Resource use efficiency in livestock: Bridging the biotechnology-livestock productivity gap in East Africa presentation by Denis Mujibi, Nelson Mandela African Institute for Science and Technology, Arusha, Tanzania

1. Resource use efficiency in livestock
Bridging the biotechnology-livestock productivity gap in East
Africa
Dr. Denis Fidalis Mujibi
The Nelson Mandela Africa Institution of Science and Technology (NMAIST), Arusha Tanzania

2. Milk Yield in Cows

3. Background: The problem
• Many Smallholder dairy farmers are milking losses.
• Using Inappropriate breeds
• Inadequate productivity optimizing technologies
• The potential contribution of appropriate genetics and new technology in
increasing yields is largely undocumented.

4. I want 30 liters!
MOVE
Crossbreed
Adaptation
Optimize
Upgrade

5. Where’s the milk?

6. Background: The problem

7. Background: The problem

8. Potential for Biotech in Dairy Cattle

9. Breed Composition of Dairy Cattle

10. Breed Composition in East Africa

11. 0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dailymilkyield(l/day)
Herd environment level
Uganda
21-35% 36-60% 61-87.5% >87.5%
7 l/day
5 l/day
7 l/day
5 l/day
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dailymilkyield(l/day) Herd environment level
Kenya
21-35% 36-60% 61-87.5% >87.5%
2.5 l/day
3.5 l/day

12. The Folly of Phenotype!
Ngobe Zerida II
73% 4.9 ltr/day Rank: 209/285 11.06 ltr/day77% Rank: 1/285

13. Conclusion
Biotechnology can offer solutions to navigate genotype by
environment interactions
The tools must be affordable to farmers
Farmers must master the basics of dairy and apply best
management practices first

14. Disease tolerance in Pigs

15. Disease tolerance in pigs
African Swine Fever virus (ASFv) is a major cause of losses in pig
production in Africa.
There is evidence to suggest that indigenous pigs are less
susceptible to ASFv.
Characterization of this tolerance is critical for development of
novel genetic control strategies

16. Disease tolerance in pigs
Domestic pig
Bushpig

17.  360 samples collected around the Lake Victoria crescent ecosystem; 34
warthogs and 14bush pigs included
 Detection of ASF viral DNA undertaken by targeting the conserved VP72
region of ASFv genome
 Animal genotyping done using the Illumina 50K and 80K SNP chips; 373
genotypes of international commercial breeds, wild European boar
sourced from collaborators.
Disease tolerance in pigs

18. Potential for Biotech in Pigs
1. Understanding gene flow and genetic structure
2. Identification of potential candidate animals for gene
mapping

19. Breed type and infection status
Indigenous Proportion ASFv Negative
(N=54)
ASFv Positive
(N=52)
< 25% 0 39
26 – 50% 0 4
51 – 75% 18 1
>75% 36 8
Proportions of pigs testing positive for ASFv given varying levels of indigenous pig ancestry

20. Potential for Biotech
Estimated membership coefficients for wild pigs and
mis-assigned domestic pigs(K = 2)
Estimated membership coefficients for
individual pigs (K = 2 to 7)

21. PIGS
Bush Pig
Homabay
Indigenous
Busia
Indigenous
Warthog
Bush Pig
Selective sweeps (iHS). The -log10(FDR-adjusted P)
values are plotted against chromosome numberDistribution for pigs showing PCA plot 1 vs 2

22. Implications for pig utilization
Biotechnology can help in managing the effects of disease if
genetic determinants are known
Much more work needs to be done to make this possible

23. Fecundity in Goats

24. Goats are compelling
Increasing demand for meat
Diminishing land sizes
Shorter generation interval
Africa has a very strong goat meat culture

25. Prevalence of “kidding type”
Type of Kidding
Agro-
Ecological
Zone
Singleton Twin Triplets Quadruplet Sextuplets Total
Western
Highlands 23 74 58 4 1 160
Forest 5 94 23 2 0 124
Total
(%)
28
(9.8)
168
(59.1)
81
(28.5)
6
(2.1)
1
(0.3)
284
Results from household survey

26. High Value Super Does

27. High Value Super Does
Njitapon-Kouonja SuperDoe Super Does
 Soper Doe 1: More than ten
kiddings = {1, 3, 4, 4, 4,…, 3} =
total 35 kids
 Super Does have the potential to
increase the efficiency of meat
offtake, reduce land degradation,
and reduce émission of methane.

28. We R
here
Association analysis of 100 - 200 superdoes versus an equal
number of normal Does (routinely deliver singletons),
genotype candidate Booroola homologue and GBS genome
scan.
Collet tissue specimen from 100 -
200 does with 3+ kids on more than
2 kiddings from Njitapon, CAM plus
100 does with 1 kid at a time for
more than 3 kiddings
Genotype at four SSR loci
{OarAE101, TGLA68, BM1329,
TGLA54, BMS2508} linked to the
sheep Fec genes
GBS of Super does and controls
on MiSeq. Genome which scan
for possible novel goat
fecundity loci
Develop and validate a
MAS DNA assay for high
fecundity to test Bucks
Discovery and utilisation of high
fecundity genes in African Goats

29. Potential for Biotech in Goats
1. Understanding the genetic basis for high litter size
2. MAS of young bucks to sire super does

30. Challenges
The potential impact of biotech cannot be realized if
farmers do not know the basics
Researchers need to engage more with farmers
Phenomic gap limits what can be done
Access to markets/inputs need to be sorted out

31. PARTNERS

32. The END