Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection

Mohammad Hossein Moradi; Ardeshir Nejati-Javaremi; Mohammad Moradi-Shahrbabak; Ken G Dodds; Rudiger Brauning; John C McEwan

doi:10.3390/ani12111423

Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection

Animals (Basel). 2022 May 31;12(11):1423. doi: 10.3390/ani12111423.

Authors

Mohammad Hossein Moradi¹, Ardeshir Nejati-Javaremi², Mohammad Moradi-Shahrbabak², Ken G Dodds³, Rudiger Brauning³, John C McEwan³

Affiliations

¹ Department of Animal Science, Faculty of Agriculture, Arak University, Arak 38156-8-8349, Iran.
² Department of Animal Science, University of Tehran, Karaj 31587-1-1167, Iran.
³ Centre for Reproduction and Genomics, AgResearch, Invermay, Mosgiel 9053, New Zealand.

Abstract

The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform. Statistical tests were then performed using different and complementary methods based on either site frequency (F_ST and Median homozygosity) or haplotype (iHS and XP-EHH). The results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that was consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. An analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113 kb, 201 kb, and 2831 kb to 28 kb, 142 kb, and 1006 kb on chromosome 5, 7, and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting of TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR, EBP, CACNA1F, HSD17B10,SLC35A2, BMP15, WDR13, and RBM3 (OAR X), and each of which could potentially be the actual target of selection. The study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed, and that fat tail animals were developed later. Overall, our results provide a comprehensive assessment of how and where selection has affected the patterns of variation in candidate regions associated with fat deposition in thin and fat tail sheep breeds.

Keywords: candidate genes; fat tail sheep; genomic scan; lipid metabolisms; selection signature.

Grants and funding

This study was funded by Animal Science Research Institute of Iran, Mobarakandish Institute and AgResearch, New Zealand, Project number: PRJ-2016/11547. The funders were not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication.