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Tropical dairy genomics

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Presented by Karen Marshall, ILRI, and Eileen Wall, Scotland's Rural College, at the CTLGH Project Management Committee Meeting, Edinburgh, 19-20 April 2017

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Tropical dairy genomics

  1. 1. Dairy Genomics Program of the Centre for Tropical Livestock Genetics and Health Tropical Dairy Genomics Karen Marshall, ILRI Eileen Wall, Scotland's Rural College CTLGH Project Management Committee Meeting, Edinburgh, 19-20 April 2017
  2. 2. Dairy Genomics Intermediate Outcome 1.1: - [current] 5 proof of concept genomic/ metagenomic predictions or algorithms developed and tested for at least 2 tropical adaptability and resilience traits to aid the selection of superior locally adapted breeding bulls for use in Africa. (restricts technology options) - [suggested] n proof of concept genomic based technologies to aid the selection of superior locally adapted breeding bulls for use in Africa. CTLGH-BMGF-DFID results tracker (March 2017) Simultaneously genetic improvement programs need to be developed to take advantage of these technologies. Need to take care that what is produced will be in demand by stakeholders
  3. 3. Define and characterize at least 5 tropical cattle adaptability/resilience traits such as heat stress, lactation persistency, tropical cow fertility and efficiency of local fodder utilization. UNDERPINS ALL OTHER OUTPUTS Heat stress, efficiency of local fodder utilization  No phenotypic data exists or currently being collected  Research infrastructure required (ILRI’s Kapiti farm) Lactation persistency, tropical cow fertility  Phenotypic data being collected by ADGG, sufficient by early 2019 Other - general disease resistance tolerance; fertility status particularly pregnancy; energy status including metabolic disorder  Additional data collection activities linked to ADGG  Novel phenomics to be developed to facilitate process Output 1.1.1 Proposal feed - heat - milk Proposal novel phenomics Proposal ADGG interface
  4. 4. Key research facilities required Equip the ILRI Kapiti station (32,000 Acres in semi-arid environment, currently running 2200 cattle and 1600 small ruminants) with:  Dairy shed with automatic milkers  Ability to measure feed intake (e.g. Growsafe)  Climate options (shade)  Various for specific tests Proposal novel phenomics Proposal feed - heat - milk
  5. 5. Step 1: Identify potential associations  Genomics Reference Resource for African Cattle  Sequence information + geo-reference co-ordinates  Can explore data for ‘signatures of selection’ for traits e.g. temperature (but power unknown)  ADGG  Can perform association studies when discovery population is sufficiently large  Other data via new projects Output 1.1.2 Proposal novel phenomics Proposal ADGG interface Generate high resolution genotypes and phenotypes on local and exotic cattle and confirm associations of at least 10 putative causal variants linked to selected traits of tropical adaptability and resilience. Proposal feed - heat - milk
  6. 6. Step 2: Confirm associations  Various approaches; timely (beyond 2020)  Direct and correlated effects need to be evaluated for use in breeding programs (suggest output is reworded to include productivity under local environments and omit step 2) Output 1.1.2 Generate high resolution genotypes and phenotypes on local and exotic cattle and confirm associations of at least 10 putative causal variants linked to selected traits of tropical adaptability and resilience.
  7. 7. Transfer at least 5 genomic/metageomic prediction algorithms for use in the African Dairy Genetic Gain program. Output 1.1.3  ADGG is employing genomic selection and thus will be developing prediction algorithms to select breeding animals within their population - CTLGH can assist by strengthening the genomic and phenomic data  Both CTLGH and ADGG have activities around a ‘smart tool for breed composition’ and can collaborate here Proposal novel phenomics Proposal ADGG interface (output rewording suggested to capture collabotative nature of ADGG – CTLGH rather than transfer; genomic tools rather than algorithms; potential use of tools outside of ADGG) Proposal ADGG interface
  8. 8. Output 1.1.4 Transfer 5 well-characterized tropical cattle adaptability and resilience genetic/ metagenomic variants to program 03 for further development into precision breeding tools.  Confirmation of (some of) the putative causal variants identified by the program will be beyond 2020  Can focus on existing (literature) options – e.g. trypanotolerance (Babboon ApoL1); ECF resistance (in discovery) (suggest revise output wording from transfer to identify to reflect that the variants may arise from literature rather than program activities; also proof of concept rather than development into precision breeding tools)
  9. 9. Summary 1.1.1 New knowledge on adaptation 1.1.2 Identification of putative causal variants 1.1.3 Tools / algorithms for strengthened genetic improvement programs OUTPUTS INTERMEDIATE OUTCOMES ACTIVITIES / PROJECTS 1.1 Proof of concept genomic based technologies to aid the selection of superior locally adapted breeding bulls for use in Africa Enhanced genomic tools  Genomics Reference Resource for African cattle  Low-cost genotyping platform  Smart tool for breed composition NEW: ‘Feed – heat – milk’ NEW: ‘Novel phenomics’ NEW: ‘ADGG interface’ Selection signatures for traits of interest (building on the Genomics Reference Resource)
  10. 10. ‘Feed – Heat – Milk’ deliverables General idea: Characterize the interaction between feed efficiency, heat stress and milk production for dairy cattle with different proportions indigenous / exotic Deliverables  Assessment of key genotype by environment (GxE) interactions relevant to dairy cattle production in Africa  Initial data towards identification of causal variants  Practical recommendations at various levels - policy makers, breeding program implementers, farmers Ballpark budget: 2-3m USD (due to need for facilities) Could potentially expand to include rumen microbiome characterisation
  11. 11. ‘Novel Phenomics’ deliverables General idea: develop field-suitable novel phenomics on-station and introduce into ADGG to strengthen its program Deliverables  New phenomic tools pilot-tested in-situ  ADGG field recording program extended to new traits  Enhanced ADGG selection algorithms  Undertaken gene discovery activities on key adaptability traits Ballpark budget: 0.5m USD
  12. 12. ‘ADGG Interface’ deliverables General idea: Leverage of CTLGH and ADGG investments through a set of 4 activities (see CN) Deliverables  Reduced SNP sets for breed composition and gEBV estimates* for any African population *when combined with reference population data  Known limits of breed composition tool to refine to underlying breeds (rather than breed-groups e.g. Zebu, Taurus)  Undertaken gene discovery activities for milk productivity & other traits at higher accuracy than currently possible  Understanding of breed effect on calf mortality, and undertaken gene discovery activities for calf mortality
  13. 13. ‘ADGG Interface’ deliverables General idea: Leverage of CTLGH and ADGG investments through a set of 4 activities (see CN) Deliverables  Reduced SNP sets for breed composition and gEBV estimates* for any African population *when combined with reference population data  Combine ADGG, SDG and CTLGH (Malawi) data; additional genotyping + analysis needed  Known limits of breed composition tool to refine to underlying breeds (rather than breed-groups e.g. Zebu, Taurus)  Use of commercial dairy data with known breed proportion; additional genotyping + analysis needed  Undertaken gene discovery activities for milk productivity & other traits at higher accuracy than currently possible  Extend ADGG genotyping to HD: additional genotyping + analysis needed  Understanding of breed effect on calf mortality, and undertaken gene discovery activities for calf mortality  Extend ADGG phenotyping to follow calves for first year of life; additional phenotyping, genotyping + analysis needed
  14. 14. 1.1 2 proof of concept genomic based technologies to aid the selection of superior locally adapted breeding bulls for use in Africa 1.1.1 Define and characterize at least 2 cattle adaptability/resilience or productivity traits such as heat tolerance, lactation persistency, tropical cow fertility and efficiency of local fodder utilization 1.1.2 Generate high resolution genotypes and phenotypes on local and exotic cattle and identify at-least 5 putative causal variants linked to cattle adaptability/resilience or productivity traits 1.1.3 In collaboration with the African Dairy Genetics Gain (ADDG) program develop genomic tools and/or prediction algorithms to aid the selection of superior dairy cattle 1.1.4 Identify (including from literature) 5 cattle adaptability/resilience or productivity genetic/ metagenomic variants for program 03 to use as proof of concept in relation to producing gene-edited cattle Target numbers still to be discussed Suggested revised outcomes and outputs
  15. 15. The Centre for Tropical Livestock Genetics and Health (CTLGH) is a joint venture between the International Livestock Research Institute, the University of Edinburgh, & Scotland’s Rural College., currently funded by the Bill and Melinda Gates Foundation and the CGIAR Livestock and Fish CRP. CTLGH Dairy Genomics Program co-leads  Karen Marshall, the International Livestock Research Institute, kmarshall@cgiar.org.  Eilleen Wall, Scotland’s Rural College, Eileen.Wall@SRUC.ac.uk

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