Utilizing Genomics in genetic improvement Molecular genetics as a tool in wildlife breeding,...
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Transcript of Utilizing Genomics in genetic improvement Molecular genetics as a tool in wildlife breeding,...
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..
…
AACGTGTTGACGCCGTAATGCATAATCTHISWILLEVENTUALLYDRIVEYOUCRA
ZYCGCTAGCCTTCGGCAATC...
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. HiP
99% 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
40L
og li
kel
ihoo
d of
ass
ignm
ent
to H
iP
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