RGCA GIFT SELECTIVE

BREEDING PROGRAMME

Mathews Varkey
Asst. Project Manager
INTRODUCTION

• Majority of cultured fish in the world are based on unimproved strains

– Rely on wild fish stocks for broodstock

– Chances of recruiting diseased animals

– Uncertain availability

– Uncertain growth rate

– Depletion of genetic stock in natural environment

– Eg: Seabass, Grouper, Mudcrab

– Only about 10% are genetically improved

– Eg: Salmon, L .vannamei, GIFT, Tiger Shrimp ?
WHAT IS SELECTIVE BREEDING AND WHY IS IT NECESSARY ?

 Never or rarely recruit from wild broodstock except after

development of founder stocks.
 Stocks can be made Specific Pathogen Free (SPF)

 Every generation is more genetically improved.

 Availability whenever required.

 Adequate diversity is maintained in the stock after every

generation.
 Pedigree is known.

 Controlled inbreeding with known value.

 Offers traceability, a prerequisite for marketing finished

products
WHY GENETIC IMPROVEMENT
PROGRAMS?

• Have the power to modify the animal to suit a

purpose
• Can increase productivity
• Gain is permanent
• Large return on investment
• Can help fill gap between demand and supply
• Manage inbreeding in the captive stock
 STATUS OF SELECTIVE BREEDING AND SUBSEQUENT
GENETIC IMPROVEMENT…

Chicken grow twice as fast on half of the feed as the chickens of 50 years
ago…

Domestication and selective breeding has led to

substantial genetic improvement in livestocks…

But… benefits accrued from the selective breeding and genetic

improvement of shrimp/fish lag far behind than that of livestocks…

Rajiv Gandhi Centre for Aquaculture (MPEDA, Ministry of Commerce & Industry, Govt. of India)
HOW DOMESTICATION WITH GENETIC IMPROVEMENT
.
HAS LED TO SUBSTANTIAL INCREASE IN PRODUCTIVITY …

Chicken

300
Cattle
Productivity, % (Ref. 1940)

Pig

Norw. Salmon
200

GIF Tilapia L.vannamei

100

1940 1950 1960 1970 1980 1990 2000 2010

Year
Over the last 40 years, the growth rate of broilers has increased around 300%, and studies have
shown that 78% of this gain is due to genetic selection…
Gene flow through the lock-and-copy aquaculture system

Shrimp-breeding
programs release
only a small
fraction of their
genetic material
to clients for
grow-out.

Solid arrows represent the flow of genetically locked material authorized by the
breeder (authorized hatchery). Broken arrows represent gene flow from
genetically locked PLs used as breeders without authorization (copy hatchery).
Courtesy: Argue et.al., 2014; Doyle,
R.W., 2014
Central Aquaculture Genetics Lab, Rajiv Gandhi Centre for Aquaculture (MPEDA)
Decrease performance of the lock-and-copy aquaculture system…
(adopted from Argue et al., 2014)

1st generation Inbreeding:

(one generation of brother-sister
mating: 25% inbreeding)
2nd generation Inbreeding:
(mating of 25%-inbred shrimps:
37.5% inbreeding)
3rd generation Inbreeding:
(mating of 37.5%-inbred
shrimps: 50% inbreeding)

Generation Growth Survival Breeding performance

difference difference
(%) (%)

1st 24 5 Spawning was ~10% less in inbred shrimp

2nd 56 49 Spawning rate was comparable, but nauplii production was one-
third.

3rd 29 28 None of the 50%-inbred shrimp spawned

 Breeding Program Design…
•Genetic improvement typically takes place in a very small fraction of the population, which
is multiplied and disseminated to the production systems…

Genetic improvement
Nucleus
1000 Selection (Breeding centres)

Gene flow
Multipliers/Hatcheries Breeding animals
1 million

Commercial producers/ Farmers

10 million

Pyramid breeding structure

BREEDING PROGRAMME IN A NUTSHELL…

Where to go?
Breeding objectives…

To increase growth To conserve a rare

How to go? species

Use of Quantitative Genetics/ Selection

Getting there/Implementation

• Breed from the best only, select accurately,

not all from the same family
Rajiv Gandhi Centre for Aquaculture (MPEDA, Ministry of Commerce & Industry, Govt. of India)
WHICH ANIMALS TO SELECT?

A: 70 g

B: 100 g

C: 90 g
Ans: B ???

Rajiv Gandhi Centre for Aquaculture (MPEDA, Ministry of Commerce & Industry, Govt. of India)
Environmental factors influencing quantitative traits:
Stocking density
Water temperature
Water quality
Feed quality

PHENOTYPIC VARIANCE (VP)

 Phenotypes of quantitative traits are influenced by environmental factors.
(water quality, feed quality, stocking density, water temp etc.)

 Phenotypic variance can be observed and measured

V P = V G + VE
Rajiv Gandhi Centre for Aquaculture (MPEDA, Ministry of Commerce & Industry, Govt. of India)
WHICH ANIMAL HAVE TO SELECT ?
A: 70 g
A: 70 = 60 + 10
B: 100 g
B: 100 = 70 + 30
C: 90 g
C: 90 = 80 + 10
B ???
C?
VP = V G + V E

VG = VA + VD + VI
(Additive-; Dominance-; Epistatic genetic variance)
Rajiv Gandhi Centre for Aquaculture (MPEDA, Ministry of Commerce & Industry, Govt. of India)
Several approaches to genetic
improvement feasible with fish

hybridization transgenesis
cross-breeding
chromosome
manipulation

selective breeding
only approach where gains are
cumulative and permanent
age unknown
pedigree and genetic
relationships unknown
individuals selected on
high risk of phenotype only
inbreeding (measurable alive)

μ
150 g 300 g 550 g

1. Individual selection
selection done within inbreeding limited by
cohort or group mating between cohorts

(fe)males rotate

field personnel comfortable with this design

2.Cohort selection
 requires family
identification

families reared in separate

tanks, hapas, cages

high within-family selection

intensity possible

inbreeding easily controlled

by rotational mating

3. Within-family selection
 utilizes information from
individual plus relatives,
linked by pedigree

uses Best Linear Unbiased

Prediction (BLUP) to estimate
breeding values (EBVs)

 BLUP accounts for systematic effects (e.g. sex, batch, age)

and maternal, common environmental effects
4.Combined selection
Rajiv Gandhi Centre for Aquaculture (MPEDA, Ministry of Commerce & Industry, Govt. of India)
 successfully applied
in tilapia

genetic gain for body

weight estimated at 12%
per generation after 12
generations

easily managed but

requires greater inputs
INBREEDING

Inbreeding is rising of offspring by mating closely related pairs.

The resultant individual of these crosses are called Inbred.

Inbreeding depression (F)

Inbreeding can bring deleterious recessive alleles together

in homozygous genotypes,

Result –Reduced fitness, Stunted growth etc.

G
I
F
T
Selective Breeding Programme in RGCA

Started in the August 2011 by importing 60 families of G0 Generation from

World Fish Centre, Malaysia.

Successfully completed the production of G1, G2, G3, G4, G5 and G6

generations.

Imported 40 additional families during 2016 from WFC to strengthen the

ongoing programme.

Presently holding fry from G6 generation for All male seed/Brood stock
development and production of G7 Generation
DESIGN SYSTEM FOR MULTIPLICATION
AND DISSEMINATION
• Genetic improvement typically takes place in a very small fraction of
the population, which is multiplied and disseminated to the
production systems

Selection (breeding nuclei)

RGCA

Flow of genes
Multiplication (hatcheries)

Production (farmers)
MAJOR STEPS

The selective breeding programme involves three major

steps.

1. Tagging

2. Harvesting

3. Mating
PIT - TAGGING

PASSIVE INTERGRATED TRANSPONDER.

o Individual tagging
o Automated
o unique ID
o Dimensions: Dia. 2.12; Length 11.5 mm (0.08 x 0.45 in.)
Individual tagging of GIFT-RGCA with PIT…

Central Aquaculture Genetics Lab, Rajiv Gandhi Centre for Aquaculture (MPEDA)
TAGGING PROTOCOL
DATA SHEET
Maintain the data of each fish for further use.

Observe the animal in indoor and open pond hapa for 24 hours and
observe for post tagging mortalities

Retag if required
HARVESTING
Harvest the animals
after rearing in
communal rearing
ponds.

Record the Harvesting

morphometry of
individual animals.

Stock them in labeled

hapa for easy retrieval.
Stocking
MATING LIST
Design a mating programme with families that will give maximum EBV and
minimum inbreeding depression.

Select the best 3 animals from each family for one mating.
MATING PROGRAMME

Allow the fish to mate with respective pairs 1X1 mating hapa.

Check for egg or fry resulted in the mating hapa in fixed day interval.

Stock the egg or fry in breeding jar until free swimming stage.

Normally tale 2-3 month to complete.

SINGULAR HATCHING JAR
OPEN POND NURSERY UNIT
Stock the egg or fry in breeding jar until free swimming stage.

Transfer the fry to open pond nursery hapa to grow to tagging size.
 SELECTIVE BREEDING - PROCESS FLOW
Rearing of Fry obtained from
each representative family in
Hapas in Ponds
Resultant fry are designated with
family numbers and stocked in
Nursery Hapas
Egg collection is carried every
10 days and incubated to hatch
out the fry
Selected fish are identified from
Mating Hapas are set up for
breeding the Top three
representatives from each
families
injuring females during mating
Random selection of stocks from
each family and tagging them
individually using PIT Tags
10 – 11 months for the development of a generation
the stocks using their PIT tags A mating list is prepared
and conditioned for Breeding. based on this data by keeping
Males are subjected to Lip the Inbreeding coefficient at
clipping to prevent them from minimum
Communal rearing of all these
fish in the same environment till
they reach breeding sizes
Harvesting the pond and
recording the individual data of
each fish
Sending the consolidated data to
WFC for preparation of the
Mating List
Based on the grow-out
performance of each Individual
& after analyzing their pedigree
records, the top three male
38 &
Female representatives of each
family are identified
Thank you…..