resource use efficiency in livestock: bridging the biotechnology-livestock productivity gap in east...
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Resource use efficiency in livestockBridging the biotechnology-livestock productivity gap in East Africa
Dr. Denis Fidalis Mujibi The Nelson Mandela Africa Institution of Science and Technology (NMAIST), Arusha Tanzania
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Milk Yield in Cows
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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.
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I want 30 liters!
MOVE
Crossbreed
Adaptation
Optimize
Upgrade
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Where’s the milk?
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Background: The problem
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Background: The problem
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Potential for Biotech in Dairy Cattle
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Breed Composition of Dairy Cattle
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Breed Composition in East Africa
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Level-1 Level-2 Level-30
2
4
6
8
10
12 Uganda
21-35% 36-60% 61-87.5% >87.5%
Herd environment level
Daily
milk
yie
ld (l
/day
)
7 l/day
5 l/day
7 l/day
5 l/day
Level-1 Level-2 Level-30
2
4
6
8
10
12
Kenya
21-35% 36-60% 61-87.5% >87.5%
Herd environment levelDa
ily m
ilk y
ield
(l/d
ay)
2.5 l/day3.5 l/day
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The Folly of Phenotype!
Ngobe Zerida II
73%
4.9 ltr/day
Rank: 209/285 11.06 ltr/day
77%
Rank: 1/285
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Conclusion
Biotechnology can offer solutions to navigate genotype by environment interactions
The tools must be affordable to farmersFarmers must master the basics of dairy and apply best
management practices first
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Disease tolerance in Pigs
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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
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Disease tolerance in pigs
Domestic pigBushpig
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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
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Potential for Biotech in Pigs
1. Understanding gene flow and genetic structure2. Identification of potential candidate animals for gene mapping
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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
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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)
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PIGS
Bush Pig
Homabay Indigenous
BusiaIndigenous
Warthog
Bush Pig
Selective sweeps (iHS). The -log10(FDR-adjusted P) values are plotted against chromosome number
Distribution for pigs showing PCA plot 1 vs 2
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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
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Fecundity in Goats
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Goats are compelling
Increasing demand for meatDiminishing land sizesShorter generation intervalAfrica has a very strong goat meat culture
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Prevalence of “kidding type”
Type of Kidding
Agro-EcologicalZone
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
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High Value Super Does
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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.
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We R here
FecGOATDesign
DEC 2013
FECGOATGBS Data
MAR 2014
FECGOATMAS TOOL
DEC 2013
CandidateFecGOAT
GeneFecGOATSamples ReadySEP 2013
JUL 2013
DEPLOY
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
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Potential for Biotech in Goats
1. Understanding the genetic basis for high litter size2. MAS of young bucks to sire super does
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Challenges
The potential impact of biotech cannot be realized if farmers do not know the basics
Researchers need to engage more with farmersPhenomic gap limits what can be doneAccess to markets/inputs need to be sorted out
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PARTNERS
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The END