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Status of livestock genomics research in Ethiopia and its implementation into the breed improvement programs


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Presented at the Twenty Sixth Ethiopian Society of Animal Production Annual Conference, Bahir Dar Ethiopia, 23-25 August 2018

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Status of livestock genomics research in Ethiopia and its implementation into the breed improvement programs

  1. 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. 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. 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. 4. Sayad Osman et al. (2016) Pereira et al (2009) Ethiopia: the gate way of livestock species to Africa
  5. 5. ..
  6. 6. • Objective: ☞The paper summarizes the status of livestock genomics research in Ethiopia and implicates its importance for the breed improvement programs. ..
  7. 7. Level of diversity • Diversity from autosomal genomic information perspective a) Cattle Sisay (1996) Dadi et al (2008)
  8. 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. 9. Dadi et al (2009) Tarekegn et al (2018) Haplogroup T Maternal origins of the indigenous cattle
  10. 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. 11. Tarekegn et al. (2018) Fig. Regression analysis of heterozygosity vs geographic distances from possible entry points ?
  12. 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. 13. Adhena et al. (Unpublished) Aman et al. (Unpublished)
  14. 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. 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. 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. 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. 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. 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. 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. 21. Ongoing whole genome scanning efforts
  22. 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. 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. 24. ‹ 4) Availability of databases storage facilities 5) Reduction of genotyping and sequencing costs
  25. 25. The way forward a) b) 𝛿2 𝐺 𝛿2 𝐺𝑥𝐸 𝛿2 𝐸 𝛿2 𝑃 𝑆𝑢𝑐𝑐𝑒𝑠𝑠 = ෍(𝛿2 𝐺 +𝛿2 𝐺𝑥𝐸 +𝛿2 𝐸)
  26. 26. Thank you