1- Department of Animal Science, Faculty of Agriculture Engineering, University of Kurdistan, Sanandaj, Iran
2- Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
3- Department of Animal Breeding and Genetic , Animal Science Research Institute of Iran, Agricultural Research, Education & Extension Organization (AREEO), Karaj, Iran
4- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful, Iran
2- Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
3- Department of Animal Breeding and Genetic , Animal Science Research Institute of Iran, Agricultural Research, Education & Extension Organization (AREEO), Karaj, Iran
4- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful, Iran
Abstract: (963 Views)
Extended Abstract
Background: Investigating genetic diversity and the population structure using genealogical information and molecular markers can reveal patterns of genetic differences resulting from past breeding methods, geographic separation, and human-mediated selection. Understanding the population structure is crucial for implementing corrective, conservation, breeding, and management programs. One of the important tools for investigating the structure of populations is the analysis of pedigree information, which plays a pivotal role in identifying genetic diversity and tracking changes across generations. It also provides estimates of essential population parameters, including increasing homozygosity, decreasing heterozygosity, inbreeding, and effective population size. While numerous studies have explored the population structure of various horse breeds worldwide using pedigree information, research specific to Iranian horses has been limited to Iranian Asil (Iranian Arab) and Turkmen horses. Furthermore, the Caspian horse, recognized as one of Iran’s significant native breeds, holds the distinction of being one of the world’s oldest horse breeds. Surprisingly, despite its historical significance, no study has yet explored the population structure of this breed using pedigree information. In this research, this gap is addressed by examining the Caspian horse population structure based on two information sources: pedigree records from the Caspian Conservation Society (CCS) and the International Caspian Society (ICS).
Methods: This study examined data from 1034 and 2264 horses registered in CCS and ICS pedigrees. After correcting errors in the pedigrees, important demographic parameters were calculated for each of the information sources separately. Initially, general information were extracted from the pedigrees using CFC software. Furthermore, inbreeding coefficients were estimated using the AGHmatrix package in the R programming language for both populations, and their changes were investigated over different years. The effective population size (Ne) in both pedigrees was calculated based on the method of individual increase in inbreeding using purgeR. The Ne was estimated using two distinct scenarios. All individuals in the pedigree were included in the first case, while the second case considered only the horses that were currently alive. Subsequently, the number of founders (Nf) and ancestors (Na), the number of founder genomes equivalents (Ng), and the deviation from Hardy-Weinberg were calculated for both pedigrees. The generation distance was calculated based on the average age of parents for four selected paths: 1) stallion to male foal, 2) stallion to female foal, 3) mare to male foal, and 4) mare to female foal. Finally, the pedigree completeness index (PCI) was calculated using the optiSel package in the R language for both pedigrees.
Results: The value of PCI calculated based on CCS and ICS information was above 70% until the 2nd and 4th generations, respectively, but its value showed a great decrease in the later generations. The rate of inbreeding observed for the whole population was estimated at 0.794% (for CCS) and 4.373% (for ICS), and a positive trend of changes was observed in inbreeding in both sources of information. The estimated observed inbreeding in the CCS pedigree was lower than that in the ICS pedigree. This discrepancy can be attributed to the incomplete genealogical information available in the CCS data source. Overall, the Ne calculated for both pedigrees was less than 100. When considering the entire pedigree, the Ne for the ICS pedigree (68.33 ± 13.03) was nearly twice that estimated for the CCS pedigree (32.86 ± 0.88). The estimated Ne values for the CCS and ICS populations, considering only live horses, were 66.43 ± 14.39 and 32.40 ± 0.93, respectively. Notably, the Ne estimates based on genealogical information aligned with those from previous studies that utilized genomic data. The values of Na and Nf calculated in the two pedigrees showed a huge difference, which indicates the relatively strong influence of a population bottleneck in the past. Additionally, given the substantial differences observed in Ng (110.12 for CCS versus 13.25 for ICS) and other metrics, such as Nf (333 for CCS and 155 for ICS) and Na (516 for CCS and 996 for ICS), it is evident that genetic drift has significantly impacted reducing population diversity. The estimated deviation from the Hardy-Weinberg equilibrium was observed to be positive in two pedigrees, which indicates the presence of a small amount of positive mating between relatives in both pedigrees.
Conclusion: Although the origin of this breed is in Iran, the registered genealogy was of lower quality than its international pedigree, indicating a serious need for more accurate genealogy registration in Iran. According to Ne's estimates, the Caspian horse population is in an endangered condition, and a specific program should be designed to conserve the genetic diversity of this breed. Despite the smaller number of horses registered in the CCS pedigree, the study of the reference population structure reveals that the genetic diversity is superior within the Iranian population. Consequently, this genetic resource holds promise for enhancing the overall condition of the Caspian horse worldwide. Moreover, the presence of inbreeding can worsen the existing situation; thus, a controlled breeding program to reduce inbreeding for both populations can be considered a solution.
Background: Investigating genetic diversity and the population structure using genealogical information and molecular markers can reveal patterns of genetic differences resulting from past breeding methods, geographic separation, and human-mediated selection. Understanding the population structure is crucial for implementing corrective, conservation, breeding, and management programs. One of the important tools for investigating the structure of populations is the analysis of pedigree information, which plays a pivotal role in identifying genetic diversity and tracking changes across generations. It also provides estimates of essential population parameters, including increasing homozygosity, decreasing heterozygosity, inbreeding, and effective population size. While numerous studies have explored the population structure of various horse breeds worldwide using pedigree information, research specific to Iranian horses has been limited to Iranian Asil (Iranian Arab) and Turkmen horses. Furthermore, the Caspian horse, recognized as one of Iran’s significant native breeds, holds the distinction of being one of the world’s oldest horse breeds. Surprisingly, despite its historical significance, no study has yet explored the population structure of this breed using pedigree information. In this research, this gap is addressed by examining the Caspian horse population structure based on two information sources: pedigree records from the Caspian Conservation Society (CCS) and the International Caspian Society (ICS).
Methods: This study examined data from 1034 and 2264 horses registered in CCS and ICS pedigrees. After correcting errors in the pedigrees, important demographic parameters were calculated for each of the information sources separately. Initially, general information were extracted from the pedigrees using CFC software. Furthermore, inbreeding coefficients were estimated using the AGHmatrix package in the R programming language for both populations, and their changes were investigated over different years. The effective population size (Ne) in both pedigrees was calculated based on the method of individual increase in inbreeding using purgeR. The Ne was estimated using two distinct scenarios. All individuals in the pedigree were included in the first case, while the second case considered only the horses that were currently alive. Subsequently, the number of founders (Nf) and ancestors (Na), the number of founder genomes equivalents (Ng), and the deviation from Hardy-Weinberg were calculated for both pedigrees. The generation distance was calculated based on the average age of parents for four selected paths: 1) stallion to male foal, 2) stallion to female foal, 3) mare to male foal, and 4) mare to female foal. Finally, the pedigree completeness index (PCI) was calculated using the optiSel package in the R language for both pedigrees.
Results: The value of PCI calculated based on CCS and ICS information was above 70% until the 2nd and 4th generations, respectively, but its value showed a great decrease in the later generations. The rate of inbreeding observed for the whole population was estimated at 0.794% (for CCS) and 4.373% (for ICS), and a positive trend of changes was observed in inbreeding in both sources of information. The estimated observed inbreeding in the CCS pedigree was lower than that in the ICS pedigree. This discrepancy can be attributed to the incomplete genealogical information available in the CCS data source. Overall, the Ne calculated for both pedigrees was less than 100. When considering the entire pedigree, the Ne for the ICS pedigree (68.33 ± 13.03) was nearly twice that estimated for the CCS pedigree (32.86 ± 0.88). The estimated Ne values for the CCS and ICS populations, considering only live horses, were 66.43 ± 14.39 and 32.40 ± 0.93, respectively. Notably, the Ne estimates based on genealogical information aligned with those from previous studies that utilized genomic data. The values of Na and Nf calculated in the two pedigrees showed a huge difference, which indicates the relatively strong influence of a population bottleneck in the past. Additionally, given the substantial differences observed in Ng (110.12 for CCS versus 13.25 for ICS) and other metrics, such as Nf (333 for CCS and 155 for ICS) and Na (516 for CCS and 996 for ICS), it is evident that genetic drift has significantly impacted reducing population diversity. The estimated deviation from the Hardy-Weinberg equilibrium was observed to be positive in two pedigrees, which indicates the presence of a small amount of positive mating between relatives in both pedigrees.
Conclusion: Although the origin of this breed is in Iran, the registered genealogy was of lower quality than its international pedigree, indicating a serious need for more accurate genealogy registration in Iran. According to Ne's estimates, the Caspian horse population is in an endangered condition, and a specific program should be designed to conserve the genetic diversity of this breed. Despite the smaller number of horses registered in the CCS pedigree, the study of the reference population structure reveals that the genetic diversity is superior within the Iranian population. Consequently, this genetic resource holds promise for enhancing the overall condition of the Caspian horse worldwide. Moreover, the presence of inbreeding can worsen the existing situation; thus, a controlled breeding program to reduce inbreeding for both populations can be considered a solution.
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2024/05/16 | Accepted: 2025/09/4
Received: 2024/05/16 | Accepted: 2025/09/4
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