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Asmare S, Alemayehu K, Mwacharo J, Haile A, Abegaz S, Ahbara A. Genetic diversity and within-breed variation in three indigenous Ethiopian sheep based on whole-genome analysis. Heliyon 2023; 9:e14863. [PMID: 37089312 PMCID: PMC10119558 DOI: 10.1016/j.heliyon.2023.e14863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The objective of this work was to study genetic diversity by comparing whole genome sequence data of Rutana, Gumuz and Washera sheep found in Amhara and Benishanguel gumuz regional states of Ethiopia. We employed variant calling format tools version 0.1.15 to calculate some genetic diversity indices such as observed heterozygosity, expected heterozygosity, inbreeding coefficient, and nucleotide diversity. The results revealed that, observed heterozygosity ranged from 0.33 in Gumuz to 0.34 in Rutana and Washera sheep. Expected heterozygosity ranged from 0.37 in Rutana to 0.38 in Gumuz and Washera sheep. Expected heterozygosity was found to be higher than observed heterozygosity. Higher inbreeding coefficient (0.12) was recorded for Gumuz sheep compared to 0.09 of Rutana and Washera sheep. Mean nucleotide diversity values were 0.0029, 0.0030 and 0.0028 for Gumuz, Rutana and Washera sheep, respectively. Higher values of nucleotide diversity were recorded. Population structure analysis using principal component analysis revealed no clear separation between Gumuz, Rutana and Washera sheep populations with possibility of gene flow attributed to geographical location proximity. The smaller population size, closed breeding system, genetic drift and uncontrolled (non-random) mating might lead to higher rate of inbreeding in Gumuz, Rutana and Washera sheep, requiring timely intervention. This intervention helps to prevent inbreeding depression and extinction of these valuable breeds of sheep, which helps in sustaining the livelihood of sheep keepers in lowlands and highlands. Nevertheless, the whole-genome analysis revealed high within-breed variation. Uncovered areas of studies like mapping quantitative trait loci, identifying genes underpinning productivity traits such as carcass quantity and meat quality could be carried out on diversified sheep resources identified by the current study. Identifying the genomic regions and biological pathways that contribute to explaining variability in these traits is of great importance for selection purposes. Designing conservation-based within-breed sheep selective breeding programs are recommended considering economically important traits into account.
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Affiliation(s)
- Sisay Asmare
- Debre Markos University, Burie Campus, P.O. Box 18, Ethiopia
- Bahir Dar University, College of Agriculture and Environmental Sciences, Department of Animal Production and Technology, Bahir Dar, Ethiopia
- Biotechnology Research Institute of Bahir Dar University, Ethiopia
- Corresponding author. Debre Markos University, Burie Campus, P.O. Box 18, Ethiopia.
| | - Kefyalew Alemayehu
- Bahir Dar University, College of Agriculture and Environmental Sciences, Department of Animal Production and Technology, Bahir Dar, Ethiopia
- Biotechnology Research Institute of Bahir Dar University, Ethiopia
| | - Joram Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Aynalem Haile
- International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Solomon Abegaz
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Abulgasim Ahbara
- Animal and Veterinary Sciences, SRUC, The Roslin Institute Building, Midlothian, Edinburgh, UK
- Departments of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
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Asmare S, Alemayehu K, Abegaz S, Haile A. On-farm evaluation of growth and reproductive performances of Washera and Gumuz sheep in northwestern Ethiopia: Basics for setting up breeding objectives/goals. PLoS One 2021; 16:e0254924. [PMID: 34283870 PMCID: PMC8291677 DOI: 10.1371/journal.pone.0254924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/06/2021] [Indexed: 11/18/2022] Open
Abstract
Growth and reproductive performance traits are traits of economic importance for sheep selection and productivity improvement interventions. This study aimed at comparative evaluation of growth and reproductive performance traits of sheep in the highland and lowland agro-ecologies of northwestern Ethiopia. Data on growth performance traits were collected from 144 Washera (78 males and 66 females) lambs and 72 Gumuz (37 males and 35 females) lambs. Data on reproductive performance traits were collected from 260 Washera (130 rams and 130 ewes) sheep and 150 Gumuz (75 rams and 75 ewes) sheep. General linear model univariate procedure was employed to analyze the collected data. Breed, the interaction effect between breed and season of birth as well as the interaction effect between breed and type of birth all exerted very high significant effect (P<0.001) on live weight at all age groups. Breed type affected pre-weaning average daily weight gain significantly (P<0.01). Pre-weaning average daily weight gain of Washera (70 g/day) was found much better performance than 60 g/day of Gumuz. Breed type exerts significant (P<0.05) effect on age at first lambing, lambing interval, annual reproductive rate and number of lambs born per ewe life time. Average age at first lambing and lambing interval of Washera sheep were 11.69 months and 9.27 months, respectively. The corresponding values for Gumuz sheep were 12.51 months and 10.43 months, respectively. Production and reproduction performance values of traits varied across the two breeds and sexes as well. These values can be used to set up breeding objectives or goals for selective breeding of sheep giving special emphasis to growth traits believed to have medium heritability values.
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Affiliation(s)
- Sisay Asmare
- Debre Markos University, Burie Campus, Debre Markos, Ethiopia
- * E-mail:
| | - Kefyalew Alemayehu
- Department of Animal Science and Technology, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Solomon Abegaz
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Aynalem Haile
- International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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