Genetic Diversity and Admixture Study of Ethiopian Thin-Tailed and Fat-Tailed Sheep Populations Using Morphological Traits and Low-Density Snp Markers
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Date
2020-06-06
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Addis Ababa University
Abstract
The study was conducted to characterize the fat-tailed and thin-tailed sheep breeds based on morphological traits and low-density SNP markers. Six hundred and five animals were used from both fat-tailed and thin-tailed sheep breeds for phenotypic observation and body linear measurements and two hundred and seventeen animals were used for molecular studies. Both qualitative and quantitative data were collected and analyzed using SAS 9.4. The measure of the genetic diversity within the breed and genetic relationships and distance between breeds were analyzed using ARLEQUIN 3.5.2 software. Genetic structure among breeds was analyzed using a model-based clustering algorithm implemented in the software ADMIXTURE v. 1.2.3 and the pattern of breed admixture was further analyzed through principal component analysis (PCA) using the GenABEL R package. Diverse coat color pattern and coat color type were observed in both fat-tailed and thin-tailed sheep breeds. Least square means and standard error of body weight and linear body measurements of fat-tailed and thin-tailed female sheep showed a significant (p<0.05) variability between breeds and age groups. Discriminant analysis of variance revealed tail length, rump length, ear length, and body weight were the most discriminating variables among the studied sheep breeds. The canonical discriminant analysis revealed that the greatest Mahalanobis distance was observed between Begayit and Afar sheep populations and least Mahalanobis distance was observed between Begayit and Rutana sheep populations living more closely. A dendrogram based on quantitative traits and the molecular analysis of PCA and admixture results at k=2 were identified two main clusters that separate fat-tailed (Afar, Tumele and SSFT) and thin-tailed (Gumz, Rutana and Begayit) sheep populations. The observed heterozygosity was estimated at 0.36 ± 0.15 for Begayit and Gumz, 0.37 ± vii
0.15 for Rutana, Afar, Tumele, and SSFT. The expected heterozygosity values were 0.37 ± 0.14 for Begayit, Gumz, Afar and SSFT and 0.38 ± 0.14 for Rutana and Tumele. All sheep populations demonstrated positive FIS values ranged from 0.004 (Afar) to 0.032 (Begayit). The analysis of molecular variance results revealed that the greatest variation existed within the individual across all populations (93.37%). FST values for all pairs of populations were significantly different from zero (P<0.001). The highest FST values were observed between Begayit and Afar (FST = 0.062) breeds, similar to mahalanobis distance while the lowest one was observed between Afar and Tumele populations (FST = 0.015). The Afar and small short fat-tailed sheep breeds in the fat-tailed sheep had the minimal case of admixture while thin-tailed sheep population and Tumele sheep had a high level of admixture. The FIS result showed low to moderate inbreeding coefficient. Both the PCA and genetic admixture analysis indicated that the thin-tailed and Tumele sheep population had high level of admixture. The present morphometric information, inbreeding coefficient (FIS), genetic differentiation (FST), population pattern and level of admixture found in this study will have paramount importance for future decision on the management, conservation, and improvement of the studied sheep genetic resources.
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Keywords
Genetic Diversity, Morphological Characterization, Fat-Tailed and Thin-Tailed Sheep