Disentangling the origin of chemical differences using GHOST
Genomic techniques to profile and improve productivity and resilience in buffalo
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.
better lives through livestock
ilri.org
ILRI thanks all donors and organizations which globally support its work through their contributions to
the CGIAR system
Editor's Notes
There MUST be a CGIAR logo or a CRP logo. You can copy and paste the logo you need from the final slide of this presentation. Then you can delete that final slide
To replace a photo above, copy and paste this link in your browser: http://www.flickr.com/photos/ilri/sets/72157632057087650/detail/
Find a photo you like and the right size, copy and paste it in the block above.