APPLICATIONS OF BIOINFOMATICS

IN AQUACULTURE
Lecturer: Dr. Nguyen Minh Thanh
Date of presentation: Tuesday, December 24th, 2019.
Group 8 Members
Trương Thanh Ngọc BTBTIU15162
Hoàng Thị Hồng Hạnh BTBTIU16168
Lê Nguyễn Hoàng Việt BTBTIU16155
Trân Ngọc Như Ý BTBTIU16161
I. OVERVIEW
01 BIOINFOMATICS AND AQUACULTURE

II. BIOINFORMATICS
APPLICATIONS IN AQUACULTURE
01 MARKER-ASSISTED SELECTION IN AQUACULTURE

02 RAD-seq ANALYSIS PIPELINE

III. SUMMARY
 I. OVERVIEW
BIOINFORMATICS
The use of computer databases and computer
algorithms to analyze proteins, genes, and the
complete collection of deoxy- ribonucleic acid
(DNA) that comprises an orga nism (the
genome).
Bioinformatics and Functional Genomics (3rd Ed)

“research, development, or application of

computational tools and approaches for
expanding the use of biological, medical,
behavioral, or health data, including those to
acquire, store, organize, analyze, or visualize such
data.”
National Institutes of Health (NIH )
I. OVERVIEW
AQUACULTURE
Aquaculture: Farming of aquatic organisms, including fish, molluscs,
crustaceans and aquatic plants.
Farming: Intervention in the rearing process to enhance production, such as
regular stocking, feeding, protection from predators, etc. Ownership
of the stock being cultivated.

Aquaculture: owned throughout their rearing period,

Harvest of fisheries: aquatic organisms which are exploitable by the public as
a common property resources
(FAO, 1988)
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
01 MARKER-ASSISTED SELECTION IN AQUACULTURE
White spot disease in shrimp

Why?
• Diseases are major threats to
sustainable aquaculture, in Sustainable aquaculture
crustacean farming, especially
shrimps farming, and in the farming
of some molluscs, especially
oysters.

• Diseases also affect the farming of

many types of fishing, including
carps, catfish and salmonids.
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
01 MARKER-ASSISTED SELECTION IN AQUACULTURE

Why?
• Although rich genetic resources must exit among aquaculture
species for resistance to major fish diseases, for fast growth and
for efficient feed conversion, genomic research is required to
identify and then utilize these.
• Direct selection of disease resistance has proven to be very
difficult in aquaculture.
• Genome-based technologies for increasing and identifying
disease resistance have proven safe, reliable, and
environmentally sound for livestock.
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
01 MARKER-ASSISTED SELECTION IN AQUACULTURE
Principles
• Marker-assisted selection or marker-aided selection (MAS) is a process
whereby a selection decision is made based on the genotypes of DNA markers.
MAS is especially useful for traits that are difficult to measure, lethal to measure, exhibit low
heritability, and/or are expressed late in development.

• Its implementation requires information of DNA markers that are tightly linked
to QTL for traits of interest based on QTL mapping or association studies. Ideally,
the DNA markers should be the causative mutation underlying the phenotypic
variation.
In order to implement MAS, QTLs need to be mapped and validated within the breeding
populations.
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
01 MARKER-ASSISTED SELECTION IN AQUACULTURE
Applications
MAS has been applied mostly with plants and livestock animal species, but less so with
aquaculture species, although a few good examples do exist for application in aquaculture.
Japanese flounder.
 A microsatellite locus, Poli9-8TUF, was mapped to be near the major QTL for
resistance to lymphocystis disease. Additional analysis indicated that the disease
resistance was controlled by a single gene, and the resistance allele was
dominant.
 Based on the marker linkage information, Fuji et al. (2007) developed a new
population of Japanese flounder using MAS with the marker Poli9-8TUF.
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
01 MARKER-ASSISTED SELECTION IN AQUACULTURE
Applications
Japanese flounder.
 They selected a female homozygous for the
favourable allele (B-favourable) and a male with
a higher growth rate and good body shape, but
without the resistant allele as parents.

 In the females, the marker Poli9-8TUF is tightly

linked to the QTL for resistance to lymphocystis
disease; therefore, a female was selected as the
linkage disequilibrium-resistant parent.
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
01 MARKER-ASSISTED SELECTION IN AQUACULTURE
Applications
Japanese flounder.
 The 40 B-favourable allele was transmitted from the mother to the progeny.
All the progeny are heterozygotes with the resistance allele, and the progeny
was entirely resistant to lymphocystis disease, while the control group
without B-favourable alleles showed incidences of 4.5 and 6.3 percent of
mortality due to lymphocystis disease.

 These results clearly demonstrate that MAS is an efficient strategy for

breeding. MAS lymphocystis disease-resistant flounder had a market
penetration rate of 35 percent in Japan in 2012.
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
02 RAD-seq ANALYSIS PIPELINE

 How about in
Aquaculture?
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
02 RAD-seq ANALYSIS PIPELINE

- A wealth of software is available

for analyzing data originating from
the RAD family of techniques.
--> Is there a comprehensive
overview of all available tools?
Maybe but not enough!!
- Instead, a general framework for
data analysis is proposed: RAD
bioinformatic analyses.
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
02 RAD-seq ANALYSIS PIPELINE
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
02 RAD-seq ANALYSIS PIPELINE

Experimental design and simulation

• Choice of the RE
• Desired read coverage per locus
-->R‐based package SimRAD: simulation‐based prediction of the
expected number of loci for each RE (or their combination) and the
genome of study.
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
02 RAD-seq ANALYSIS PIPELINE
Name Abbreviation Datatype #Samples #Reads Read Expected # Expected # Reference
Length of Loci of pop.

SE RAD SE-RAD single-end 12 480,000 100 2,000 3 [1]

Tutorial v.3.0 RAD

SE ddRAD SE-ddRAD single-end 12 240,000 100 1,000 3 [2]

Tutorial ddRAD
v.3.0.4

PE ddRAD PE-ddRAD paired-end 12 480,000 2x100 2x1,000 3 [3]

Tutorial ddRAD
v.3.0.4

E ddRAD w/ PE-ddRAD m paired-end 12 81,613 2x100 340 3 [4]

merged reads ddRAD
Tutorial
v.3.0.4

Figure 1. Summary of the simulated data sets.

II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
02 RAD-seq ANALYSIS PIPELINE

Demultiplexing libraries SNP identification

• De novo assembly
• FastQ files: generated by
• Stacks software does not currently
sequencer.
support SNP identification and
Demultiplexing into individual
genotyping in the paired‐end (P2) read,
samples based on nucleotide
unless anchored to a second RE.
barcodes: Stacks (Catchen et al.  • pyRAD, allow the identification of
2011) and pyRAD (Eaton 2014).
insertion/deletion polymorphisms (indels)
and identification of SNPs in the P2
reads.
II. BIOINFORMATICS APPLICATIONS IN
AQUACULTURE
02 RAD-seq ANALYSIS PIPELINE

Potential bias and sources of error: there remains potential intrinsic barriers

• Salmonid species: Distinguish between genuine allelic SNPs and paralogous
variants.
• Problem of RAD allele dropout: mutations within the recognition sequence
for the RE segregating in the population are a common source of null alleles.
• Concept of PCR duplicates: one allele is overrepresented--> Problems with
differentiating homozygous and heterozygous individuals at that locus. 
II. SUMMARY
 References 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6128402/
https://www.biosearchtech.com/services/sequencing/genotyping-by-sequencing-gbs
https://experiment.com/u/MCGNEA
https://cran.r-project.org/web/packages/SimRAD/SimRAD.pdf

[1] Eaton DA. Example de novo RADseq assembly using pyRAD.

http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD_3.0.ipynb, Date accessed: 18.10.2016.

[2] Eaton DA. Tutorial: single-end ddRAD analysis (or other two-cutter based datatypes) pyRAD v.3.0.4.
http://nbviewer.ipython.org/dc6241083c912519064e/tutorial_ddRAD_3.0.4.ipynb, Date accessed: 18.10.2016. 71
Bibliography

[3] Eaton DA. Tutorial: paired-end ddRAD analysis w/ merged reads (or other two-cutter based datatypes) pyRAD v.3.0.4.
http://nbviewer.ipython.org/dc6241083c912519064e/tutorial_pairddRAD_3.0.4. ipynb, Date accessed: 18.10.2016.

[4] Eaton DA. Tutorial: paired-end ddRAD w/ merged reads (or other two-cutter based datatypes) pyRAD v.3.0.4.
http://nbviewer.ipython.org/gist/dc6241083c912519064e/tutorial_pairddRAD_3. 0.4-merged.ipynb, Date accessed:
18.10.2016.
Thank You For Your Attention!
Merry Christmas!