Identification of selective signatures, detection of ROH Islands and related genes associated with the number of lambs per lambing in Zandi ewes

Document Type : Research Paper

Authors

1 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Environmental Sciences, Arak University, Arak, Iran.

2 Assistant Professor, Department of Animal Sciences, University College of Agriculture and Natural Resources, University of Tehran

3 Associate Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.

Abstract

Abstract
Objective
The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. Also, selection not only increases the frequency of new-useful mutations but also remains some signals throughout the genome. Since these regions are often control economically important traits, identifying and tracking these regions is the most important subject in the animal genetics.
Materials and methods
In order to identify the signatures of selection and ROH Islands, 81 native Zandi sheep including prolific ewes (42 animal) and others with only singleton records (39 animal) were genotyped using the medium-density Illumina Ovine SNP50 array. Theta unbiased statistical method in R software was used to identify selection signatures. Candidate genes were identified by SNPs located at 0.1% upper range of Theta using BioMart software in ensemble 109. Also the detectRUNS package of R was useful to find the proportions of the homozygous genome and one percent of SNP with the highest frequency in ROH were considered as ROH Islands.
Results
Based on the results of obtained Theta values genomic regions on chromosomes 1(3 regions), 2 (2 regions), 5, 6 (2 regions), 8 (2 region), 10 and 25 were identified. A total of 17 ROH Islands with length: 270.46 Kb to 8.25 Mb related to studied trait were identified, which covering less than 1% of the sheep genome. The ROH Islands was not distributed across the genome uniform. The highest number ROH Island was observed on chromosome 1, while the lowest was on chromosome 24. Candidate genes PER2, KCNH7, CLCN3, UTG8 and EPHA5 obtained these regions. Further investigation using bioinformatics tools showed these genomic regions overlapped with the genes associated with development of ovarian granulosa cells, ovulation rate, lipid transport in Sertoli cells and early growth fetus.
Conclusions
The results of this study revealed that, the selection processes in different sheep breeds for economic traits during several years, has led to the formation of many ROH islands in sheep genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.

Keywords

References

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Agricultural Biotechnology Journal
Volume 15, Issue 3
September 2023
Pages 277-294

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