Nutrigenomics is the emerging application of genomics tools to nutritional research. It allows studying how foods affect genes and how genetic differences impact nutrient responses. This is important for aquaculture, which has lagged medical research in genetics but is now a rapidly changing field. Recent nutrigenomics studies in fish include examining gene expression changes from replacing fish oil/meal with vegetable alternatives, and identifying genes involved in lipid metabolism and digestion to inform sustainable aquaculture feed development. The high-throughput data requires bioinformatics analysis to develop diets that optimize production economics and animal welfare.

1. NutrigeNomics: the emergiNg face of
aquaculture
NutritioN
NutrigeNomics: the emergiNg face of
aquaculture
NutritioN
SMIT R. LENDESMIT R. LENDE
Dept. of AquacultureDept. of Aquaculture

2. Content

3. •Aquaculture has lagged far behind medical research
in applying genetics improvement technique but this
is rapidly changing field.
•However last 25 year was favorable period for
development aquaculture genomics.
•Nutritional science has long tradition for
recommending specific diets to the farmed fishes for
getting more production.
IntroductionIntroduction

4. • Nutrigenomics is the application of high throughput genomics
tools in nutritional research.
• Nutrigenomics is the study of “how foods affect genes and
how individual differences in genetic makeup affect the ways
in which animals respond to nutrients with regard to health”.
• Communication is an essential part of scientific life and many
would regard research that is not passed on to others as being
incomplete.
• Hence the present discussion is the bridge in between genome
based technology and aquaculture nutrition programs.

5. Brief history of fish nutrition
* Prior to 1950s:
-Empirical feed formulation research with a variety of ingredients
-Nutritional diseases quite prevalent
-Little solid information on nutritional requirements
* 1950s and 60s:
-“Golden age” due to development of semi-purified diet that
allowed single nutrients to be deleted and added back (Halver’s
PhD work)
-Vitamin and amino acid requirements of salmon and trout were
discovered
-Common nutritional diseases eliminated

6. Cont…
*1970s :
-Essential nutrient list expanded to other species
-Refinement of nutrient requirement estimates using new approaches to
assess nutritional adequacy
*1980s and 90s: Aquaculture production takes off
-Need for economical and efficient grow-out feeds
-New species including those with larval stages
-Low-pollution feeds (low-phosphorus, highly digestible)
*2000
-Main story is alternative protein and lipid sources
-Sub-plot is supplements to enhance disease resistance, provide “semi-
essential nutrients” and to produce healthful products (low in POPs, high
in omega-3 fatty acids)

7. Origin of Nutrigenomics
• The concept that diet influences health is an ancient one.
• Nutrigenomics includes known interactions between food
and inherited genes, called inborn errors of metabolism,
that have long been treated by manipulating the diet.
• The Human Genome Project of the 1990s, which
sequenced the entire DNA in the human genome, jump-
started the science of nutrigenomics.

8. • Nutrigenomics brings along new terminology, novel
experimental techniques and a fundamentally new
approach to nutrition research, such as high-
throughput technologies that enables the global
study of gene expression in a cell or organism.
• Hence to see how molecular approach is useful in
fish nutrition the current discussion is with some
recent studies on nutritional regulation of candidate
gene expression.

9. Genomics and Aquaculture
• Functional genomics – the combination of genomics,
proteomics, transcriptomics, and metabolomics has expanded
rapidly over the last decade, but research on important
aquaculture species is still relatively uncommon.
• Nutrigenomics uses a number of “omic” disciplines, including
1. Transcriptomics: The complete collection of gene
transcripts in a cell or a tissue at
a given time.
2. Proteomics : The study of proteomes (the
complete collection of proteins in
a cell or tissue at a given
time),which attempts to determine
their role inside cells and the
molecules with which they interact.

10. 3. Metabolomics : The study of the metabolome,
which is the entire metabolic
content of a cell or organism, at
a given time.
4. Epigenomics : Epigenomics is the study of the
complete set of epigenetic
modifications on the genetic
material of a cell, known as the
epigenome.
• The huge data sets generated by this research rely
heavily on the field of bioinformatics, which has
developed new methods to acquire, store, share,
analyze, present, and manage the information.

11. BIOACTIVE FOOD COMPONENTS CAN MODIFY TRANSCRIPTION,
TRANSLATION AND METABOLISM

13. Candidate Gene Approach in Fish
Nutrition
1. Nutritional regulation of digestive physiology at a
molecular level
suppression of live diets and replacement by
inert-formulated diets in marine fish larvae
*Production of marine fish larvae and juveniles
European sea bass, Gilthead seabream, Red sea
bream, in commercial hatcheries still depends on
the supply of live prey, such as rotifers and Artemia.

14. • Compound diet substitution for live prey is crucial
for lowering production costs and for sustaining
production of high and constant quality juveniles.
• A number of studies have attempted to determine
the timing of initiation of feeding and/or
gastrointestinal functionality in fish larvae.

15. How molecular techniques may help
to answer to this question
How molecular techniques may help
to answer to this question
• This adaptation may be due to a molecular
regulation of their gene expression.
• Coordinated decrease between specific activity and
mRNA levels of amylase enzyme is
transcriptionally regulated during larval
development.
• As such, amylase mRNA and activity are very high
during young larval stages and decrease during the
development of larvae.

16. 2. Nutritional regulation of lipid metabolism
suppression of fish oil/fishmeal by vegetable
products without negative consequences on fish product
quality
• Increased demand for fish oils in feed industries.
• Only sustainable alternative to fish oils is plant
(vegetable) oils.
• Plant oils rich in C18 but devoid of the essential fatty
acids such as Eicosapentaenoic acid (EPA) or
docosahexaenoic acid (DHA),compromising their
nutritional value.

17. • Understanding the molecular basis of fatty acid
biosynthesis and its regulation in fish is indeed
necessary to enable efficient and effective use of
vegetable oils in aquaculture.

18. Genomics research initiative in farmed
fish
• Teleosts are diverse groups of more than 23,000
species.
• Fish undergone whole genome duplication at one or
other point of their evolution (Taylor et al., 2003).
• Initially, model fish species for genomics were
zebrafish and medaka (Oryzias latipes), two
freshwater species – models for developmental and
genetic research – and the pufferfish (Fugu rubripes
and Tetraodon nigroviridis) (Cossins and Crawford,
2005).

19. • Over the past 5 years, genomics programmes1 have
been initiated for ‘model’ farmed fish species
(Thorgaard et al., 2002; Liu, 2003; Rise et al., 2004)
• Carnivorous fish salmonids (rainbow trout and
Atlantic salmon) and striped bass Morone saxatilis
• Omnivorous channel catfish Ictalurus punctatus
• Semi-carnivorous tilapia Oreochromis mossambicus

21. Case study ICase study I

23. • Methods
1. cDNA microarrays
2. Hybridisation: scanning and quantifications of
microarrays
3. Microarray data analysis
4. Data mining
5. Real-time RT-PCR
Duration of experiment: 9.5 weeks

25. ResultsResults

27. Result

31. Conclusion
• Total removal of ingredients of marine origin is not
essential for sustainable aquaculture development,
knowledge on potential implications of such
extreme diets is useful.
• The use of transcriptomics data obtain from these
investigation helpful for the development of novel
aquafeeds.

32. Future DirectionsFuture Directions
• By increasing understanding of dietary manipulation
effects on fish production, scientists can develop
elite feeds with positive effects on production
economics and animal welfare, and develop
“designer fish” that target specific market demands.
• One important challenge concerning our future is to
establish and maintain sustainable and profitable
food production.

33. THANK YOU FOR ATTENTION