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

Milk Yield in Cows

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.

I want 30 liters!

MOVE

Crossbreed

Adaptation

Optimize

Upgrade

Where’s the milk?

Background: The problem

Background: The problem

Potential for Biotech in Dairy Cattle

Breed Composition of Dairy Cattle

Breed Composition in East Africa

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

The Folly of Phenotype!

Ngobe Zerida II

73%

4.9 ltr/day

Rank: 209/285 11.06 ltr/day

77%

Rank: 1/285

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

Disease tolerance in Pigs

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

Disease tolerance in pigs

Domestic pigBushpig

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

Potential for Biotech in Pigs

1. Understanding gene flow and genetic structure2. Identification of potential candidate animals for gene mapping

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

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)

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

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

Fecundity in Goats

Goats are compelling

Increasing demand for meatDiminishing land sizesShorter generation intervalAfrica has a very strong goat meat culture

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

High Value Super Does

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.

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

Potential for Biotech in Goats

1. Understanding the genetic basis for high litter size2. MAS of young bucks to sire super does

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

PARTNERS

The END