This document summarizes the status of livestock genomics research in Ethiopia and its implementation in breed improvement programs. It finds that Ethiopia has highly diverse livestock genetic resources due to its varied agro-ecologies. Genomic studies show high genetic diversity within populations for cattle, goats, sheep, and chickens. Efforts are exploring the genetic potentials through genome-wide association studies identifying genes related to adaptation, productivity, and disease resistance. Opportunities now exist to apply molecular tools in breeding programs through initiatives prioritizing livestock development and reducing genotyping costs. Overall, the document outlines the genomic research conducted on Ethiopian livestock to date and its potential application in breed improvement.

1. Status of livestock genomics research in
Ethiopia and its implementation into the
breed improvement programs
GM Tarekegn1,2, E Strandberg1, DJ De Koning1
1SLU, Uppsala Sweden
2Bahir Dar University, Ethiopia
Ethiopian Society of Animal Production (ESAP), 26th Annual
conference
Bahir Dar Ethiopia August 23-25th, 2018

2. Introduction
Diversified agro-ecologies:  18 major and 19 sub
agro-ecological zones
with diversified flora and
fauna gene pool.
 70% of the total land mass
is arid, semi arid and
sub-humid.

3. • The livestock sector contributes up to 47% of the agri. GDP
• Livestock population (CSA, 2017).
11.1 million
1.2 million59.5 million
30.2 million
30.7 million
59.5 million

4. Sayad Osman et al. (2016) Pereira et al (2009)
Ethiopia: the gate way of livestock species to Africa

5. ..

6. • Objective:
☞The paper summarizes the status of livestock genomics
research in Ethiopia and implicates its importance for the
breed improvement programs.
..

7. Level of diversity
• Diversity from autosomal genomic information
perspective
a) Cattle
Sisay (1996) Dadi et al (2008)

8. Low density SNP chip
• High admixture due to gene
flow (Fedilu, 2007; Solomon
et al. 2011; Zerabruk et al.,
2007 and 2011 and Zewdu,
2010).
☞Nm= 19 (Edea et al., 2013)
Edea et al (2015)
Edea et al (2013)
Based on autosomal markers

9. Dadi et al (2009) Tarekegn et al (2018)
Haplogroup T
Maternal origins of the indigenous cattle

10. Tarekegn (2016)
• Both studies uncovered high
levels of within-population
genetic diversity and high
level of admixture among the
goat populations.
This goes inline with Guangul
(2014) with SNP chip panel
Tucho (2004)
b) Indigenous goat populations

11. Tarekegn et al. (2018)
Fig. Regression analysis of heterozygosity vs
geographic distances from possible entry points
?

12. • Isolation-by-distance model explained
most of the observed genetic variation
c) Sheep
Gizaw et al (2007)
Edea et al. (2017)
 Clustered according to tail-type and
geographical origin.
 Explained by historical events and
selection for ecological adaptation

13. Adhena et al. (Unpublished) Aman et al. (Unpublished)

14. • Dessie (2003) assessed genetic
variation of 5 ecotypes.
– Moderate genetic variation
– Observed distinct alleles, e.g. Tilili
and Chefe ecotypes showed better
performance in growth and feed
utilization.
d) Indigenous chicken
Lawal et al (2013)
• Higher variation b/n
Jarso & village chicken.

15. Efforts towards exploring genetic potentials of the
indigenous livestock genetic resources
• Noyes et al. (2011) detected
ARHGAP15 gene for
trypanotolerance in Sheko
cattle.
 A genome-wide SS analysis revealed
816 loci (p < 0.01) associated to
candidate genes to adaptation (Edea et
al., 2014).
 The candidate genes are involved in
metabolism, hypoxia response and
heat stress.

16. ☞Taye et al. (2017) identified 583 candidate genes
involved in 41 biological processes and pathways
which include heat shock response, feed intake
and metabolism, and reproduction functions, etc.
Kim et al. (2017)
African cattle populations whole genome scan

17. Gene: HSPH1
MF: ATP Binding
Gene: MAP2K5
MF: ATP Binding
Gene:SPATA5
MF: ATP Binding
21 breeds of goats
• We observed a total of 132 pathways
(P<0.05), contain 1825 candidate
genes (Tarekegn et al).
 ARHGAP15, hair follicular
development, etc.

18. • In the association analysis of
polymorphic SNPs detected on
Kisspeptin gene on Woyto-
Guji and Gondar goat
populations we observed 18-
31% increment of litter size
(Tarekegn et al., 2017).

19. .
• In Ethiopian indigenous chicken ecotypes, Dessie
(2003) reported presence of strong association
between ecology and morphological characters.
• This warrants further use of the ecotypes for
selection and crossbreeding.
• The integration of EAV-HP in domestic chicken and
functional annotation clustering of genes reveals
enrichment for immune-related functions
(P < 0.05) in Horro and Jarso (Wragg et al., 2015).

20. • Whole genome of Horro chicken has
been fully sequenced and
documented in “The Book of
Genome” (Vanmechelen, 2017).
• The variants explored in the entire
genome could be used as a
reference to fine map and utilize the
genetic potentials of the local
ecotypes.
The Book of Genome (Vanmechelen, 2017)

21. Ongoing whole genome scanning efforts

22. Opportunities to apply molecular tools in the
breeding programs in Ethiopia
1) The emerging breeding platforms suits to small holder farming system
b) Open nucleus breeding scheme
Fig. Fogera cattle ONB scheme
2) Established farms, multiplication centers and ranches
• Potential technology incubation centers to generate improved genotypes
☞ The schemes link and transfer the improved genotypes to small holder farmers
Source: Haile et al., 2011
a) Community based breeding program

23. Livestock Development
Technology Roadmap
Tarekegn GM, Hailu F, Mekonnen A,
Assefa Y, Degefa T, Animut G,
Tegegne A, 2016
3) Livestock development initiatives as a priority in the country

24. ‹
4) Availability of databases
storage facilities
5) Reduction of genotyping
and sequencing costs

25. The way forward
a) b)
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26. Thank you