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The science of genomics and livestock genetic improvement


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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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The science of genomics and livestock genetic improvement

  1. 1. The science of genomics and livestock genetic improvement Dirk Jan de Koning, Getinet Mekuriaw Tarekegn & Erling Strandberg Department of Animal Breeding and Genetics, SLU
  2. 2. Advances from breeding in the devloped world Species Trait 60s 2005 %- increase Broilers Days till 2 kg 100 40 60 Fillet, % 12 20 67 FCR 3,0 1,7 43 Layers Eggs/year 230 300 30 Eggs/ 1000 kg feed 5000 9000 80 Source: Table 1 i Van der Steen et al. J. Anim. Sci. 2005. 83:E1-E8 woodleywonderworks under Creative Commons
  3. 3. Thanks to plant and animal breeding 60s 2005 Reduced acreage Feed(kg) Ha Feed (kg) Ha 1000 kg lean pork 11750 6,5 5880 2,6 2,5x 1000 kg broiler meat 3000 1,7 1700 0,37 4,6x 10000 eggs 2000 1,1 1111 0,24 4,6x Creative Commons: Neil Palmer Creative Commons: woodleywonderworks Creative Commons: jere-me/
  4. 4. The observed trait is sum of many genes and environmental factors Complex Traits
  5. 5. Classical model Genotype environment Phenotype
  6. 6. Genomics Era Model Phenotype Environment QTL QTL QTL QTL QTL QTL Genotype
  7. 7. Marker Assisted Selection Accelerate genetic progress Measure DNA Markers early in life Even in embryos Sex limited traits Milk Litter size Traits measured in relatives Meat quality traits!
  8. 8. Three starting points for MAS Ease of Detection Use Functional mutations - known genes Q q M m Q q Markers in pop.-wide LD with functional mutation Markers in pop.-wide LE with functional mutation Q q M m genes GAS LD-markers LD-MAS LE-markers LE-MAS
  9. 9. Genomic Selection Phenotype Environment Q T L Q T L Q T L Q T L Q T L Q TL Q T L Q TL Q TL Q T L Q T L Q T L Q T L Q T L Q T L QTL QTL QTL QTL QTL Whole genome SNP genotypes A better Black box
  10. 10. Genomic Selection
  11. 11. MAS • Find QTL or genes and select specifically for favourable alleles • Need strategy to combine with EBV • LE-MAS computationally intensive • LE-MAS has major genotyping requirements Genomic Selection • Estimate effects across all markers and select on the sum of effects • Replaces EBV • Can be very computationally intensive • Major genotyping requirements
  12. 12. Genomic Selection: Accuracy Very important when considering Genomic Selection: What accuracy can I achieve? How many animals do I need for training? How many markers do I need? What is the cost-benefit ratio?
  13. 13. Genomic Selection: A little example
  14. 14. Livestock state of play
  15. 15. Generation intervals reduced dramatically Sires for bulls: ~7 => 2,5 years Dams for bulls: 4 => 2,5 years Selection differentials quite constant Genetic trends improved a lot Genetic gains increased 50-100% for yield traits 3x – 4x for traits with low heritability
  16. 16. International efforts for tricky traits Some traits are very expensive or difficult to measure. For example methane emission and individual feed intake. Large collaborations: each country (including Sweden) measures a number of cows Concern: genetic differences and GxE
  17. 17. Genomic Selection • Has doubled genetic progress for yield traits in dairy, 2-4- fold improvement for health traits! • Other species following suit. • Special case for crossbreeding species. • Crop breeding has been turned on its head by genomic selection • How do we deliver the benefits of modern breeding to low-income countries? • Faster in crops because seeds are easily stored and distributed!
  18. 18. Options for genomic selection in low income countries • Nucleus breeding programs • Centrally organized • Generic breeding goal • Good potential for species like poultry • Community based breeding programs • Locally organized • Use locally adapted genetic resources • May struggle to get suitable reference population • Any participatory approach needs immediate benefits for the participating farmers: not in the future.
  19. 19. Current examples • African Dairy Genetics Gains • Funded by ‘GATES’ foundation • Strong stakeholder involvement • Farmers submit data to the ADGG platform • Farmers receive feedback via iCOW: => 3 SMS/week  Drip feeding manuals to farmers  Mainly improved farm health • IlRI’s Livestock Genetics program: LiveGene
  20. 20. Useful links Misperceptions about livestock: smithoct17 TED talk on ADGG: genetics-program-works-with-farmers-to-boost-nutrition-in- africa/ B3 Africa: