Estimating the Effective Population Size of Sangsari Sheep Using Different Methods Based on Pedigree Analysis

پژوهشهای علوم دامی ایران

Article 5, Volume 10, Issue 2 - Serial Number 34, June 2018, Pages 237-247   

Document Type: Genetics & breeding

DOI: 10.22067/ijasr.v10i2.62343

Authors

Mohammadreza Sheikhlou^{* 1}; Einollah Abdi Ghezeljeh¹; Rashid Safari¹; Zabihollah Nemati²

¹Department of Animal Sciences, Ahar Faculty of Agriculture and Natural Resources, University of Tabriz, Tabriz, Iran

²Department of Animal Science, Ahar Faculty of Agriculture and Natural Resources, University of Tabriz, Tabriz, Iran

Abstract

Introduction: The practices that make breeding programs effective in generating genetic gain results the reduction in genetic diversity. The loss of diversity and the resulting increase in homozygosity may result in decreased production and fitness of inbred animals. One of the important parameters in assessing the level of genetic diversity of population is effective population size. Effective population size is a key parameter in population and conservation genetics due to its direct relationship with the rate of inbreeding and the amount of genetic variation lost because of random genetic drift. As a consequence, effective population size is usually considered as a useful criterion for classifying the livestock breeds according to the degree of endangerment. Classically, effective population size can be estimated from the rate of inbreeding between two successive generations. However, in real populations with overlapping generations, the definition of a ‘previous’ generation is quite difficult to establish and assignment of animals to various generations is not simple. A number of methods are available to estimate the effective population size on the basis of pedigree in livestock populations. However, when it comes to monitoring animal genetic resources not all methods are equally well suited and depending on the conditions in the population under consideration, different methods may have to be chosen. The objective of this study was to estimate effective population size in the breeding flock of sangsari sheep using different methods and to select the best estimates among them according to the pedigree structure.
Material and Methods: In this study the pedigree information of Sangsari sheep collected in 28 years (1988-2015) at breeding station of Damghan were used to estimate effective population size. The quality of available pedigree information is of great importance when interpreting the results of pedigree analysis. Thus, the degree of completeness of pedigree was assessed before analysis. For the whole file, the proportion of animals with both parents known was computed by simple counting. The pedigree completeness index (PCI) was used to describe the degree of completeness of pedigree. In addition, for each individual, the number of equivalent complete generations (EqG) was computed. Effective population size was estimated using the six different methods. The best method was selected considering some criteria such as time period used, subpopulation stratification, stability of estimates and negative estimate for effective population size.
Results and Discussion: The proportion of animals from the whole file with two known parents was 70%. The completeness of pedigree was low in the early years of the foundation of the center, however, pedigree filling improved over time, with the most recent cohort of lambs having pedigree completeness index of 0.61 and equivalent complete generations of 4.1. Accordingly, the pedigree had an acceptable completeness level for estimation of the effective population size. Estimates for effective population size were different according to the methods used for estimation. Estimated effective population size from and Ne-Coan resulted negative values for some years in the time period of last generation interval, which is clearly meaningless and leads to the rejection of these estimates. Another criteria for choosing the best method is the variability of estimates that should be as small as possible. Here, we consider the square root of the residual after fitting a linear regression to the yearly Ne estimates that should not be greater than 20. In all methods this criteria was greater than the critical value (20) except for the methods Ne-Cens and Ne-Ecg, and Ne-Ecg has the smaller value between the methods. Considering the necessary criteria, estimates from the method of individual increase in inbreeding (Ne-Ecg) were chosen as the best estimates for effective population size in this pedigree. Average estimated effective population size using this method was 131 animals.
Conclusion: Estimated realized effective population size was greater than the critical levels reported by FAO (50) and Meuwissen (100). Also, the estimated effective population size in this study was in the range of estimates for some foreign and Iranian sheep breeds. Considering the closed nucleus with no entry of animals from other herds, implementation of methods for preventing the losses of effective population size in the future such as optimum contribution of parents is suggested.

Material and Methods: In this study the pedigree information of Sangsari sheep collected in 28 year (1988-2015) at breeding station of Damghan were used to estimate effective population size. The quality of available pedigree information is of great importance when interpreting the results of pedigree analysis. Thus, the degree of completeness of pedigree was assessed before analysis. For the whole file, the proportion of animals with both parents known was computed by simple counting. The pedigree completeness index (PCI) proposed by MacCluer et al. (1983) was used to describe the degree of completeness of pedigree:
〖PCI〗_animal=(2C_sire C_dam)/(C_sire+C_dam )
Where Csire and Cdam are contributions from the paternal and maternal lines respectively: C=1/d ∑_(i=1)^d▒a_i
Where ai is the proportion of known ancestors in generation i; and d is the number of generations that is taken into account. In addition, for each individual, the number of equivalent complete generations (EqG) was computed as the sum of (1/2)n , where n is the number of generations separating the individual to each known ancestor (Maignel et al., 1996). Effective population size was estimated using the six different methods. The best method was selected considering some criteria such as time period used, subpopulation stratification, stability of estimates and negative estimate for effective population size.
Results and Discussion: The proportion of animals from the whole file with two known parents was 70%. The evolution of the pedigree completeness index (PCI) and equivalent complete generations (EqG) of animals in the studied years are given in Figuer 1. The completeness of pedigree was low in the early years of the foundation of the centre, however, pedigree filling improved over time, with the most recent cohort of lambs having pedigree completeness index of 0.61 and equivalent complete generations of 4.1. Accordingly, the pedigree have an acceptable completeness level for estimation of the effective population size. Table 3 shows the actual estimates of effective population size for the years in last generation interval using different methods. Estimates for effective population size were different according to the methods used for estimation. According to the Table 3, estimated effective population size from N_e -ΔF_p and Ne-Coan resulted negative values for some years in the time period of last generation interval, which is clearly meaningless and leads to the rejection of these estimates. Another criteria for choosing the best method is the variability of estimates that should be small as possible. Here, we have chosen the square root of the residual after fitting a linear regression to the yearly Ne estimates that should not be greater than 20 (7). According to the Table 3 in all methods this criteria were greater than the critical value (20) except for the methods Ne-Cens and Ne-Ecg, and Ne-Ecg has the smaller value between the methods. Considering the necessary criteria, estimates from the method of individual increase in inbreeding (Ne-Ecg) were chosen as the best estimates for effective population size in this pedigree. Average estimated effective population size using this method was 131 animals.
Conclusion: Estimated realized effective population size was greater than the critical levels reported by FAO (50) and Meuwissen (100). Also, the estimated effective population size in this study was in the range of estimates for some foreign and Iranian sheep breeds. Considering the closed nucleus with no entry of animals from other herds, implementation of methods for preventing the losses of effective population size in the future such as optimum contribution of parents are suggested.

Keywords

Effective population size; Inbreeding; Pedigree analysis; Sangsari Sheep

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