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Resource Use Efficiency: Applications
of Biotechnology in Genetic
Improvement in Tropical Aquaculture
David J Penman
Insti...
Scope of talk
• This talk will cover biotechnologies (as understood
from prior FAO definitions) related to genetic
improve...
Relevant biotechnologies
• Chromosome set manipulation
• Sex ratio manipulation
• Cryopreservation
• DNA markers, linkage ...
Relationship with selective breeding
• Selective breeding is not included in the scope of
this talk (not considered as a b...
Biotechnologies in Global Aquaculture
• Most of the relevant biotechnologies that I will
describe have been applied to a g...
The context of applying
biotechnologies in aquaculture
• Use of chromosome set and sex ratio manipulation in
controlling m...
Triploidy
• Widely used in rainbow trout, Pacific oyster,
Atlantic salmon in temperate aquaculture to
control maturation/r...
Grass carp – biological containment
Although no requirement for triploidy in grass carp aquaculture
in major producing cou...
Alternative method of control of exotic
species (silver and bighead carp in USA)!
African catfish
(Clarias gariepinus)
• Culture is booming, particularly in Nigeria, with
interesting peri-urban production...
Control of sex ratio
• Desirable in species where one sex grows more
slowly and/or matures earlier than the other, or
wher...
Monosex Female Production in XX/XY Species
XX FEMALES
ALL-FEMALE PROGENY (XX)
COMMERCIAL ONGROWING
XX NEOMALES
MIXED SEX
F...
Monosex female production in the
silver barb (Barbonymus gonionotus)
• Female grows faster than male, ovaries also eaten
•...
Mixed Sex v’s Monosex Tilapia
(photo by GC Mair)
MST SRT/GMT ®
MST = mixed sex tilapia; SRT = sex-reversed tilapia; GMT = ...
Control of Maturation/Reproduction in Nile
Tilapia (Oreochromis niloticus)
Hormonal masculinization (MT in-feed)
• Can be ...
Genomic Location of
XX/XY locus in Nile
tilapia in LG1
Palaiokostas et al (2013)
Monosex Male Production in WZ/ZZ Species
ZZ MALES
“ALL-MALE” PROGENY (ZZ)
COMMERCIAL ONGROWING
ZZ NEOFEMALES
MIXED SEX
FRY...
Genetic sex control in a WZ/ZZ species – the
giant freshwater prawn
• Males grow faster than females in the giant
freshwat...
Cryopreservation
• Not widely used in commercial aquaculture
• Useful for gene banking of founder populations,
efficient f...
Use of DNA markers in genetic
management of captive populations
• Many species of fish can be stripped of eggs and
sperm m...
Use of DNA markers in genetic
management of captive populations
Catla catla
hormonal induction of ovulation (above)
Stripp...
Use of DNA markers in genetic
management of captive populations
Strip
spawning
In vitro
fertilization
Single
family
Separa...
Consequences
• For many highly fecund species, eggs are small and
survival rates very variable, generally low
• No control...
Example - Milkfish (Chanos chanos)
• Important aquaculture species in SE Asia: > 1 million t p.a.
• Catadromous, high fecu...
Use of DNA markers/genomics as tools
in enhancing selective breeding
Genetic Improvement of Farmed Tilapia (GIFT)
• The first major breeding programme for a tropical
aquaculture species – Nil...
Genetic Improvement of Farmed Tilapia (GIFT)
• Multinational, public funding, dissemination to many
countries
• Core breed...
DNA markers for parental allocation in
common carp (Vietnam)
• Earlier mass selection programme showed gain for five
gener...
DNA markers for parental allocation in
common carp (Vietnam)
• Heritabilities moderate to high in both
environments
• Redu...
QTLs and MAS
• Marker-assisted selection (MAS) for quantitative trait loci (QTL)
affecting complex traits such as disease ...
QTLs and MAS
• Many other QTL have been mapped in aquaculture species
• E.g. pearl traits in pearl oyster Pinctada maxima ...
Very long-running evaluation for food safety in USA
FDA issued “Preliminary Finding of No Significant Impact” (May 2012)
h...
Transgenics v’s “gene editing”
• Sledgehammer v’s scalpel?
• Range of techniques (e.g. CRISPR/Cas9)
• Can be used to modif...
Summary
• Aquaculture covers species from well-deloped
breeding programmes to wild seed
• A range of biotechnologies are b...
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Resource use efficiency in fish: Application of biotechnology in genetic improvement in tropical aquaculture

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Resource use efficiency in fish: Application of biotechnology in genetic improvement in tropical aquaculture presentation by David Penman, University of Stirling, Stirling, United Kingdom

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Resource use efficiency in fish: Application of biotechnology in genetic improvement in tropical aquaculture

  1. 1. Resource Use Efficiency: Applications of Biotechnology in Genetic Improvement in Tropical Aquaculture David J Penman Institute of Aquaculture University of Stirling, Scotland, UK
  2. 2. Scope of talk • This talk will cover biotechnologies (as understood from prior FAO definitions) related to genetic improvement in tropical aquaculture • It will attempt to look at these in the context of (improving) resource use efficiency • Focus on (fin)fish species • Globally, aquaculture ranges from well-established domesticated species to capture and ongrowing of wild organisms – this talk will try to reflect this
  3. 3. Relevant biotechnologies • Chromosome set manipulation • Sex ratio manipulation • Cryopreservation • DNA markers, linkage mapping, QTLs, etc • GM technologies
  4. 4. Relationship with selective breeding • Selective breeding is not included in the scope of this talk (not considered as a biotechnology) • However, many of the relevant biotechnologies are used in the context of managing captive breeding programmes and genetic improvement by selective breeding • So, several aspects of the talk will require reference to breeding programmes in relevant species
  5. 5. Biotechnologies in Global Aquaculture • Most of the relevant biotechnologies that I will describe have been applied to a greater extent in non-tropical aquaculture, particularly well- established, high-value species such as salmonids • I will this draw on some examples from such species/culture systems, to illustrate the current trends and the directions that may be followed in tropical aquaculture.
  6. 6. The context of applying biotechnologies in aquaculture • Use of chromosome set and sex ratio manipulation in controlling maturation and reproduction • Use of cryopreservation in gene banking, transfer of genetic material and assessing genetic gain • Use of DNA markers in understanding population structure of wild genetic resources • Use of DNA markers in genetic management (Ne, inbreeding) of captive populations • Use of DNA markers/genomics as tools in enhancing selective breeding • Use of GM and related technologies in enhancing performance in aquaculture
  7. 7. Triploidy • Widely used in rainbow trout, Pacific oyster, Atlantic salmon in temperate aquaculture to control maturation/reproduction • Needs unfertilised eggs and sperm to allow pressure or temperature shocking of newly fertilised eggs • Has been tested in Nile tilapia, including field trials in Africa, with very promising results but incompatible with breeding systems in commercial hatcheries (many females, produce small batches of eggs frequently and asynchronously: embryos or fry collected later) • Potential in other species (PTO)
  8. 8. Grass carp – biological containment Although no requirement for triploidy in grass carp aquaculture in major producing countries, triploidy is widely used in the southern USA where grass carp is an exotic species used to control aquatic plant growth (diploids banned in some states) Juvenile grass carp Screening blood samples to test triploidy
  9. 9. Alternative method of control of exotic species (silver and bighead carp in USA)!
  10. 10. African catfish (Clarias gariepinus) • Culture is booming, particularly in Nigeria, with interesting peri-urban production systems growing • Only one formal breeding programme (WFC, Egypt) – this aspect needs development in SS Africa to support sustainable growth • Genomics/genetics resources being developed (Hungary/UK/Nigeria/Netherlands) • Where market size is large (> 1 kg), ovarian development in females can be significant (20% of total weight): triploidy could eliminate this
  11. 11. Control of sex ratio • Desirable in species where one sex grows more slowly and/or matures earlier than the other, or where both sexes mature and breed before harvest • Sex determination in fish is very varied – sometimes XX/XY or WZ/ZZ, can be polygenic or influenced by environment (temperature during differentiation), also find hermaphroditic species (e.g. grouper, barramundi)
  12. 12. Monosex Female Production in XX/XY Species XX FEMALES ALL-FEMALE PROGENY (XX) COMMERCIAL ONGROWING XX NEOMALES MIXED SEX FRY (XX, XY) MT XX NEOMALES, XY MALES MT Commercial production cycle MT = 17α-methyltestosterone (or other androgens, depending on species)
  13. 13. Monosex female production in the silver barb (Barbonymus gonionotus) • Female grows faster than male, ovaries also eaten • Technique for monosex female production developed in Thailand in 1990s, used in aquaculture but not now used due to decline in popularity of species in aquaculture (snipview.com)
  14. 14. Mixed Sex v’s Monosex Tilapia (photo by GC Mair) MST SRT/GMT ® MST = mixed sex tilapia; SRT = sex-reversed tilapia; GMT = genetically male tilapia
  15. 15. Control of Maturation/Reproduction in Nile Tilapia (Oreochromis niloticus) Hormonal masculinization (MT in-feed) • Can be very effective (but often not very well done!), most commonly used technique, banned in several major countries (not always enforced) GMT (YY males x XX females -> XY males) • Has been used on a small scale commercially, hindered by complexities of sex determination: XX/XY locus, but other genes and temperature [in some families] can affect sex determination, YY production process complex. • Genomic analysis being used to develop sex-linked markers and marker-assisted selection to improve GMT
  16. 16. Genomic Location of XX/XY locus in Nile tilapia in LG1 Palaiokostas et al (2013)
  17. 17. Monosex Male Production in WZ/ZZ Species ZZ MALES “ALL-MALE” PROGENY (ZZ) COMMERCIAL ONGROWING ZZ NEOFEMALES MIXED SEX FRY (WZ, ZZ) WZ FEMALES, ZZ NEOFEMALES Commercial production cycle
  18. 18. Genetic sex control in a WZ/ZZ species – the giant freshwater prawn • Males grow faster than females in the giant freshwater prawn Macrobrachium rosenbergii. • Feminization of ZZ males achieved by surgical removal of androgenic gland. • Developed by Amir Sagi’s group: mass production 2006, used on small scale in Thailand, India, Vietnam… • More recently developed RNAi technique (Aflafo et al 2015) for feminization: double- stranded RNA injection caused temporary silencing of expression of insulin-like androgenic gland hormone (dsRNA degraded rapidly) • Argue that RNAi is a safe biotechnology for this and other uses in aquaculture ZZ neofemale prawn (above) and harvest of all-males (below) (U. Na-nakorn)
  19. 19. Cryopreservation • Not widely used in commercial aquaculture • Useful for gene banking of founder populations, efficient for assessing genetic gain (cryo x current gen v’s current x current) • Interesting case study in Nigeria: o Cryopreserved milt used to transfer genetic material from Netherlands o Males need to be killed to obtain milt – problems with sperm quality o Infrastructure exists for use of cryopreservation in cattle
  20. 20. Use of DNA markers in genetic management of captive populations • Many species of fish can be stripped of eggs and sperm manually, then individual families can be set up and maintained • For some, this is feasible experimentally but not on a commercial scale • For others, mass spawning is still the only feasible way of producing fry • The way fish are bred has consequences for establishing pedigree and controlling Ne/inbreeding
  21. 21. Use of DNA markers in genetic management of captive populations Catla catla hormonal induction of ovulation (above) Stripping of eggs (right)
  22. 22. Use of DNA markers in genetic management of captive populations Strip spawning In vitro fertilization Single family Separate tanks or hapas PIT tags Pedigree data  Stripping and in vitro fertilization make control over pedigree feasible:  Mass spawning makes this impossible without the use of DNA markers: Mass spawning and fertilization Mixed families Single Tank or hapa No family i.d. No pedigree data PIT tags Biopsy sample DNA profiling Pedigree data
  23. 23. Consequences • For many highly fecund species, eggs are small and survival rates very variable, generally low • No control over family contribution to next generation of broodstock -> uneven contribution, lower Ne, inbreeding starts • Control allows more even contribution, higher Ne, also basis for sustainable selective breeding programmes
  24. 24. Example - Milkfish (Chanos chanos) • Important aquaculture species in SE Asia: > 1 million t p.a. • Catadromous, high fecundity, small eggs, long generation time (5-7 years), large broodstock – high investment in broodstock • DNA microsatellite markers developed for parental allocation to allow control of family size/Ne in captive-reared broodstock • Sex-linked markers (not developed yet) would aid in ensuring both males and females retained in all families
  25. 25. Use of DNA markers/genomics as tools in enhancing selective breeding
  26. 26. Genetic Improvement of Farmed Tilapia (GIFT) • The first major breeding programme for a tropical aquaculture species – Nile tilapia • Started 1988, now >20 generations Rearing of separate families in hapas (GIFT Manual, WorldFish Center)
  27. 27. Genetic Improvement of Farmed Tilapia (GIFT) • Multinational, public funding, dissemination to many countries • Core breeding programme run by WorldFish Centre (Penang) • Pedigree established using single pair matings, separate family rearing, PIT tags (no DNA markers) • First private offshoot uses DNA markers, claims faster progress (hard to verify – little information) • Several other secondary breeding programmes in a range of countries, plus other tilapia breeding programmes
  28. 28. DNA markers for parental allocation in common carp (Vietnam) • Earlier mass selection programme showed gain for five generations then stopped (inbreeding/loss of genetic variation) • More recent family-based programme: (i) separate or (ii) communal rearing with parental assignment using DNA markers? • Tested in parallel – same families, split Ninh et al. (2011) Ninh et al. (2013)
  29. 29. DNA markers for parental allocation in common carp (Vietnam) • Heritabilities moderate to high in both environments • Reduced maternal and common environmental effects under communal rearing • Fish grew faster under communal rearing – reduced generation time • Greater response to selection under communal rearing • Perhaps surprisingly, communal rearing and use of DNA markers was cheaper than separate rearing (hapas, extra labour costs)
  30. 30. QTLs and MAS • Marker-assisted selection (MAS) for quantitative trait loci (QTL) affecting complex traits such as disease resistance offers more efficiency than phenotypic selection • MAS for Infectious Pancreatic Necrosis (viral) in Atlantic salmon, in both Scotland and Norway, was the first example of such an application in a commercial breeding programme in aquaculture. QTL in LG21 • Patent has been applied for based on this (WO 2014006428 A1) Houston et al. (2010)
  31. 31. QTLs and MAS • Many other QTL have been mapped in aquaculture species • E.g. pearl traits in pearl oyster Pinctada maxima (also GWAS) • Slow uptake so far, expect to see many more over next few years • Also now seeing many SNP chips being developed (including for tilapia), application of these in breeding programmes being developed • Also seeing breeding companies developing use of genome- wide selection (still in early stages in aquaculture)
  32. 32. Very long-running evaluation for food safety in USA FDA issued “Preliminary Finding of No Significant Impact” (May 2012) http://www.fda.gov/AnimalVeterinary/DevelopmentApprovalProcess/GeneticEngineering/GeneticallyEngineeredAnimals/ucm280853.htm AquaBounty cleared to produce salmon eggs in Canada for commercial purposes (Nov 2013) http://aquabounty.com/wp-content/uploads/2014/02/2013-11.25-AquAdvantage-Salmon-Cleared-for-Production.pdf Aquabounty fined by Panama for regulatory failures in its Panama plant (The Guardian, 29/10/14) If successful in coming to market, this could be a watershed for the development of GM animals – many other developments in the pipeline GM Atlantic Salmon
  33. 33. Transgenics v’s “gene editing” • Sledgehammer v’s scalpel? • Range of techniques (e.g. CRISPR/Cas9) • Can be used to modify/knockdown genes or alleles of genes • Could be used to affect a wide variety of traits in a cost- effective fashion, including disease resistance, sexual development, ….. • Should this be treated in the same way as transgenic organisms (poorly targeted introduction of modified genes, often from other organisms)? Li et al. (2014) Germ cell development manipulation in Nile tilapia via Nanos genes
  34. 34. Summary • Aquaculture covers species from well-deloped breeding programmes to wild seed • A range of biotechnologies are being applied in commercial aquaculture • Most advanced in temperate/high-value species • Relatively limited application in many tropical aquaculture species to date • Genomics and NGS are contributing to the scope and pace of development of new biotechnologies and application to aquaculture • Bright future?

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