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Ben Greyling ARC-API, Irene

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 w ildlife management/conservation/breeding The ABC of DNA

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Ben Greyling ARC-API, Irene

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  1. Utilizing Genomics in genetic improvementMolecular genetics as a tool in wildlife breeding, management and conservation (An African Buffalo case study) Ben Greyling ARC-API, Irene

  2. 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

  3. 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

  4. 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..

  5. …AACGTGTTGACGCCGTAATGCATAATCTHISWILLEVENTUALLYDRIVEYOUCRAZYCGCTAGCCTTCGGCAATC...…AACGTGTTGACGCCGTAATGCATAATCTHISWILLEVENTUALLYDRIVEYOUCRAZYCGCTAGCCTTCGGCAATC... The value of Mol Gen tools: Making sense of “useless information”

  6. 3000 000 000 letters per cell… T Point mutation (SNP) deletion A A C G C T T A G C T A G C T C A T T G C G AAT C G A T C G A G T insertion

  7. 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

  8. Case studies: Population structure • KNP vs. HiP 99% accurate assignment of individuals to pops due to genetic distance

  9. 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

  10. 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

  11. 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?

  12. 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..

  13. 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

  14. 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

  15. 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

  16. 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…

  17. Requirements for Genomics: • Accurate pedigrees • Phenotypic records • Reference populations • DNA (SNP) profiles • Test populations

  18. The future is now with this technology Are we ready to adopt?

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