This document summarizes a study that used genomics approaches to investigate the molecular basis of sex maturation in Atlantic salmon. The researchers manipulated photoperiod to initiate maturation in female salmon during a specific time window. They collected tissue samples from the brain, pituitary, ovaries and other tissues before, during and after the maturation process to generate transcriptomic and epigenomic data. The goal was to gain mechanistic insights into the triggers for sexual maturation onset in Atlantic salmon, which has implications for the salmon aquaculture industry dealing with issues like early maturation.

1. Molecular
basis
of
sex
matura1on
in
Atlan1c
salmon:
Integrated
genomics
approach
Amin
Mohamed1,
Antonio
Reverter1,
Peter
Kube2,
Brad
Evans3,
Harry
King2,
James
Kijas1
AGRICULTURE
AND
FOOD

2. 2
|
Tasmania
Atlan1c
salmon
farming
industry
• Commercially
important
species
• Annual
output
valued
at
~
$500
million
in
Tasmania
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO

3. 3
|
key
performance
traits
in
Tasmania's
AtlanKc
salmon
stocks:
Ø growth
Ø resistance
to
amoebic
gill
disease
Ø late
matura1on
Salmon
selec1ve
breeding
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO

4. 4
|
Early
matura1on
a
challenge
for
the
salmon
aquaculture
industry
• Salmon
can
mature
early
aUer
their
1st
sea
winter
• Early
matura1on
can
reduce
growth
and
affect:
Ø product
quality
Ø suscepKbility
to
disease;
significant
stock
loss
Journal of the World Aquaculture Society
Volume 47, Issue 5, pages 605-632, 9 AUG 2016 DOI: 10.1111/jwas.12342
http://onlinelibrary.wiley.com/doi/10.1111/jwas.12342/full#jwas12342-fig-0002
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO

5. 5
|
Biology
of
sex
matura1on
The
brain-­‐pituitary-­‐gonad
(BPG)
axis
Neuron
sKmulaKon
of
the
brain
gonadotropin
releasing
hormone
(GnRH)
sKmulaKon
of
the
pituitary
gonadotropins
Follicle
sKmulaKng
hormone
(FSH)
Luteinising
hormone
(LH)
to
the
gonads
(effector
Kssue)
Sex
hormones
Sex-­‐related
physiology
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO

6. 6
|
Matura1on
types
in
Atlan1c
salmon
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO
parr
Precocious
Early
matura1on
1SW
Marine
matura1on
2-­‐3
SW

7. 7
|
Photoperiod
manipula1on
for
matura1on
control
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO
Ø Animal
exposure
to
arKficially
increased
day
lengths
between
the
winter
and
summer
solsKces
effecKvely
advances
maturaKon
Ø Animals
to
make
early
assessment
of
their
energeKc
status
and
reproducKve
fitness
Ø Meets
the
necessary
energeKc
thresholds
• maturaKon
is
accelerated
• If
not:
maturaKon
is
suspended
(adapted
from
Bromage
et
al.,
1993)

8. 8
|
Project
aim
Approach
Ø MechanisKc
insights
into
the
triggers
for
sexual
matura1on
onset
in
AtlanKc
salmon
Ø Photoperiod
manipula1on
to
narrow
the
1me
window
during
which
maturaKon
ini1ated
Ø Next
generaKon
sequencing
to
obtain
transcriptome,
DNA
methyla1on
and
epigenomic
data:
during
and
aSer
the
matura1on
process
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO

9. 9
|
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO
Experimental
design
4
1me
points
T1-­‐T4
Before,
during
and
aUer
maturaKon
signal
Animals
used:
• ♀broodstock
• 3
yrs
at
1st
sampling
1st
priority
Ø Brain
Ø Pituitary
Ø Ovary
2nd
priority
Ø Pineal
Ø Liver
Ø Spleen
Ø Muscle
Target
1ssues:
Day$Length$(hrs)$
Jan$ Feb$ Mar$ Apr$ May$ Jun$ Jul$ Aug$ Sep$ Oct$ Nov$ Dec$ Jan$ Feb$ Mar$ Apr$ May$
8$
16$
2017$ 2018$
Summer$
sols4ce$
Winter$sols4ce$
2017$
T1$
T2$ T3$ T4$
Natural$photoperiod$
Long$day$photoperiod$to$ini4ate$matura4on$of$+3$females$for$sampling$at$T2$–$T4$
Spawning$
+4$females$

10. 10
|
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO
Tissue
sampling
T1,
Before
Matura1on:
4
replicate
fish
x
7
1ssues
F1
F2
F3
F4
Mean
Length
(cm)
69.5
86
69
75.5
75
Total
weight
(gram)
5570
8230
6270
7300
6842.5
Gonad
Weight
(gram)
22
30
30
54
34
Liver
Weight
(gram)
52
70
62
64
62
Gonadosoma1c
Index
(GSI)
0.39
0.36
0.47
0.71
0.48
Hepatosoma1c
Index
(HSI)
0.93
0.85
0.98
0.84
0.9
Confirma1on
GSI
<
1
%

11. 11
|
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO
DNA
methyla1on
Histone
modifica1on
Transcriptomic
mRNA
Lin
et
al
2016
(Nature)
Reference
Genome
Assembly
Omics
data
Transcriptome,
Epigenome,
Methylome

12. 12
|
FixaKon
in
RNA-­‐Later
gDNA
Bisulfite
treatment
Libraries
prep
High-­‐throughput
sequencing
Total
RNA
Quality
Control
mRNA
enrichment
RRBS
RNA-­‐Seq
ChIP-­‐Seq
FixaKon
in
LN2
pulverizaKon
ChIP-­‐DNA
prep
Next-­‐gen
sequencing
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO

13. 13
|
Histone
ModificaKons
ChIP-­‐Seq
Gene
Expression
RNA-­‐Seq
DNA
MethylaKon
RRBS
Integrated
Analysis
Gene
co-­‐expression
networks
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO
Mul1
Omics
Integrated
Analysis

14. 14
|
Outcomes
• Insights
into
the
molecular
mechanisms
deriving
onset
of
sex
maturaKon
in
AtlanKc
salmon
• Gene
co-­‐expression
networks
during
the
maturaKon
process
• Tissue-­‐specific
expression/regulaKon
of
some
genes
of
interest
• Developing
novel
approach
for
management
of
unwanted
early
maturaKon
within
the
salmon
industry
• ContribuKon
to
the
FAASG
iniKaKve
to
annotate
the
AtlanKc
salmon
genome
Impacts
Molecular
basis
of
sex
maturaKon
in
AtlanKc
salmon
|
Amin
Mohamed,
CSIRO

15. AGRICUTURE
Acknowledgement
James
Kijas
Aquaculture
geneKcs
and
phenomics,
CSIRO,
Brisbane,
Queensland
Antonio
Reverter
ComputaKonal
and
Systems
Biology,
CSIRO,
Brisbane,
Queensland
Peter
Kube,
Harry
King
CSIRO,
Hobart,
Tasmania
Brad
Evans
SALTAS
Ltd.,
Hobart,
Tasmania