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Genomic techniques to profile and improve productivity and resilience in buffalo

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Presented by Karen Marshall and Rahman Habibar, ILRI, at the ILRI-ICAR Annual Review Meeting, New Delhi, 24-25 January 2019

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Genomic techniques to profile and improve productivity and resilience in buffalo

  1. 1. Genomic techniques to profile and improve productivity and resilience in buffalo Karen Marshall and Rahman Habibar, ILRI ILRI-ICAR Annual Review Meeting, New Delhi, 24-25 January 2019
  2. 2. Genomic techniques to profile and improve productivity and resilience in buffalo Project Goal: To increase buffalo productivity through the use of superior buffalo genetics that meets the needs and preferences of women and men smallholder buffalo keepers as well as other value chain actors. Working with the existing ICAR-CIRB Murrah buffalo breeding program
  3. 3. Project activities and achievements (1) Review the Murrah buffalo breeding program + recommendations re incorporation of genomic selection Recommendations:  Data digitization  Best linear unbiased prediction (BLUP)  Optimal contribution theory  Reference population  Genomic selection  Reduced genotyping array  Restructure of breeding program re genomics selection  Continual review and refinement Marshall, K., Mrode, R., Sikka, P., Singh, K.P., Singh, I. and Bhardwaj, A. 2017. Incorporation of genomic selection into the Murrah buffalo breeding program. ILRI Manual 27. Nairobi, Kenya: ILRI.
  4. 4. Project activities and achievements (2) Digitization of Murrah buffalo records into a database  Years of details records on performance of the Murrah buffalo in the CIRB-led breeding program in hard-copy (books)  Efforts to digitize these led by Network Project on Buffalo Improvement, with backstop support from this project  Achievements:  Database structure to harbor digitized data of daughter’s first lactation records for all the network centers are in place & its structure framing, front end development and apps programming completed  Database installation at central portal (CIRB) & its testing in process.
  5. 5. Project activities and achievements (3) Test the suitability of the currently available buffalo genotyping tool for the Indian Murrah buffalo population  176 Murrah buffalo genotyped with the Axiom Buffalo genotyping array, by local genotyping company (Imperial Life Sciences, Hiryana)  Result indicated the array is suitability for use in genomic selection in Murrah buffalo  High number informative SNPs, n=93,860  Normal distribution of minor allele frequency  Observed heterozygosity close to expected
  6. 6. Project activities and achievements (4) Strengthen the field progeny testing scheme via automating data capture  Open Data Kit (ODK) tools developed, piloted and finalised  Training of staff from CIRB and other centers in tool  Tool implementation Animal sample data recorded on-site (farms) using ODK software on mobile phone or netbook Data transferred to a central server at CIRB Data immediately available to ICAR scientists in different locations
  7. 7. Project activities and achievements (5) Strengthen the field progeny testing scheme by incorporation of parentage testing based on genomic information  Pilot to determine the benefit of genotyped based parentage testing underway  Blood samples collected from ~100 field progeny animals from three different field units (GADVASU, CIRB, NDRI) with genotyping in progress(Imperial Life Sciences, Hiryana)  ILRI staff will support result analysis and interpretation in 2019
  8. 8. Project activities and achievements (6) Incorporation of genomic selection in to the Murrah buffalo breeding program  Capacity building: 1 week training course November 2017, delivered by Drs Mrode and Ducroq, 17 participants - 4 female- from different ICAR centers  Movement to use of Best Linear Unbiased Prediction (BLUP) to estimate breeding values (a pre-requisite for genomic selection)  Implementation of an new analytical platform [WOMBAT]  Estimation of breeding values for 140 bulls (over sets 1 to 12) using the WOMBAT software  Unable to full implement genomic selectin due to lack of genotyping funds – ILRI and CIRB will continue efforts to raise these funds
  9. 9. This presentation is licensed for use under the Creative Commons Attribution 4.0 International Licence. better lives through livestock ilri.org ILRI thanks all donors and organizations which globally support its work through their contributions to the CGIAR system

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