performance of selection programs in the future. The objective of this study was to identify the genomic regions that have been under selection in skin and wool sheep breeds. In general, it can be said that selective signatures provide information about the stages of evolution of different species, including sheep, which lead to changes in their genomes over many years. The aim of this study was to identify the signs of selection in the Iranian sheep genome in the highlands.

 

Materials and methods

In the present study, Illumina ovine SNP600K BeadChip genomic arrays of 58 sheep from 4 breeds were used, two breedsIn the present study, Illumina ovine SNP600K BeadChip genomic arrays of 58 sheep from 4 breeds were used, two breeds scattered in the highlands (Lori Bakhtiari and Afshari) and two breeds scattered in the lowlands (Karkul and Siah Kabud). Unbiased method of Weir and Cockerham’s FST (Theta) and hapFLK were used to detect the selection signatures. Also, to check the genes and QTLs in the selected regions, the Biomart database, OAR 3.1 version of the sheep genome, was used, and the function of the identified genes was analyzed through a wide search in different databases such as Genecards and OMIM. And finally, the list of genes related to the selected regions was reported. For this purpose, the chromosomal position of SNPs with high numerical value of theta and hapFLK, as well as the 250 kbp region around these markers, were further investigated. Then, DAVID database online search was used to investigate the biological and functional processes of genes and to study the ontology. Finally, Cytoscape software was also used to determine gene networks.

Results

The results of Theta revealed 22 genomic regions and the results of hapFLK revealed 15 genomic regions. Bioinformatics analysis demonstrated that many of genes had important effects on adaptation to hypoxia conditions e.g. rheumatoid arthritis (TXNDC5), hematopoiesis (FANCA), immunity and fighting infection (LEF1, NMUR1, PTMA and COPS7B), regulating blood pressure and responding to pain and inflammation (NMUR1) and suppressing cancer (CD82, GAS8, PRMT1, B3GNT7). For example, TXNDC5 and FANCA functional genes, which are located on chromosome 13 and 14, were related to reacts to hypoxic conditions and hematopoiesis. Also, genes such as LEF1, NMUR1, PTMA and COPS7B are effective in immunogenicity and fighting infection. Study of the reported QTL in these regions of the sheep genome showed that they overlapped with QTL of economically important traits such as corpuscular hemoglobin concentration, hematocrit, traits related to meat, carcass, milk, body weight, bone density, and the total number of lambs born.

 

Conclusion

Due to the fact that little research has been done regarding adaptation to altitude in sheep, the results of this research may facilitate the identification of genes affecting adaptation to altitude. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.

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Iranian Journal of animal Science
Volume 55, Issue 1
March 2024
Pages 143-162

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History

  • Receive Date: 31 January 2023
  • Revise Date: 13 May 2023
  • Accept Date: 29 May 2023

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