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Mousavi SF, Razmkabir M, Rostamzadeh J, Seyedabadi HR, Naboulsi R, Petersen JL, Lindgren G. Genetic diversity and signatures of selection in four indigenous horse breeds of Iran. Heredity (Edinb) 2023:10.1038/s41437-023-00624-7. [PMID: 37308718 PMCID: PMC10382556 DOI: 10.1038/s41437-023-00624-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 06/14/2023] Open
Abstract
Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.
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Affiliation(s)
- Seyedeh Fatemeh Mousavi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mohammad Razmkabir
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Jalal Rostamzadeh
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Hamid-Reza Seyedabadi
- Animal Science Research Institute of Iran, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Rakan Naboulsi
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, Tomtebodavägen 18A, 17177, Stockholm, Sweden
| | | | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium.
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Pérez JRS, Palacios DM, Garro JM. Genetic characterization of the Colombian Creole Horse population via STR markers used in filiation tests and equine certification. FORENSIC SCIENCE INTERNATIONAL: ANIMALS AND ENVIRONMENTS 2023. [DOI: 10.1016/j.fsiae.2023.100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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Sadeghi R, Moradi-Shahrbabak M, Miraei Ashtiani SR, Schlamp F, Cosgrove EJ, Antczak DF. Genetic Diversity of Persian Arabian Horses and Their Relationship to Other Native Iranian Horse Breeds. J Hered 2020; 110:173-182. [PMID: 30590570 DOI: 10.1093/jhered/esy061] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2018] [Indexed: 11/13/2022] Open
Abstract
The principal aims of this study were to explore genetic diversity and genome-wide selection signatures in Persian Arabian horses and to determine genetic relationship of Persian Arabians with other Iranian horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to 47 mares from the mid to late 19th century, using the equine 670k single nucleotide polymorphism (SNP) BeadChip. Mean observed and expected heterozygosity were (0.43) and (0.45), respectively, average inbreeding measures (inbreeding estimates based on runs of homozygosity and pedigree information) were low, indicating high genetic diversity in Persian Arabian horses. Analysis of population genetic structure using STRUCTURE and principal component analysis suggested that Persian Arabian horses can be divided into 3 groups, however the groups do not match traditional matrilineal strains. In total, 15 genomic regions were identified by at least 2 of the 3 implemented methods, Tajima's D, H, and H12, as potentially under selection in Persian Arabian horses. Most of these peaks were found on chromosome 9, overlapping with QTLs previously associated with horse temperament. Biological function analysis of identified candidate genes highlighted enrichment of GO term "response to lipopolysaccharide" and KEGG pathway "chemokine-mediated signaling pathway," which are associated with immune responses and may have been targets of selection in Persian Arabian horses. Independent analyses of SNP data from 30 horses of 4 other Iranian breeds suggested distinct population structure between Persian Arabian, and Turkemen and Caspian horse breeds. Overall, the results of this study suggest a rich genetic diversity in the Persian Arabian horses and a clear genetic differentiation with Turkemen and Caspian breeds.
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Affiliation(s)
- Raheleh Sadeghi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.,Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Mohammad Moradi-Shahrbabak
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Seyed Reza Miraei Ashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Florencia Schlamp
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY
| | - Elissa J Cosgrove
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY
| | - Doug F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY
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