This study delves into the genetic landscape of four major Iranian horse breeds: Caspian, Turkmen, Persian Arabian, and Kurdish. By analyzing SNP data from 275 genotyped samples, researchers aimed to understand the genetic distances, effective population sizes, population structure, and selective pressures shaping these unique breeds. The findings provide valuable insights into their evolutionary history and potential for future conservation and breeding programs.
Genetic Distances and Population Structure
Genetic distance analyses revealed distinct relationships among the Iranian horse breeds. The Persian Arabian and Kurdish breeds exhibited the lowest genetic distance, suggesting a closer evolutionary relationship. Conversely, Persian Arabian horses showed the greatest divergence from Turkmen and Caspian breeds. Pairwise FST values, a measure of genetic differentiation, indicated that all breeds were distinguishable, with Turkmen and Persian Arabian samples displaying the highest divergence. Interestingly, breeds originating from geographically similar regions, such as Turkmen and Caspian, or Kurdish and Persian Arabian, showed lower genetic differentiation.
Principal Component Analysis (PCA) further elucidated the population structure. The first principal component (PC1) separated breeds based on their geographical origin, clustering northern Iranian breeds (Caspian and Turkmen) apart from southwestern/western breeds (Persian Arabian and Kurdish). PC1 also helped differentiate Persian Arabian from Kurdish breeds. Subsequent PCs further resolved relationships within these broader clusters, with PC2 separating breeds within the geographic origins and PC3 distinguishing Caspian from Turkmen breeds. Relatedness analysis, using identity-by-descent measures, supported these findings, showing the closest relationship between Caspian and Turkmen breeds, and highlighting potential subpopulations within the Kurdish breed. Admixture analysis, assuming varying numbers of ancestral populations, indicated that the most likely ancestral structure involved two or three genetic clusters, generally aligning with the geographic groupings observed in PCA.
Effective Population Size and Linkage Disequilibrium
Estimates of effective population size (Ne) revealed a general decrease over time across all breeds, with a more pronounced decline in recent generations. The Caspian breed presented a unique historical Ne pattern, with the lowest Ne in recent generations and a higher Ne in older generations compared to other breeds. The Kurdish population exhibited the largest historical Ne. Contemporary Ne estimates, based on linkage disequilibrium (LD), indicated that the Turkmen breed had the lowest Ne, while the Kurdish breed possessed the highest. LD decay analysis showed a rapid drop in LD within approximately 100 kbps for all breeds, with the Persian Arabian population exhibiting the slowest LD decay.
Runs of Homozygosity and Genomic Inbreeding
Runs of homozygosity (ROH), segments of the genome where an individual is homozygous for all sites, were analyzed to assess genomic inbreeding. The Kurdish breed had the highest number of ROH segments, followed by Persian Arabian, Turkmen, and Caspian breeds. However, direct comparison of absolute ROH numbers is limited due to differences in sample size. Genomic inbreeding estimates (FROH) were similar across breeds, ranging from approximately 21% in Turkmen to 26% in Persian Arabian. Kurdish and Caspian breeds showed very similar inbreeding levels around 22-23%.
Selective Signals and Gene Associations
Selective signal analyses, using the DCMS method, identified significant SNPs and candidate genes associated with specific pairwise comparisons between breeds. Across these comparisons, genes previously linked to human height were frequently identified, including LLPH, HMGA2, MSI2, and TGFB2. Gene ontology (GO) enrichment analyses revealed terms related to molecular function, cellular components, and biological processes, such as chemokine receptor activity and thiolester hydrolase activity.
Several Quantitative Trait Loci (QTLs) were also found in regions showing signs of selection. These included QTLs for wither height, alternate gaits, and various health-related traits like chronic progressive lymphedema and osteochondrosis.
Overlapping Signatures
Significant overlaps were observed in selective signals, particularly among breeds sharing geographical proximity or potential common ancestry. For instance, SNPs significant in both Caspian vs. Kurdish and Caspian vs. Persian Arabian comparisons were also found in the Turkmen vs. Caspian comparison. Candidate genes such as HMGA2 and LLPH appeared in multiple Caspian pairwise comparisons. Genes associated with human height, like TRIM2 and CSMD1, were also identified as overlapping candidates.
QTL analysis highlighted common regions related to wither height across Caspian pairwise comparisons, and navicular bone morphology QTLs were consistently found in comparisons involving the Kurdish breed. GO term analyses revealed shared biological processes, such as dendritic spine development, in comparisons involving the Caspian breed.
This comprehensive genetic analysis underscores the distinct evolutionary trajectories and shared genetic heritage of Iranian horse breeds, providing a foundation for informed conservation and breeding strategies.
