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

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. 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. 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. 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. 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. 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. 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. 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. This presentation is licensed for use under the Creative Commons Attribution 4.0 International Licence.
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ILRI thanks all donors and organizations which globally support its work through their contributions to
the CGIAR system