Utilizing Genomics in genetic improvement

Molecular genetics as a tool in wildlife breeding, management and conservation

(An African Buffalo case study)

Ben Greyling ARC-API, Irene

Menu Role of Mol. Gen. in wildlife management/conservation/breeding

The ABC of DNA

The African buffalo: A case study

Genomics: Where do we stand?

The Cattle model: from genetic variation, to marker assisted

selection to quantitative variation

Cape buffalo – recent developments

Primary objective of conservation and management

To protect diversity, ensure sustainable use of the resource Driving forces: need to qualify and quantify

Role of Mol tools: Supply baseline info Levels of genetic variation, inbreeding Pop structure – genetic distances/assignment? Gene flow between populations? Effective population size vs. census size Admixture (Genomics..) Relationship between variation and fitness/adaptation Gene regulation/expression under environmental control

More applications…

Forensics and traceability: Individual ID

Parentage verification (selection and management tool)

Hybrid identification

Genomics: Quantitative variation – from genotype to

phenotype

Epigenetics: Environments effect on genes - heritable

trait expression..

…AACGTGTTGACGCCGTAATGCATAATC

THISWILLEVENTUALLYDRIVEYOUCRAZYCGCTAGCCTTCGGCAATC...

The value of Mol Gen tools:Making sense of “useless information”

A A C G C T T A G C T A G C T C A

T T G C G A A T C G A T C G A G T

T

insertion

deletionPoint mutation (SNP)

3000 000 000 letters per cell…

African buffalo: A major role player in our ecosystems/metapopulation

Largest populations confined to conservancies

Model species with regard to pop. dynamics - factors

affecting it Genetic variation, structure, gene flow, disease status, etc.

Contributed immensely to conservation and

management strategies

Case studies: Population structure

KNP vs. HiP99% accurate assignment of individuals to pops due to genetic distance D is tributio n o f the L o g lik e liho o d o f a s s ig nm e nt fo r K N P a nd H iP

0 5 10 15 20 25 30 35 40

Log lik e lihood of as s ignme nt to K N P

0

5

10

15

20

25

30

35

40Lo

g lik

elih

ood

of a

ssig

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HiP

HiPKNP

Case studies: Genetic variation

Periods of low Ne for some populations in SA:?? sustainability of genetic variation?? compromised adaptation in response to changing

environment?

Example: Genetic erosion in HiP: 1% per year

East vs. southern African subpopulations?

Little genetic differentiation

East/southern African population a separate management unit, differ substantially from central/west African lineage

Substantial variation in both sub-populations

Gene expression/regulation: The Y-Chromosome

Its raining men

Environment and body condition: switch on/switch off…

Sex ratio distorted: more males in the wet season

Particular genotypes dominate depending on

environment (season) – affect sex ratio

Sex ratio and BTB-link?

Heterozygote-fitness-correlation (HFC)

Low genetic variation = low body condition – affect genes

on the “Y”

Bad genes expressed in southern KNP, link to BTB, what

the Y is going on?….

Females can also affect sex ratio…

Epigenetic factors?

BTB susceptibility may have an epigenetic link –

heritable..

Ranches: management-scenario’s

Small populations, restricted gene flow

Controlled breeding (non-random mating)

Fragmented populations and “lines”

Breeding and selection among “lines”, e.g. Addo-Lowveld

Preference for market-desired phenotypes

Potential consequences of ranching

Reduction in genetic variation (inbreeding?)

Increase in frequency of deleterious alleles

Loss of adaptive genes/fitness

disease resistance, reproduction, growth etc.

Reduction in effective pop size – sustainability of

variation?

Admixture – potential outbreeding depression

Compromised adaptability

Genomics to the rescue: Linking the DNA code to

performance and phenotype (amongst others…) SNP vs. full genome sequences – from a good amount of

info to a desired amount of info

Powerful tools to address needs of wildlife industry

Substantially applied to livestock

Quantitative genetics: Selection tool for superior

genetics

Fast track genetic improvement

Genomics for buffalo?

3K SNP panel already developed identified using

next generation sequencing technology

Projects in pipeline using the 3K panel = more

powerful approach

Buffalo and quantitative genetics: Breeding values

on the horizon?

Scope for genomic breeding values…

Requirements for Genomics:

Accurate pedigrees Phenotypic records Reference populations DNA (SNP) profiles Test populations

The future is now with this technology

Are we ready to adopt?