Drawing from the indigenous african livestock genomes a dart aimed at sustainability

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Sustainability
 Farmers – sustainable populations uphold Darwinian
adaptations in indigenous breeds
 Scientists – sustainable use of Africa’s genetic resources
landscape genomics, genomic selection
 Breed improvement programs – sustainable productivity
match projects to environments
 Governments/policy makers (AU-IBAR) – policies driving
sustainability – CAIS stock indigenous breeds genetic material,
sharing genetic material across borders

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Drawing from the indigenous african livestock genomes a dart aimed at sustainability

  1. 1. Drawing from the indigenous African livestock genomes - a dart aimed at sustainability Dr. Mary Ndila Mbole-Kariuki
  2. 2. ”It’s been proven that of all the interventions to reduce poverty, improving agricultural productivity is the best. All the other different economic activity — yes it trickles down. But nothing as efficiently as in ” – Bill Gates (2013) Small-holder farmers Over 500 million small-holder farmers ~2 billion depend on it for livelihoods Produces 80% of food consumed in Asia, sub- Saharan Africa
  3. 3. Challenges livestock production faces in Africa – small holder farmers “Negative selection” Prevalence of disease and disease vectors Continual ineffective traditional animal husbandry practices Evident knowledge gap - BIP Poor extension services Eminent climate change
  4. 4. Effects on the genetic resources Loss of genetic diversity Loss of adaptive traits Endangered
  5. 5. Why has sustainability continued to be evasive in Africa? Needle in haystack
  6. 6. In 2009 ….. Indigenous East African Shorthorn Zebu (EASZ) – Western Kenya An Admixed population – indicine and taurine Well adapted to aridity and heat Resistant/tolerant to infectious diseases (ECF) and vectors (Ticks) Embarked on, Characterizing on a genome level the population structure of EASZ Identifying imprints of genetic selection through phenotype- genotype associations for disease and non-disease traits
  7. 7. Study site
  8. 8. Study design Recruitment flow chain 552 (3-7 days old) calves and followed-up for 1 year period Calves were exposed to natural disease and vector challenges No veterinary intervention was administered apart from euthanasia of critically ill animals Routine rural farm practices Chiefs AHA Farmers
  9. 9. Genotypic data Illumina® BovineSNP50 Mapped against University of Maryland genome 3.1 assembly Number of SNPs Mapped autosomal SNPs 54436 (96%) Unmapped autosomal SNPs 1066 Unknown chromosomes 104 Sex chromosome 1341 Total SNPs 56947
  10. 10. Genetic characterization Population structure
  11. 11. PCA analysis 65% variation 14%variation
  12. 12. Evidence of European taurine introgression CATEGORY 1 CATEGORY 2 CATEGORY 3 Pure from European introgression (x≤1.56%) 6 or more generation Moderate European introgression (1.56%>x<12. 5%) 4-5 ET generation Substantial European introgression (x≥12.5%) 2-3 ET generations N=425 N=94 N=29
  13. 13. Key: proportion of calves with“SUBSTANTIAL” European introgressionper sub location Legend: Average proportion of European taurine introgression per sub locations
  14. 14. Key: proportionof calves with“MODERATE” European introgressionper sub location. Northtosouthgeneticcline Legend: Average proportion of European taurine introgression per sub locations r = 0.82 P < 0.0001
  15. 15. Breed Improvement programmes Rural Development Project (1979-1989)- Kitinda dairy Bungoma Kenya – Finland Livestock Development Programme (1991-2003) Services offered: AI upon request, in-calf heifers, bull schemes Breeds used: Holstein, Aryshire, Jersey, Guernsey Impacts Offspring boom Bull schemes 84,749
  16. 16. Key: proportionof calves with“MODERATE” European introgressionper sub location. Selection against Northtosouthgeneticcline Legend: Average proportion of European taurine introgression per sub locations
  17. 17. Present Western Kenya EASZ genetic state Economically important traitsEcologically important traits This shift of focus is to a perceived economically beneficial animal as opposed to an ecologically fit one
  18. 18. Impact on the indigenous EASZ genome integrity All calves (n = 548) Moderate and substantial calves (n = 123) Non- introgressed calves (n = 425) Between calves ET < 2.2e-16 *** <2e-16 *** - AT 1 1 1 AZ <2e-16 *** < 2e-16 *** 1
  19. 19. 1 2 3 6 4 5 7 EAST AFRICAN SHORTHORN ZEBU
  20. 20. R2 value Correlation coefficient P value Easz AT /sheko AT 0.7869 0.887 6.668e-11 R² = 0.7869 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 shekoAT Linear (shekoAT) chr x
  21. 21. Case studies Farm – Africa dairy goat project - Ojango et al. 2010a Kenya Dual Purpose Goat Development project (KDPG) Ojango et al. 2010b Dairy Goat development programme (DGDP) – Ayalew 2010 Establishment of synthetic populations? Lack of continual financial and extension services support? Beneficial genotypes in wrong environment?
  22. 22. Ecologically important traits Economically important traits Strike a balance – 3 E’s Exotic * Indigenous? Indigenous * Indigenous? Environment
  23. 23. Calls for Conservation - utilisation Effective population size – important genetic measure and fundamental in understanding conservation. Reflects effects of drift or inbreeding Characterizes the population diversity Highlight events that shape a population Used a marker-based approach using linkage disequilibrium E(r2)=[1/(1+4Nec)]+(1/n) Indicator of genetic decline – small Ne predicates low genetic diversity unsuitable for population survival
  24. 24. Fst statistics Autosomes P value Fst (subpopulations/total) 0.0033 0.09 Fit (Individual/total) 0.0217 0.07 Fis (Individual/subpopulations) 0.0185 0.03 Fst statistics
  25. 25. Stop the genetic diversity melt-down and seek out the adaptive traits before they are entirely lost and make them work to the farmers’ advantage For if one link in nature’s chain might be lost, another might be lost until the whole of things will vanish piecemeal – T. Jefferson
  26. 26. Sustainability Farmers – sustainable populations uphold Darwinian adaptations in indigenous breeds Scientists – sustainable use of Africa’s genetic resources landscape genomics, genomic selection Breed improvement programs – sustainable productivity match projects to environments Governments/policy makers (AU-IBAR) – policies driving sustainability – CAIS stock indigenous breeds genetic material, sharing genetic material across borders
  27. 27. Success stories Carora-Holstein crosses - Carora (composite venezuelan breed) - slick hair gene and exotic Holstein Girlando – Gir (zebu breed in Brazil) and exotic Holstein Kurolier chicken (indigenous and exotic crosses) Kenya Dual purpose goat – crosses of indigenous East African and Galla with exotic Toggenburg and Anglo- Nubian
  28. 28. DISCLAIMER
  29. 29. Acknowledgements Prof. Olivier Hanotte (UoN) Dr. Miika Tapio (MTT) Dr. Tad Sonstegard (USDA) Farmers Wellcome Trust IDEAL fraternity
  30. 30. THANK YOUTHANK YOUTHANK YOUTHANK YOU

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