A landscape genomics approach in unravelling adaptive genetic diversity in goats: A case study of South Africa presentation by Farai Muchadeyi, Agricultural Research Council, Pretoria, South Africa

1. Landscape genomic approach to
investigate genetic adaptation in South
African indigenous goat populations
FC Muchadeyi1; K Mdladla1;2 & EF Dzomba2;
1Biotechnology Platform, Agricultural Research Council, South Africa
2Department of Genetics, University of kwaZulu Natal, Pietermaritzburg, South Africa

2. Indigenous Animal Genetic
Resources (AnGR)
• An important resource for smallholder
communal farmers
• Food security
• Income generation
• Risk aversion
• Social cultural roles
• Improved livelihoods

3. SA GOAT PRODUCTION
• South Africa has over 6 million goats
• Raised either by commercial farmers or by the
small-scale and emerging farmers
The SA Boer Goat, Savanna and Kalahari Red are
the commercial meat breeds
Angora goats ---hair production
• Indigenous uncharacterised goats represent the
majority (63%) of the goats in SA
• Tankwa goat….feral goat population originating
in the karoo desert ….now moved to a
conservation unit

4. Challenges on indigenous goat
production
• Raised under extensive systems of production
Low input production systems
Feed, water, housing, veterinary
• Exposed to harsh and fluctuating conditions
Environmental extremities
Insufficient and low quality feed supply
Exposure to disease pathogens

5. Impact of goat production system
• Low productivity
• High mortality
Therefore -:
• Farmers’ livelihoods not improved
• Local genetic resources are threatened

6. How do we improve the situation?
• Strategies to change the production environment
 Improved feed resources, housing and general management
 Veterinary interventions
• But not sustainable
 Farmers have limited capacity to improve production environment
 Most will depend on donors
• Improved genetics by identifying animals that can produce
optimally under the existing production environment
 Animals resistant or tolerant to local disease pathogens
 Animals able to utilize locally available low quality feed resources
• Minimise production cost but make the smallholder livestock
enterprises viable

7. Landscape genomics as a strategy
• Communal and feral goats thrive under a host of harsh
environmental, climatic & nutritional conditions, &
impediments to gene flow
• Allele frequencies for selected genes are shifted ultimately
leading to local adaptation
• Morphological traits linked to differentiation of goat
populations according to breed and may explain adaptation to
local environmental conditions
The genetic mechanisms underlying local adaptation in
these marginal populations is crucial for goat genetic
improvement strategies and conservation of adaptated
genetic resource

8. Working Hypotheses
• Indigenous AnGR are seen as an important genetic reservoir
developed over thousands of years and successful in
extreme and unusual environments with limited veterinary
and management input.
• AnGR are expected to have developed genetic adaptation
mechanisms that help them to survive the harsh and diverse
production environments
 Landscape genomics::: Genes and genomic regions have
been selected in response to selection imposed by the
environment and production systems
 Footprints of selection associated with specific environments

9. Aim
• To evaluate the indigenous goat genetic
resources of South Africa for adaptation
using a landscape genomics approach for
their proper utilization and conservation

10. Production systems
• Flock composition and size
• Role of goats at household
levels
• Management
• Feeding and water
• Housing
• Health and interventionsQuestionnaire surveys
Understanding the dynamics of populations

11. Phenotypic characterisation
Horns/polled
Coat colour
Beard/Goatee
Morphological characterisation
Chest girth
Pin bone
Chest width
Texture/length of hair
Coat patterns
Ears
Height
Length

12. Population based clustering using
morphometric linear body measurements

13. Geographical information systems (GIS)
data
e.g. Annual rainfall distribution
Intermediate
rainfall
Low rainfall
High temperature
High
rainfall
High rainfallDry desert- Tankwa
High rainfall
Limpopo
Eastern Cape
Northern Cape
Kwazulu-Natal
North West
• Climatic data

14. Tick burden
Tick-borne diseases-
Heartwater
Vegetation and feed resources
Environmental Data
Disease pathogens
• Prevalence?
Viral diseases-ORFV
Bacterial pathogens
E. coli 0157
Salmonella sp.
Tick vector distribution
Availability...Scarce/ abundant
Spread
Role of
vegetation

15. Factors influencing sero-prevalence
Risk factors to heartwater infection
• Breed
• Indigenous and Savannah at more risk relative to Boer
• Province
• Limpopo
• Production system
• Smallholder

16. Commercial
meat type breeds
B: Savanna
C: Kalahari Red
D: Boer
Developed breeds
E-G: Village ecotypes phenotypic representations
Kwazulu-Natal (Zulu)
North West (Tswana)
Limpopo (Venda)
Eastern Cape (Xhosa)
Local language
and does not
represent breeds
Naming system
H: Feral goat population
Tankwa
Genotyping of SA indigenous goat populations
Nguni ecotype
• SA Veld goats
• Indigenous
ecotypes
• Kept by breeders
in Kwazulu-Natal
192 goats

17. PC1 vs PC2
Boer
Savanna
Kalahari Red
Zulu
Venda
Tswana
Xhosa
Tankwa
Commercial
Village ecotypes
Nguni
PC
A
Population
PC1 Commercial vs
Indigenous
PC2 Tankwa
PC3 Zulu/Venda vs
Tswana/Xhosa
PC4 Tswana vs Xhosa
PC5 Outliers of Savanna
and KR
Principle Component analysis

18. Population pairwise Fst
Tankwa
Boer
Savanna
KR
Nguni
Venda
Zulu
Tswana
Xhosa
Tankwa Boer Savanna KR Nguni Venda Zulu Tswana Xhosa

19. Per Marker Fst
a) Tankwa vs commercial and ecotypes
• Morphometric measures
 1223 significant SNPs
 CW = 403 SNPs
 H = 455 SNPs
 CG = 179 SNPs
 L = 102 SNPs
 PB = 84 SNPs
• GIS information
 Identified 619 SNPs possible for
adaptive selection
 Long = 428
 Winter mean Tmin= 163
 Annual mean Tmax = 15
 Alt = 13

20. Summary & Implications of Results
• Heterogeneous production systems each imposing unique
selection pressures on the goat genetic resources
• Populations clustered according to their production systems
• Genetic differences between commercial, village and feral
goat populations
 Diverse gene pool with indications of unique set of alleles prevailing in
different production systems
 Next step towards determination of alleles and genotypes conferring
genetic adaptation
• Alleles and genotypes fixed towards certain production
systems and geographical landscape

21. Acknowledgements
African Goat
Improvement
Network