Landscape genomic approach to investigate genetic adaptation in South

African indigenous goat populationsFC Muchadeyi1; K Mdladla1;2 & EF Dzomba2;

1Biotechnology Platform, Agricultural Research Council, South Africa2Department of Genetics, University of kwaZulu Natal, Pietermaritzburg, South Africa

Indigenous Animal Genetic Resources (AnGR)

• An important resource for smallholder communal farmers

• Food security• Income generation• Risk aversion• Social cultural roles• Improved livelihoods

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 breedsAngora 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

Challenges on indigenous goat production

• Raised under extensive systems of productionLow input production systems

Feed, water, housing, veterinary

• Exposed to harsh and fluctuating conditionsEnvironmental extremitiesInsufficient and low quality feed supplyExposure to disease pathogens

Impact of goat production system

• Low productivity• High mortalityTherefore -:• Farmers’ livelihoods not improved• Local genetic resources are threatened

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

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

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

Aim

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

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

Phenotypic characterisation

Horns/polled

Coat colour

Beard/Goatee

Morphological characterisationChest girth

Pin bone

Chest width

Texture/length of hair

Coat patterns

Ears

Height

Length

Population based clustering using morphometric linear body measurements

Geographical information systems (GIS) data

e.g. Annual rainfall distribution

Intermediate rainfall

Low rainfallHigh temperatures

High rainfall

High rainfallDry desert- Tankwa

High rainfall

Limpopo

Eastern CapeNorthern Cape

Kwazulu-Natal

North West

• Climatic data

Tick burden

Tick-borne diseases-Heartwater

Vegetation and feed resources

Environmental Data

Disease pathogens• Prevalence?

Viral diseases-ORFV

Bacterial pathogensE. coli 0157Salmonella sp.

Tick vector distribution

Availability...Scarce/ abundant

Spread

Role of vegetation

Factors influencing sero-prevalence

Risk factors to heartwater infection• Breed

• Indigenous and Savannah at more risk relative to Boer• Province

• Limpopo• Production system

• Smallholder

Commercial meat type breedsB: SavannaC: Kalahari RedD: BoerDeveloped breeds

E-G: Village ecotypes phenotypic representationsKwazulu-Natal (Zulu)North West (Tswana)Limpopo (Venda)Eastern Cape (Xhosa)

Local language and does not

represent breeds

Naming system

H: Feral goat populationTankwa

Genotyping of SA indigenous goat populations

Nguni ecotype• SA Veld goats• Indigenous

ecotypes• Kept by breeders

in Kwazulu-Natal

192 goats

PC1 vs PC2

BoerSavannaKalahari Red

ZuluVenda

TswanaXhosa

Tankwa

Commercial

Village ecotypes

NguniPCA

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

Population pairwise Fst

Tankwa

Boer

Savanna

KR

Nguni

Venda

Zulu

Tswana

Xhosa

Tankwa Boer Savanna KR Nguni Venda Zulu Tswana Xhosa

Per Marker Fsta) 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

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

Acknowledgements

African Goat Improvement Network