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Genetic diversity and population genetic structure in native Ethiopian donkeys (Equus asinus) inferred from equine microsatellite markers

Tropical Animal Health and Production volume 53, Article number: 334 (2021) Cite this article

Abstract

We investigated the genetic diversity and population genetic structure of six morphologically distinct Ethiopian donkey populations using 12 equine microsatellite markers. The donkey populations were Abyssinian (AB), Afar (AF), Hararghe (HA), Ogaden (OG), Omo (OM) and Sinnar (SI). Blood samples were collected from 180 genetically unrelated donkeys (30 individuals per population). Population genetic diversity estimates showed that total number and mean number of observed alleles, average observed and expected heterozygosity were 94, 5.208 ± 0.0229, 0.555 ± 0.023 and 0.588 ± 0.022, respectively. Highly significant deficiency in heterozygote was detected within the overall samples (FIS = 0.055 ± 0.021; P < 0.001). Though highly significant (P < 0.001), heterozygote deficiency within populations relative to total population was moderate (FST = 0.046 ± 0.016), suggesting a higher diversity within the populations (95.4%) than between populations. Various genetic distance estimation methods produced a similar topology of un-rooted dendrograms that grouped the overall Ethiopian donkeys into lowland (Ogaden, Omo and Sinnar) and highland (Abyssinian, Afar and Hararghe) genetic lineages. Likewise, Bayesian clustering analysis produced a similar pattern of clustering that was highly concordant with traditional donkey classification systems in Ethiopia.

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Funding

This work is part of a Ph.D. project granted to the first author by the German Academic Exchange Services (DAAD) in collaboration with the International Livestock Research Institute (ILRI) in their regional program. It was also partially supported by the Portuguese Foundation for Science (FCT) through the project PTDC/BIA-BDE/64111/2006.

Author information

Authors and Affiliations

  1. Department of Animal Genetics and Breeding, Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia

    E. Kefena

  2. Research Center in Biodiversity and Genetic Resources (CIBIO), University of Porto, Campus Agrario de Vairao, Rua Padre Armando, Quintas 7, 4485-661, Vairao, Portugal

    S. Rosenbom & A. Beja-Pereira

  3. Department of Geosciences, Environment and Spatial Planning (DGAOT), Faculty of Sciences, University of Porto, Rua Campo Alegre 687, 4169-007, Porto, Portugal

    A. Beja-Pereira

  4. Department of Animal and Range Sciences, Haramaya University, P.O. Box 38, Dire Dawa, Ethiopia

    M. Yusuf Kurtu

  5. CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People’s Republic of China

    J. L. Han

  6. Department of Animal Biosciences, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia

    J. L. Han & T. Dessie

Authors
  1. E. Kefena
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  2. S. Rosenbom
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  3. A. Beja-Pereira
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  4. M. Yusuf Kurtu
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  5. J. L. Han
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  6. T. Dessie
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Contributions

Effa Kefena (Ph.D.): conceived and designed the study, performed the research, analyzed the data and prepared the draft manuscript.

S. Rosenbom (Ph.D.): assisted and performed lab analysis

A. Beja-Pereira (Prof.): hosted the first author at his lab, provided logistic and funding support and edited the manuscript before submission.

J. L. Han (Prof.): provided kits for field sample collections, supported in data analysis and edited the final manuscript before submission.

M. Yusuf Kurtu (Prof.): hosted the first author at Haramaya University and facilitated logistic supports during field data collection.

T. Dessie (Ph.D.): hosted the first author at the International Livestock Research Institute (ILRI) as a PhD student, facilitated logistic supports during field data collection.

Corresponding author

Correspondence to E. Kefena.

Ethics declarations

All ethical standards for the phenotypic characterization of farm animal genetic resources have been strictly followed and applied.

Conflict of interest

The authors declare no competing interests.

Statement of animal rights

The study has been performed in accordance with the ethical standards laid down in the 1964 Declaration of Helsinki and its later amendments as well as following a guideline “Phenotypic Characterization of Animal Genetic Resources” (2012) developed by Food and Agricultural Organization of the United Nations.

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Supplementary Information

ESM 1

Supporting Figure S1 Un-rooted neighbor-joining dendrogram summarizing the genetic relationships between six donkey populations of Ethiopia. (PNG 205 kb)

High Resolution (TIF 64 kb)

ESM 2

Supporting Figure S2 Plot of Evanno et al.’s (2005) ad hoc statistic ΔK. (PDF 10 kb)

ESM 3

Supporting Figure S3 Genetic structure and individual membership of Ethiopian donkeys (K = 2 to 6). (PNG 81 kb)

High Resolution (TIF 12858 kb)

ESM 4

Supporting Figure S4 Genetic structure and population membership of Ethiopian donkeys (K = 2 to 6). (JPG 366 kb)

ESM 5

Supporting Table S1 Modified laboratory protocol used to extract nuclear DNA from Whatman FTA Classic Cards. (DOC 68 kb)

ESM 6

Supporting Table S2 Oligonucleotide sequence, fluorescent label and annealing temperature of 12 microsatellites used in this study. (DOC 33 kb)

ESM 7

Supporting Table S3 P-values of Hardy-Weinberg equilibrium tests. (DOC 40 kb)

ESM 8

Supporting Table S4 Estimates of within-population inbreeding co-efficient (FIS) for each locus and overall loci in six Ethiopian donkey populations. (DOC 104 kb)

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Kefena, E., Rosenbom, S., Beja-Pereira, A. et al. Genetic diversity and population genetic structure in native Ethiopian donkeys (Equus asinus) inferred from equine microsatellite markers. Trop Anim Health Prod 53, 334 (2021). https://doi.org/10.1007/s11250-021-02776-2

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  • DOI: https://doi.org/10.1007/s11250-021-02776-2

Keywords

  • Ethiopian donkey
  • Genetic diversity
  • Geographic clustering; Microsatellite marker

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