APFA

1. Genetic technologies to support a transformation to profitability and competitiveness in F. merguiensis and P. monodon2009/724 Presented by Wayne Knibb, University of Sunshine Coast APFA

3. 2nd June 2012 profitability and competitiveness Beyond means of ordinary Australians on a regular basis Local 50$/kg Local

4. 2nd June 2012 Imports of seafood now overtaken our exports both in $ and volume This creates issues about food security at a national level

5. 2nd June 2012 profitability and competitiveness Can genetics make prawns more competitive?

6. Genetics Can genetics make prawns more competitive? Compare prawns with chickens: Genetics Close life cycle

7. Genetic technologies to support a transformation to profitability and competitiveness in F. merguiensis and P. monodon 2009/724 Objective 1 Understand if past and existing breeding practices led to significant inbreeding, and ...

8. Objective 1 Understand if past and existing breeding practices led to significant inbreeding, and ... 23% • 2000: ≈ 20 fertilized wild females • about 20 different mitochondrial haplotypes • Mass selected for size over 15 generations • 2012: domestic > wild • after 7 generations of selective breeding we see now only 4 haplotypes remaining in this line • after 12 generations there were 2 haplotypes • Repeated work with DNA microsatellites • Multiple ‘pure’ lines • with similar loss of mt DNA haplotypes and microsats • Estimate very approximately 12.5% inbreeding depression or loss • After controlling for : • stocking density • days of production during the wet season • year stocked • year harvested • age • pond area • feed amount • feed type • total days in production. • This corresponds to about 1-2% increase per generation

9. Objective 1 Understand if past and existing breeding practices led to significant inbreeding, and ... 14% 37% • Estimate very approximately 12.5% inbreeding depression or loss • However, there is a possibility to merge the “pure” lines so that inbreeding is removed, and diversity restored • This is being done, and first comparisons of pure vs crossbred lines available: • cross breds > pure • consistent with inbreeding • without inbreeding, • selection response ≈ 2-3% per generation • can this be further improved on current mass selection methods?

10. Genetic technologies to support a transformation to profitability and competitiveness in F. merguiensis and P. monodon 2009/724 Objective 1 Understand if past and existing breeding practices led to significant inbreeding, and ... Objective 2 What is the genetic basis for commercial traits (estimate genetic heritabilities and correlations for commercially important traits). 

11. Objective 2 What is the genetic basis for commercial traits • To maximize selection response: • determine which traits can respond to selection and which won’t, or • to what degree is the variation due to environmental vs geneticvariation (demystify) Mum 1 Mum 2 Mum 3 ? Look at offspring raised in same environment:

12. Objective 2 What is the genetic basis for commercial traits Mum 1 Mum 2 Mum 3 Development of genetic markers to make pedigree 2nd generation transcriptome and genome sequencing Result: 10 high quality, polymorphic loci for each species Designed primers for 70 loci Agarose gel and genotyping to identify best loci Identified 800+ microsatellites • To maximize selection response: • determine which traits can respond to selection and which won’t, or • to what degree is the variation due to environmental vs genetic variation 25% we need a pedigree on the farm – first for prawns?? NB: can track to farm, pond, grandma!!!

13. Objective 2 What is the genetic basis for commercial traits Mum 1 Mum 2 Mum 3 • To maximize selection response: • determine which traits can respond to selection and which won’t, or • to what degree is the variation due to environmental vs genetic variation 40% 25% after correction for fixed effects apply for monodon?

14. Objective 2 What is the genetic basis for commercial traits Mum 1 Mum 2 Mum 3 • To maximize selection response: • manage adverse genetic correlations • and develop selection index (that maximizes the $ return from selection) The decision to use this information will depend on Seafarm

15. Genetic technologies to support a transformation to profitability and competitiveness in F. merguiensis and P. monodon 2009/724 Objective 1 Understand if past and existing breeding practices led to significant inbreeding, and ... Objective 2 What is the genetic basis for commercial traits (estimate genetic heritabilities and correlations for commercially important traits). Objective 3 Can we find commercial genes (Determine if functional markers for a range of commercial traits are commercially feasible).  

16. Different ways to identify markers. Our group has focused on DNA microarrays Previously........ Vs WILD – good spawner Pond Reared – poor spawner

17. reduced pmLSD levels detected in oocytes of captive-reared may play a role in reduced lipid accumulation in oocytes in/of captive-reared animals. Gene Expression Profiling of the Cephalothorax and Eyestalk in PenaeusMonodon during Ovarian Maturation Philip Brady, Abigail Elizur,  Richard Williams, Scott F. Cummins, and Wayne Knibb. Int J Biol Sci. 2012; 8(3): 328–343.

18. So confident this technology can find genes associated with traits, but can it be used in genetic selection ...

19. Detection of colour genes in bananas with DNA microarrays Vs Light raw and cooked colour Darker raw and cooked colour Label cDNA (from RNA) with fluorescent dye Hybridize to microarray slides

20. Detection of colour genes in bananas with DNA microarrays Vs Light raw and cooked colour Darker raw and cooked colour Label cDNA (from RNA) with fluorescent dye Hybridize to microarray slides

21. Microarray technology Light raw and cooked colour Darker raw and cooked colour Label cDNA (from RNA) with fluorescent dye 3 chips (one here), 8 fields per chip, 15,000 spots per field, 4 fields for dark, 4 fields for light

22. Microarray technology Light raw and cooked colour Darker raw and cooked colour Label cDNA (from RNA) with fluorescent dye Gene expression levels for one gene explains most of the variation in colour

23. Microarray technology Light raw and cooked colour Darker raw and cooked colour Does the gene segrate with hi and lo colour families?

25. HPV High HPV titre Low HPV titre Find families with hi and lo titre (if they exist)

26. Genetic technologies to support a transformation to profitability and competitiveness in F. merguiensis and P. monodon 2009/724 Objective 1 Understand if past and existing breeding practices led to significant inbreeding, and ... Objective 2 What is the genetic basis for commercial traits (estimate genetic heritabilities and correlations for commercially important traits). Objective 3 Can we find commercial genes (Determine if functional markers for a range of commercial traits are commercially feasible).  

27. Conclusions: • New transformational technologies • genetics “on the farm” • new high quality DNA pedigree markers • Breeding values and selection index for new aquacultured species • inbreeding restoration • Discoveries/ basic science • heritabilities for colour in crustacea and other traits • candidate genes for commercial traits • prawns are monogamous • Insights from Seafarm regarding science for price, growth, survival: • Colour selection, tracking with microsats • Size selection, outbreed, leading to selection index • HPV acknowledgements

28. Contributors USC: Wayne Knibb, Abigail Elizur, Anna Kuballa, Paul Whatmore, Nicole Ertl, Rob Lamont, Dan Powell, Angelico Madaro, Jane Quinn, Nguyen Nguyen