Genome-Wide Scan for Selective Sweeps Reveals Novel Loci Associated with Prolificacy in Iranian Sheep Breeds in Comparison with Highly Prolific Exotic Breed

Hossein Mohammadi; Amir Hossein Khaltabadi Farahani; Mohammad Hossein Moradi; Hossein Moradi-Shahrbabak; Mohsen Gholizadeh; Abouzar Najafi; Marco Tolone; Enrico D'Alessandro

doi:10.3390/ani14223245

Genome-Wide Scan for Selective Sweeps Reveals Novel Loci Associated with Prolificacy in Iranian Sheep Breeds in Comparison with Highly Prolific Exotic Breed

Animals (Basel). 2024 Nov 12;14(22):3245. doi: 10.3390/ani14223245.

Authors

Hossein Mohammadi¹, Amir Hossein Khaltabadi Farahani¹, Mohammad Hossein Moradi¹, Hossein Moradi-Shahrbabak², Mohsen Gholizadeh³, Abouzar Najafi⁴, Marco Tolone⁵, Enrico D'Alessandro⁶

Affiliations

¹ Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran.
² Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 31587-11167, Iran.
³ Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran.
⁴ Departments of Animal and Poultry Science, College of Aburaihan, University of Tehran, Pakdasht 33916-53755, Iran.
⁵ Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 98166 Messina, Italy.
⁶ Department of Veterinary Sciences, University of Messina, Viale G. Palatucci, 98168 Messina, Italy.

Abstract

Domestication and selection significantly changed phenotypic traits in modern domestic animals. To identify the genomic regions associated with prolificacy in this study, 837 ewes from three Iranian indigenous sheep breeds, consisting of Baluchi, Lori-Bakhtiari, and Zandi uniparous breeds, and one Greek highly prolific dairy sheep, namely Chios, were genotyped using OvineSNP50K arrays. Statistical tests were then performed using different and complementary methods based on either site frequency (F_ST) and haplotype (hapFLK) between populations, followed by a pathway analysis of the genes contained in the selected regions. The results revealed that for the top 0.01 percentile of the obtained F_ST values, 16 genomic regions on chromosomes 2, 3, 4, 7, 8, 9, 13, 14, 16, 18, 19, and 20, and for hapFLK values, 3 regions located on chromosomes 3, 7, and 13, were under selection. A bioinformatic analysis of these genomic regions showed that these loci overlapped with potential candidate genes associated with prolificacy in sheep including GNAQ, COL5A2, COL3A1, HECW1, FBN1, COMMD3, RYR1, CCL28, SERPINA14, and HSPA2. These regions also overlapped with some quantitative trait loci (QTLs) linked to prolificacy traits, milk yield, and body weight. These findings suggest that future research could further link these genomic regions to prolificacy traits in sheep.

Keywords: FST; Iranian indigenous sheep breeds; candidate genes; hapFLK; prolificacy; selection signatures.

Grants and funding

This study was funded by Animal Science Research Institute of Iran, 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.