This document discusses different methods of fish breeding, including selective breeding, recombination breeding, and hybrid breeding. Selective breeding involves choosing individuals with desired traits to breed, and can result in reduced genetic variability over time. Recombination breeding combines traits from unrelated strains through techniques like crossbreeding and hybridization. Hybrid breeding aims to produce offspring that exhibit hybrid vigor or heterosis for increased performance. The genetic basis of heterosis includes dominance, overdominance, and epistasis effects between loci. Proper selection of parental lines and understanding of genetic processes is important for effective recombination and hybrid breeding in fish.

1. FISH BREEDING
Taryono
Faculty of Agriculture
Gadjah Mada University

2. Fish Breeding
Selective breeding
The choosing of individuals of a single strain and
species.
Recombination Breeding
Crossbreeding
The mating of unrelated strains of the same
species to avoid inbreeding
Hybrid breeding
The crossing of different species

3. Selective Breeding
“Artifical selection” as opposed to natural selection,
results in reducing genetic variability in a population.
a process used to produce different breeds of animals or
varieties of plants that have useful characteristics
Selective Breeding occurs when humans allow only those
organisms with desired characteristics to produce to the next
generation
Using selective breeding you can produce a specific offspring with
useful characteristics of both parents

4. Selective Breeding
The first application of genetics
If selective breeding involves excessive inbreeding
physical abnormalities, metabolic deficiencies, and
developmental abnormalities may occur.
Inbreeding depression-loss of fitness due to inbreeding
 more likely to observe occurence of recessive traits
 Decrease in heterozygosity

5. Mass Selection
Selection of individuals
Sampling seed of selected individuals to grow next
generation
Oldest method of improvement
Improvement of heterogeneous native populations or
landraces

6. • Grow population
• Allow random mating
Harvest and bulk seed
from desirable fishes
• Fish new generation
• Repeat
X X X X X X
X X X X X X
X X X X X X
X X X X X X
X X X X X X
X X X X X X
X X X X X X
X X X X X X
MASS SELECTION

7. Mass Selection
 Higher percentage of desirable genotypes
 Method can only be used in environments
where trait is expressed - may not be suitable
for off-season winter nurseries
 Effectiveness is function of heritability
 Manage field to enhance differences. For
instance feeding excessively to differentiate fast
growing individual fishes

8. Selective Breeding
Although potential for deleterious results, selective
breeding rationalized by:
 size
 color
 shape
 better FCR
 reproductive capacity
 disease resistance

9. Selective Breeding
 Mendel practiced selective breeding
 Most domesticated animals are bred for
specific traits (cows, horses, fish)
 most crops are selectively bred (rice, corn)

10. Recombination breeding
 It is a combining in the future strains the useful traits and characters
inherent in each parent separately
 it has become the predominant method of improvement of
cultivated strains due to hybrid vigor
 It is known as combination breeding
 Distinction is made between intra- and interspecific crossing
 The successful of hybridization is to great extent dependent on the
selection of parental materials and how well the breeder is familiar
with the genetic processes occurring in the segregating progenies of
hybrid populations
 The choice of parents might seem the best starting point, but in
practice, it is better to expound crossing and selection schemes first
and then to consider the source and choice of parents in the wider
context of breeding strategy

11. Recombination breeding
 The material resulting from hybridization is used in
different ways
1. For selection in the breeding of selection strains (open pollinated
strains), crossbreeding
2. Directly in the production as first generation hybrids (hybrid
strains), heterosis breeding
 The improvement of cross pollinated organisms cannot
be based on isolation of homozygous genotypes
1. As a consequence of outbreeding, any strain of outbreeding
organism has heterogenous genotypes, each being to some
extent different from the other ones in a given population
2. Induced selfing of outbreeding organisms leads to inbreeding
depression of the offspring

12. Crossbreeding
 Sexual recombination in fish might occasionally happen
in nature, but most were conducted artificially
 The principle of artificial sexual recombination is to
impose the male and female gametes of different fishes
to fuse together as a zygote by artificial methods that
does not happen in natural conditions
 Those hybrid zygotes will develop with some improved
characteristics
 The modified phenotypes appeared in those hybrids is
the result of “hybridity expression” of the newly
reconstructed genomes of the individuals

13. Crossbreeding
 Sexual recombination only generally can be done between
taxonomically closely related species
 In fish, sexual recombination not only can be successfully
made among closely related species, but also can be applied to
those fish species which belong to rather distantly related
species
1. Inter-genus sexual hybridization
Cyprinus carpio x Carassius auratus
2. Inter-subfamily sexual hybridization
Ctenophry idellus (sub-fam. Leucinae) x Megalobrama amblycephala
(Sub-fam. Abramidinae)
3. Inter-order combination
Carassius auratus (order Cypriniformes) x Oreochromis nilotica
(order Perciformis)

14. Bulk Breeding Method

15. Bulk Breeding Method
Procedure for inbreeding a segregating population
until the desired level of homozygosity is reached
Easy way to maintain populations
Natural selection permitted to occur in target
environment

16. Pedigree Breeding Method

17. Hybrid Breeding
Maximum performance under optimal conditions
 Stability of performance under stress
 Proprietary control of parents
 Often reduced time to strain development
 Joint improvement of traits
Heterosis breeding
Breeding based on the increase of growth
vigor and survival due to the increase of
heterozygosity

18. Hybrid Strains
Hybrid strains are first generation offspring after
cross between different inbred parent lines
Major steps in breeding
 develop inbred homozygous lines
 find good F1 combination between inbreds
 produce F1 seed in large scale for growers
Hybrids are uniform, reproducible and ”protected” if
parents are homozygous.

19. Major types of hybrid cultivars
Single cross hybrids (F1)
A x B = F1
Three way hybrids
(A x B) x C = Three Way Hybrid
Double cross (Four way hybrid)
(A x B) x (C x D) = Double Cross
Three way and double cross hybrids are used to
reduce seed costs when parentals are weak

20. Hybrid vigour or heterosis
Heterosis
The increase in size, vigour or productivity of a
hybrid organism over the average or mean of
its parents.
 Midparent heterosis
 High parent heterosis
 Standard heterosis

21. Measurement of Heterosis
Mid-parent heterosis
 Hybrid performance is measured relative to mean of the
parents (MP)
 (F1 - MP) / MP * 100
High-parent heterosis
 Comparison of hybrid to performance of best parent
(HP)
 (F1 - HP) / HP * 100

22. Genetic basis of heterosis
Three possible genetic causes:
 Partial to complete dominance
 Overdominance
 Epistasis
The issue for breeders - What is the Ideal genotype?
 Partial to complete dominance - Homozygote
 Overdominance - Heterozygote

23. Dominance Hypothesis
Davenport (1908)
 Hybrid vigor is due to action and interaction of
favorable dominant alleles
 Hypothesizes decreased homozygosity for
unfavorable recessive alleles (covering up)
 Conversely, inbreeding depression is due to
exposure of these recessive alleles during
inbreeding

24. Dominance Hypothesis
Example
Model AA = Aa > aa - AA=10 Aa=10 and aa=0
Parent 1 Parent 2
aaBBccDDee = 20 AAbbCCddEE = 30
F1
AaBbCcDdEe = 50
Also note that AABBCCDDEE = 50

25. Discussion of
Dominance hypothesis
Theoretically, homozygous for all favorable alleles
could be developed (AABBCCDDEE….)
Why then are there no inbred equal in performance to
hybrids??
This was considered a until it was recognized that only
1 in 4n individuals in a population would be
homozygous for all loci -
For 10 loci that would be 410 = one individual in a
million.

26. Dominance hypothesis
Linkage
Recombination among loci could result in plants
homozygous for all favorable alleles
Repulsion phase linkages, either slow or preclude the
development of such lines
Empirical evidence supports dominance hypothesis,
as inbred line are improving in performance.
A b
a B

27. Overdominance
 First proposed by Shull (1908) and late expanded by
Hull (1945)
 It states that the heterozygote (Aa) at one or more
loci is superior to either homozygote (AA or aa)
 Model would be Aa > aa or AA
 They recognized importance of dominance, but it
alone cannot account for observed heterosis.

28. Overdominance
Superiority of heterozygotes may exist at the
molecular level, if the products of two alleles
have different properties, e.g. heat stability, or
advantages at different environments or
maturities - thus may result in stability.
“single locus heterosis” difficult to observe
and detect if populations are not in linkage
equilibrium.

29. Pseudo- Overdominance
In which nearby loci which have alleles that are
dominant or partially dominant are in repulsion
phase
If the populations are not in linkage equilibrium, this
could mimic the effects of overdominance
A b
a B

30. Epistasis
Epistasis - interaction among loci, may also
contribute to heterosis
Internode
Generation No. nodes length Height
Parent 1 3 1 3
Parent 2 1 3 3
Hybrid ( add) 2 2 4
Hybrid ( Dom) 3 3 9

31. Epistasis
Estimates bases on mating designs to estimate
the relative magnitude of add, dom and
epistatic components of variance indicate that
the magnitude of epistatic variance is small
compared to additive and dominance
components.
The magnitude of epistatic variance is difficult
to estimate, and may play a very important role
in heterosis.

32. Prediction of heterosis
The ability to predict heterosis of “Specific
combining ability” has been an elusive goal of
plant breeders
Combining ability - Testing of hybrids
Diallel crosses n(n-1) / 2
 General (GCA) - Average performance - additive effects
 Specific (SCA) - ability of lines to combine in specific combinations
Due to dominance effects and heterosis.

33. Genetic distance and heterosis
Moll (1965) showed a relationship between genetic
distance and heterosis for yield in maize
Heterosis
Genetic
distance

34. Nuclear transplantation
 It is a diploid nucleus into enucleated egg.
 It is to combine the nucleus and cytoplasm of different
species to produce nucleo-cytoplasmic hybrids
1. Inter-genus combination
Nucleus of common carp and cytoplasm from crusian carp.
Adult fish with essentials of common carp phenotype and
cytoplasmic influenced character at morphological, physiological
and biochemical levels were obtained. Both male and female
hybrids are fertile
2. Inter –subfamily combination
Nucleus from grass carp and cytoplasm of blunt snout bream.
Adult fishes were obtained.

35. Natural barrier in distance recombination
1. The failure of foreign sperm to penetrate the egg
2. Foreign sperm can enter the eggs but it will be degenerated and
disappear in the egg cytoplasm without performing any vital
function
3. Foreign sperm can enter the egg and enlarge as a male
pronucleus but it can not fuse with the egg to form a zygote
nucleus
4. Foreign sperm can enter the egg and enlarge as a male
pronucleus but it can fuse with the egg to form a zygote nucleus
and divide in coordinating with egg cytoplasmic division,
however due to unknown natural incompatibility which existed
between the sperm and egg, the hybrid zygote nucleus will
become heteroploid. The embryo develops abnormally

36. Open pollinated populations (OPP)
 The improvement of OPP depends essentially upon the
changing gene frequencies towards fixation of favorable
allele while maintaining a high degree of heterozygosity
 Uniformity is impossible and trueness to type is a
statistically feature of the population as a whole, not a
characteristic of individual organism
 Two types
1. Population improvement
a population is changed by the chosen selection procedures based on
purely phenotypic selection (mass selection)
2. Synthetic
population improvement which has to be reconstructed from
parental lines. It can be constructed from combining inbred, clones
as a parent

37. Heterosis
1.It implies increased vigor of the first generation
hybrids as compared to the parental forms
2.It manifests itself fully in the first generation,
whereas in the subsequent generation the hybrid
vigour goes down substantially
3.Heterotic hybrid seed can be sown commercially
once
4.Practical utilization of heterosis involves annual
crossing to produce heterotic hybrid seed

38. Attributes of F1 hybrids
Maximum performance under optimal
conditions
Stability of performance under stress
Proprietary control of parents
Often reduced time to strain development
Joint improvement of traits

39. Hybrid Strains
Hybrid strains are first generation offspring after
cross between different inbred parent lines
Major steps in breeding
 develop inbred homozygous lines
 find good F1 combination between inbreds
 produce F1 seed in large scale for growers
Hybrids are uniform, reproducible and ”protected” if
parents are homozygous.

40. Major types of hybrid cultivars
Single cross hybrids (F1)
A x B = F1
Three way hybrids
(A x B) x C = Three Way Hybrid
Double cross (Four way hybrid)
(A x B) x (C x D) = Double Cross
Three way and double cross hybrids are used to
reduce seed costs when parentals are weak

41. Hybrid vigour or heterosis
Heterosis
The increase in size, vigour or productivity of a
hybrid plant over the average or mean of its
parents.
 Midparent heterosis
 High parent heterosis
 Standard heterosis

42. Measurement of Heterosis
Mid-parent heterosis
 Hybrid performance is measured relative to mean of the
parents (MP)
 (F1 - MP) / MP * 100
High-parent heterosis
 Comparison of hybrid to performance of best parent
(HP)
 (F1 - HP) / HP * 100

43. Genetic basis of heterosis
Three possible genetic causes:
 Partial to complete dominance
 Overdominance
 Epistasis
The issue for breeders - What is the Ideal genotype?
 Partial to complete dominance - Homozygote
 Overdominance - Heterozygote

44. Dominance Hypothesis
Davenport (1908)
 Hybrid vigor is due to action and interaction of
favorable dominant alleles
 Hypothesizes decreased homozygosity for
unfavorable recessive alleles (covering up)
 Conversely, inbreeding depression is due to
exposure of these recessive alleles during
inbreeding

45. Dominance Hypothesis
Example
Model AA = Aa > aa - AA=10 Aa=10 and aa=0
Parent 1 Parent 2
aaBBccDDee = 20 AAbbCCddEE = 30
F1
AaBbCcDdEe = 50
Also note that AABBCCDDEE = 50

46. Discussion of
Dominance hypothesis
Theoretically, homozygous for all favorable alleles
could be developed (AABBCCDDEE….)
Why then are there no inbred equal in performance to
hybrids??
This was considered a until it was recognized that only
1 in 4n individuals in a population would be
homozygous for all loci -
For 10 loci that would be 410 = one individual in a
million.

47. Dominance hypothesis
Linkage
Recombination among loci could result in plants
homozygous for all favorable alleles
Repulsion phase linkages, either slow or preclude the
development of such lines
Empirical evidence supports dominance hypothesis,
as inbred line are improving in performance.
A b
a B

48. Overdominance
 First proposed by Shull (1908) and late expanded by
Hull (1945)
 It states that the heterozygote (Aa) at one or more
loci is superior to either homozygote (AA or aa)
 Model would be Aa > aa or AA
 They recognized importance of dominance, but it
alone cannot account for observed heterosis.

49. Overdominance
Superiority of heterozygotes may exist at the
molecular level, if the products of two alleles
have different properties, e.g. heat stability, or
advantages at different environments or
maturities - thus may result in stability.
“single locus heterosis” difficult to observe
and detect if populations are not in linkage
equilibrium.

50. Pseudo- Overdominance
In which nearby loci which have alleles that are
dominant or partially dominant are in repulsion
phase
If the populations are not in linkage equilibrium, this
could mimic the effects of overdominance
A b
a B

51. Epistasis
Epistasis - interaction among loci, may also
contribute to heterosis
Internode
Generation No. nodes length Height
Parent 1 3 1 3
Parent 2 1 3 3
Hybrid ( add) 2 2 4
Hybrid ( Dom) 3 3 9

52. Epistasis
Estimates bases on mating designs to estimate
the relative magnitude of add, dom and
epistatic components of variance indicate that
the magnitude of epistatic variance is small
compared to additive and dominance
components.
The magnitude of epistatic variance is difficult
to estimate, and may play a very important role
in heterosis.

53. Prediction of heterosis
The ability to predict heterosis of “Specific
combining ability” has been an elusive goal of
plant breeders
Combining ability - Testing of hybrids
Diallel crosses n(n-1) / 2
 General (GCA) - Average performance - additive effects
 Specific (SCA) - ability of lines to combine in specific combinations
Due to dominance effects and heterosis.

54. Genetic distance and heterosis
Moll (1965) showed a relationship between genetic
distance and heterosis for yield in maize
Heterosis
Genetic
distance

55. Nuclear transplantation
 It is a diploid nucleus into enucleated egg.
 It is to combine the nucleus and cytoplasm of different
species to produce nucleo-cytoplasmic hybrids
1. Inter-genus combination
Nucleus of common carp and cytoplasm from crusian carp.
Adult fish with essentials of common carp phenotype and
cytoplasmic influenced character at morphological, physiological
and biochemical levels were obtained. Both male and female
hybrids are fertile
2. Inter –subfamily combination
Nucleus from grass carp and cytoplasm of blunt snout bream.
Adult fishes were obtained.