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Chapter II.12. The structure of breeding systems

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 ANIMAL BREEDING AND HUSBANDRY
Ioan Hutu, DMV, PhD, Kor Oldenbroek, Eng, PhD, Liesbeth van der Waaij , Eng, PhD
Veterinarian (1997), animal Master in Animal Husbandry Master in Animal Husbandry (1996)
science engineer (2001), master (1973) and PhD in Animal and PhD in Animal Husbandry and
in management (2012), PhD in
animal reproduction (2002) at
Breeding and Nutrition (1988)
from Wageningen University, the
Genetics (2001) from Wageningen
University, the Netherlands. Former
ANIMAL BREEDING AND
USAMVBT. Associate Professor Netherlands. Retired, associate Assistant Professor at Animal
in the Discipline of Animal
Production, Faculty of Veterinary
specialist invited to the Center for
Genetic Resources Netherlands.
Reproduction and Genomics
Center, Wageningen University, HUSBANDRY
Medicine Timisoara, Romania. The Netherland

Ioan Hutu
Kor Oldenbroek
Liesbeth van der Waaij

I. Hutu, K. Oldenbroek, L. van der Waaij

ISBN 978-606-785-148-9

AGROPRINT - TIMISOARA, 2020

 ANIMAL BREEDING AND
HUSBANDRY
textbook

Ioan Huțu
Faculty of Veterinary Medicine, Timisoara

Kor Oldenbroek
Center for Genetic Resources, The Netherlands

Liesbeth van derWaaij

Animal Genomics and Breeding Center, The Netherlands

Agroprint Publishing House, Timisoara, Romania, 2020

Scientific references:
Prof. Emil Sas Eng. PhD
Marcel MatiutiEng, PhD
Prof. Viorel Herman, DMV, PhD
Prof.EmilTirziu, DMV, PhD

Layout and adaptation:

Ioan Hutu and Isolde Heim

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HUŢU, IOAN
Animal breeding and husbandry / Ioan Huţu, KorOldenbroek, Liesbeth van der
Waaij. - Timişoara :Agroprint, 2020
Conţinebibliografie
ISBN 978-606-785-148-9

I. Oldenbroek, Kor
II. Waaij, Liesbeth van der

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Printed: December 2020

Any part of this work can be copied and redistributed, in any medium or format.
License CC BY-NC-ND 4.0.

Recommended citation:

Hutu, I., Oldenbroek, K, van der Waaij, L., Animal breeding and
husbandry,Agroprint, Timisoara, 2020.
 Chapter II. 12
THE STRUCTURE
OF BREEDING SYSTEMS
The goal of breeding programs is to generate genetic improvement within a
population. By following the outlined steps of collecting information on selection
candidates, estimating breeding values, selecting potential candidates and fitting
the mating scheme to those it is possible to create a permanent feedback cycle.
The fulfilment of set breeding goals can be monitored.

Diagram of breeding program – structure of breeding systems

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STRUCTURE OF BREEDING SYSTEMS
Definition

A breeding program or a breeding scheme is a program aiming at defined

breeding objectives for the production of a next generation of animals. It is the
result of recording selected traits, the estimating breeding values, selecting
potential parents and setting up a mating program for the selected parents
including appropriate (artificial) reproduction methods

The structure of breeding programs differs substantially between animal

species. An important reason is the differences that exist in reproductive rate.
Sows and hens can produce many more offspring than cows and mares, and some
fish species can produce even more. Another important reason is the ownership of
the animals which may even be different for the males and females of certain
species.
Reproductive rates range from one offspring every few years to many
thousands of offspring per year or even per month. In addition, the rate often differs
between males and females. Males often have higher reproductive rates than
females. This leads some programs to focus more on selection in males. The
number of males needed is smaller which leads to higher selection intensities. An
added advantage is that with fewer animals, the cost of keeping the breeding stock
becomes smaller. Sometimes the biological reproduction rates can be enhanced by
technological interventions. In dairy cattle breeding, artificial reproduction
techniques such as artificial insemination (AI) and in vitro fertilization, in
combination with embryo implantation, are well-developed and widely used in the
breeding population. This provides the opportunity to produce large numbers of
offspring from superior sires and dams, and disseminate the genes of these
superior animals widely in the production population.
Ownership of breeding animals. In animal species that are kept for
companionship or leisure purposes, control over the breeding program by the
breed associations is very loose because the animals are owned by private
owners. These private owners each decide individually on the breeding of their
animals. In some species, like the major dairy cattle breeds, the males are owned
by a breeding company or a group of breeders, and the females are privately
owned. In both cases the breeding company or association depends on the
breeding decisions of the private owners. Breeders can only completely control the
breeding decisions when they own both the males and females in the breeding
program.

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 ANIMAL BREEDING AND HUSBANDRY

12.1. Genetic improvement in a breeding program

In a breeding program tenacity, accuracy and discipline of the active

breeders are crucial. Tenacity with respect to the breeding goal, accuracy in
collecting phenotypes, genotypes and pedigree registration and last but not least
discipline in selection and mating. All are important human factors that should be
kept under control. However, in almost all species the female animals, and
sometimes also the males, of the population under selection, are privately owned
by farmers or citizens. They decide whether they want to breed with their animal(s)
and if, which would be the mating partners. In case of private ownership, the
willingness and help of the owners are essential to be able follow the breeding
goal, collect information systematically and accurately and to perform the selection
and mating process.

12.1.1. Genetic improvement by selection

As explained already, the permanent selection response depends on the
selection intensity, the accuracy of the breeding value, the genetic variation and
the generation interval. The first three parameters are expressed in the nominator
of the formula and the last one in the denominator. The formula shows that the best
selection response is achieved if selection intensity, accuracy and genotypic
variation are high while generation interval is low. The formula is:
R i * rIH * σA,
12.1
ΔG anual = ; ΔG anual =
L L

where: ΔG year = genetic gain, R = selection response; i = selection intensity;

rIH = accuracy; σA, = genotypic variation and L = generation interval
The genotypic variation can hardly be influenced within a breeding program,
but the breeder has impact on the other three. The Parameters are interrelated,
especially the accuracy of selection and the generation interval. For example: If the
choice is made for selection with a high accuracy, collecting all information on
selection candidates takes long, which leads to a long generation interval. When
the breeder agrees to a lower accuracy, younger animals can be selected for
breeding, which results in a short generation interval. In this way breeding
programs can be optimized with respect to selection intensity, accuracy and
generation interval.
Within a specific breeding program, the selection response can be achieved
by four different pathways. The total selection response is the addition of the
selection response in these four different paths. From 1 – 4 the paths have a

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STRUCTURE OF BREEDING SYSTEMS
decreasing impact on genetic improvement. 1) sires to breed sires, 2) sires to
breed dams, 3) dams to breed sires and 4) dams to breed dams (see formula
9.10).

12.1.2. Genetic improvement by crossbreeding

Cross-breeding (see Chapter 11) aims to achieve genetic changes in
populations by restructuring offspring genotypes in the direction of heterozygosity.
Basically, the cross-breeding system is a system of directed production of
heterozygosity in the population. Crossing is especially successful in the case of
characters with low heritability in which the phenomenon of heterosis occurs and
there is complementarity (combination of the characteristics of two races / lines)
and combinability (the possibility of combining negatively correlated characters).
Heterosis is manifested by the superiority of the average performance of double,
single or reciprocal hybrids over the parent generation.

H% = [(Xf-Xp) / Xp] x 100 12.1

where: H% = heterosis effect, Xf = average of the filial generation; Xp =

average of the parental generation (maternal and paternal average).
The effect of heterosis is based on non-additive genetic interactions:
dominance, superdominance and epistaxis. The effect of heterosis is not identical
and unitary in all species and production characters and is not identical in each
breeding pair. Heterosis has a low value in the case of characters with high
heritability. Therefore, in the case of characters with high heritability, the
improvement is made by selection in purebred and in the case of characters with
low heritability, crosses will be used. Three ways can be used to obtain the
heterosis effect: i) crossing the inbred lines, ii) using the individuals that after the
mating show heterosis effect or the use of the breeds that after mating externalize
to the products the heterosis effect.

12.2. Structure of breeding programs / schemes

In animal species kept for companion or leisure purposes control over the
breeding program by the breed associations is very loose. These programs have a
flat structure: Nearly all females can be selected and in most cases the breed
association only has a strong vote in the selection of the males.

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 ANIMAL BREEDING AND HUSBANDRY
Conformation shows determine to a great extend which males are used. This
very often results in a few “champion” males which are very heavily used
throughout the whole population. In these breeding programs only the selection
paths sires to breed sires and sires to breed dams are effective in creating a
selection response in the whole population. As an example, we will outline a
breeding program for horses (the Dutch KWPN program).
On the contrary, in pig and poultry production (pork, eggs and broiler meat)
commercial breeding programs have full control over all breeding activities. They
own a limited number of breeding animals which are part of their selection lines. In
these lines the companies determine the breeding goal, perform data collection
and the breeding value estimation. They take care for the selection and mating of
parents to produce a new generation. The final product is produced by large
numbers of animals that are three- or four-way crosses from the selection lines
they own. In these breeding programs all the selection paths are effective in
creating a selection response in the whole breeding program with a pyramidal
structure. Working with different selection lines, which differ in breeding goal traits,
the breeding companies have the flexibility to produce different three- or four-way
crosses. Giving as an example pork production, where markets are different:
Requirements for slaughter weight, carcass composition and meat quality are not
equal. The globally operating companies have different sire lines for pork
production which are used to serve different markets for pork. Controlled by
contracts, farmers multiply and cross the selection lines in a pyramidal structure. A
breeding program for pork production will be outlined later on (the Topigs program).
Between breeding programs with a flat and loose structure and breeding
programs with a pyramidal structure fully under control, there are also breeding
programs with an open nucleus. In these programs a part of the population is
owned by a limited number of breeders and/or a breeding company. This part is
used to select the sires and to select the dams of the sires for the next generation.
Here only the selection path dams to breed dams is of little importance in creating
a selection response in the whole population. As an example an open nucleus for
dairy cattle breeding is outlined later on (the CRV program).

12.3. Breeding programs with a horizontal structure

In many species, like dogs, horses and meet producing sheep and goats
breeding programs have a simple structure. In such programs an intense selection
of males takes place, because only a limited number of males is necessary to
produce the next generation. Some selection in females is practised, because
many of animals are required as dams for the next generation. However, this
selection is hardly effective.

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STRUCTURE OF BREEDING SYSTEMS
The breeding animals in these species (especially the females), are privately
owned, the owners making selection and mating decisions themselves.
Consequently, breeding goals change too often and are not followed strictly,
recording of traits and pedigree is less complete, selection and mating can hardly
be influenced. This results in low genetic improvement rate over generations.
Herdbooks play a prominent role in the breeding programs of these species.
They are used for pedigree recording and set the rules for the characteristics of
males and females to be selected as parents for the next generation. The
guidelines for males are often very strict and only a limited number is approved for
breeding. Often, high emphasis is given to conformation. Rules for females, on the
other hand, are very loose, they are very seldomly disapproved.
Great efforts are made nowadays to professionalize the breeding programs
of horses. Only a limited number of stallions in the breed is approved for breeding
by the studbooks and only females with the best conformation, health and
performance traits are promoted for breeding. This results indeed in a genetic
improvement which also can be validated in analyses.
In dog breeding, shows play an important role in the selection of males. A
limited number of males with the best conformation score at shows is used for
breeding, often without any control by the breed association. Because of its
negative side effects dog breeding is under discussion nowadays. Strong selection
for conformation and high relationship among animals within the population lead to
inbreeding and frequent genetic defects.
In meat producing sheep and goat breeds the selection of rams and bucks is
most effective because only a limited number of is necessary to produce the next
generation. Simple breeding goals for these species are weight and muscularity at
a fixed age. With the use of young rams and bucks the generation interval can be
kept short and genetic improvement can be generated. From a farm economics
point of view, the ewes should produce litters as long as possible. Therefore, the
generation interval on the dam’s side is rather long. In more intense sheep and
goat production systems fertile dam breeds are crossed with males from
specialised meat breeds, resulting in many lambs with good growth and slaughter
quality.
The Dutch Texel breed is famous for these traits and is often and globally
used as a terminal sire line to produce crossbred lambs from females of local fertile
breeds. In milk producing sheep and goat breeds, the selection of dams and males
used for breeding is practised. Progeny testing of males is hardly performed due to
a low percentage of milk sheep and milk goats in milk recording schemes. Up to
now, little genetic improvement is obtained in milk sheep and goats.

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 ANIMAL BREEDING AND HUSBANDRY
12.3.1. Example of a breeding program with a flat structure
The KWPN breeding goal. Since 2006, the KWPN distinguishes four
breeding directions. Riding horses, which are subdivided into dressage and
jumping disciplines, make up the largest group (85-90%). The other two breeding
directions are the harness horse and the Gelders horse. Even though each
breeding direction has its own additional objectives, all horses fall under the
general KWPN breeding goal, which aims at:
• breeding a competition horse that can perform at Grand Prix level;
• with a constitution that enables long time usefulness;
• with a character that supports the will to perform as well as being friendly
towards people;
• with functional conformation and a correct movement mechanism that
enables good performance;
• with attractive exterior that is preferably attractive, along with refinement,
nobility and quality.
The KWPN has formulated a separate breeding standard for each breeding
direction. These standards are, in fact, descriptions of the ideal dressage-,
jumping-, harness- and Gelders horse. The breeding standard helps to evaluate
horses objectively and uniformly. It provides a framework for the jury. This reduces
the risk of pronounced personal preferences and therefore increases the
uniformity, reproducibility and the reliability of the evaluation.
A distinction must be made between mares and stallions.
The studbook supports the selection and use of the best mares by issuing
predicates. They are kind of ‘quality stamps’ which a mare can earn, based on her
own qualities (performance, conformation and heath) or based on qualities of the
offspring (performance, conformation). For stallions there is an obligatory process
to become a studbook approved stallion. The stallion route has four steps:
1. Inspections of the stallion: on hard surfaces for correctness of legs and
body and on free jumping (jumper horses) or free movement (dressage stallions).
2. Health checks: in various stages of the stallion selection process, stallions
must prove to meet minimum demands for clinical correctness of body and
functioning, X-rays, semen quality and roaring.
3. Station performance test: depending upon their age, stallions must prove
their sport ability during a central performance test of maximum 70 days
4. When a stallion has offspring, these offspring are inspected and/or followed
in sport. Based on the collected information, various breeding values are estimated
for each stallion. Based on those, stallions are evaluated at several points in live, i.
e. when their eldest offspring is 1 year, 3 years, 7 years and 11 years of age.

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STRUCTURE OF BREEDING SYSTEMS

Table 12.1.
KWPN types of information used to estimate breeding values
Types of information Types of data used to estimate
breeding values
Linear scores of conformation and 20 random foals of each new approved
movement stallions
X-rays for ostechondrose 20 random yearlings of each new approved
stallion
Linear scores on conformation, movement, all (mainly) 3 year old mares offered for
free studbook inspection
Jumping or free movement + valuing marks all young stallions offered for the stallion
selection process
Marks obtained in performance tests one day performance tests for Mares
(IBOP) and station tests (EPT) for mares
and stallions
Competition results off all registered horses

KWPN collects various types of information on many different

moments: These data are used to estimate breeding values for all stallions and
mares (see table 12.1).
Breeding values are estimated for:
• All linear scored traits (conformation, movement, free jumping)
• Osteochondrosis
• Sport dressage
• Sport jumping
These breeding values are communicated to breeders, used during selection
processes, for evaluation of the breeding program and for the best combination of
stallion and mare.

12.4. Breeding programs with selection nucleus

Nucleus programs are characterized by a limited number of female animals

with a genetic superiority. These are the dams to breed sires. They are owned by a
breeding organization or a limited number of breeders and called a nucleus
(breeding farm(s) or breeding unit(s)). They deliver the next generation of sires to
breed sires and sires to breed dams. They are recorded for a large number of
traits.

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 ANIMAL BREEDING AND HUSBANDRY
The breeding organization takes the decisions on selection and mating in the
nucleus and in the contracts. As a consequence, breeding goals are followed
steadily, recording of traits and pedigree is complete, selection and mating in the
nucleus is under full control. This results in a high genetic improvement rate over
generations. Nucleus programs can be closed, like in commercial pig and poultry
breeding. The breeding animals for the nucleus are chosen at the beginning and
no animals from outside the nucleus are added at a later stage. This is called a
closed nucleus breeding program.
In cattle breeding artificial reproduction techniques, in particular artificial
insemination and in vitro fertilization in combination with embryo implantation are
well developed and heavily used in the open nucleus. It gives the opportunity to
produce high numbers of offspring from superior sires and dams, such
disseminating the genes of these superior animals widely in the production
population. In the disseminated part of the population (mainly used for production
purposes = production population) the offspring of the sires is tested for important
traits. When the estimated breeding value of females in the production population
is comparable with (or higher than) the breeding value in the nucleus population
they can enter the nucleus. In that case they can be bought by the breeding
company or contracted by the breeding organization. This is called an open
nucleus breeding program.
Open nucleus breeding programs are an option in species where the present
breeding programs have a flat structure: horses, dogs, sheep and goats. Genetic
improvement can be generated in a controlled situation and males from the
nucleus can be used widely by individual private breeders. In dogs open nucleus
breeding programs are developed for breeding working dogs. For eye-seeing dogs
even closed nucleus programs are set up.

12.4.1. CRV dairy breeding program - an open nucleus breeding system

The breeding goal and CRV selection index
For its nucleus CRV uses as a breeding goal (2014): ‘a healthy and long
lasting dairy cow that will give the optimum contribution to farm profit’. For the
selection of bull dams and sires of sons, for the nucleus animals or potential
nucleus animals CRV in The Netherlands uses its own index. In this ‘CRV-index’
great importance is put upon health traits and longevity as can be seen below
(figure 12.1).
Each of these three categories is a sub-index in which a number of
production traits, longevity and health traits and a number of conformation traits are
combined in one single figure.

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STRUCTURE OF BREEDING SYSTEMS

Figure 12.1. The relative weight of production, healt and conformation in the RV
index
The traits for these three categories originate from several sources. An
important source is the milk recording service. For management reasons farmers
like to know individual milk production data (kg and content). Conformation data
are gathered by inspectors visiting farms in regular intervals. Longevity and health
traits are composed from milk recording and conformation data. For the bulls which
have been chosen to disseminate the genetic improvement into the production
population another selection index is used: The NVI (Table 12.2) is the total net
merit index. It is used in the Netherlands and Flanders for ranking bulls.
Table 12.2.
The genetic gain (in breeding values)

Trait Gait value

Indices INET 3% milk, 9% fat and 14% proteins

26%, din care:
Longevity 11%

Udder health 14%

Fertility 14%

Udder conformation 14%

Leg and claw 16%

conformation
Calving index 5%

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 ANIMAL BREEDING AND HUSBANDRY
This index puts those bulls at the top which are able to produce daughters
that come closest to the national breeding goal. The NVI is derived from a formula
based on three different components: Production, Health and Conformation. The
underlying traits and their contribution to the NVI are shown in the table 12.2:

The selection response obtained in Table 12.3. The genetic gain (in
the milk production population. The table breeding values)
12.3 shows the genetic gain (in breeding
values) in the production population from Trait Gain Value
selection with NVI after 1 generation (e. g. Milk 272 kg
with selection with the NVI formula the next
generation of animals will have a breeding Fat 13 kg
value for milk that is 272 kg higher than the Protein 8.7 kg
breeding value for milk of the present
generation). Longevity 200 days

The structure of the CRV breeding Udder health 2.3 pnt

program (Figure 12.2). In parallel CRV
Udder 1.8 pnt
performs a breeding program for Black and
White (B&W) and for Red and White (R&W) Feet & Legs 2.2 pnt
Holstein Friesians. The selected females
Calving interval 0.8 pnt
originate from the nucleus with animals CRV
owns (Delta donor) and from farmers in the Interval from first to last
1.0 pnt
production populations worldwide (Euro insemination
donor). Within Euro donor selected females
Calving ease (paternal) 1.4 pnt
are contracted with the essence that the
selected female is inseminated with a sire of Maternal calving
1.1 pnt
the choice by CRV and a calf born out of this process
insemination is first offered for sale to CRV.
Vitality (paternal) 0.7 pnt
This Euro donor scheme makes the CRV
nucleus an “open” nucleus. The offspring of Maternal vitality 0.9 pnt
selected Euro females at production farms
with the highest CRV index are added to the offspring of the Delta females owned
by CRV. In this group CRV selects the sires and dams to breed the next generation
of potential breeding animals. Within the Delta scheme In Vitro Fertilization (IVF) is
applied. From one year old heifers, oocytes are collected and fertilized in a lab with
semen of a selected sire. In this way full and half sib progeny (males and females)
of a donor is born out of foster dams. The best males and females, the ones with
the highest predictive value for the CRV index are selected. Males are selected to
be used as sires for the nucleus and the production population and females for the
Delta nucleus.

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STRUCTURE OF BREEDING SYSTEMS
When enough embryos become available from a heifer by IVF, the heifer is
inseminated and transported to one of the testing farms of CRV. Here, the heifers
are raised up to their first calving and subsequently tested under uniform conditions
for milk production and conformation in their first lactation. The test results (own
performance) are used to calculate a realized breeding value. Each year 100 Delta
heifers and 150 heifers from the Euro donor are tested at the farms under contract
of CRV. The very best heifers are used again as donor in their first lactation and a
part of the embryos obtained are also sold to production farms.
In the scheme below (2014) from 150 B&W test bulls only 38 came from
donors at production farms. 23 of the 50 R&W test bulls originate from such
donors. In the Delta nucleus an intense selection is applied in the one-year-old
heifer donors: 15-20 are dam of 90 test heifers and of 112 test bulls. They are
selected on their predictive breeding value, nowadays a genomic breeding value
(see later). CRV produces 5700 embryos annually within the Delta program and
3000 embryos within the Euro donor program. In addition, a few embryos are
bought on the North American market. The selection in the born male calves is
intense: 1 out of 15 is used as a young sire in the production population.

Figure 12.2. Genomic selection in the CRV breeding program for dairy cattle
Personal communication Marieke de Weerd, November 2013.

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 ANIMAL BREEDING AND HUSBANDRY

12.4.2. CRV1 genomic breeding program

For commercial breeding companies the attractiveness of genomic selection
consists of two factors. First, it is possible to calculate differences in breeding value
between full sibs before they have their own phenotypic records or records from
their progeny. The SNP analysis makes clear which genes of the parents are
transmitted to each full sib. Second, young animals that should have been progeny
tested before they obtain an accurate breeding value, can be used intensively
directly after puberty. The accuracy of the genomic breeding value comes close to
the accuracy obtained after progeny testing. In this way the generation interval in
breeding programs with genomic selection can be very short. This speeds up the
genetic gain of the breeding programs (Figure 12.3).
In the past CRV applied progeny testing to breed the bulls that were
intensively used by the dairy farmers. On average dairy farmers bought
approximately 25 per cent of semen from young unproven bulls. CRV sold in a
short term 1000 doses of semen from those. Four years later this resulted in at
least 50 daughters of such an unproven bull with a completed first lactation. Then,
the selection of the best bulls took place and the best proven bulls were used
heavily by the dairy farmers (75 per cent of the inseminations performed at dairy
farms).

Figure 12.3. Reliability of breeding value for milk production

1
Personal communication Marieke de Weerd, November 2013.

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STRUCTURE OF BREEDING SYSTEMS
In this traditional testing scheme, the selection of young bull dams and
young bull sires takes place in year 0, the birth of the young proven bulls is in year
1, their semen is collected and used in year 2, their calves are born in year 3, their
heifers start to produce milk in year 5 and finish their first lactation in year 6. Then,
the proven bulls are selected on the first lactation data of their daughters. After
year 6, they are intensively used and their progeny becomes productive in year 10.
In this traditional testing scheme it takes 10 years before the selection of the young
dams and sires leads to an increase in profit for the dairy farmers.
Nowadays (2014) genomic selection is used and leads to a rise in use of
young bulls by the dairy farmers. This is due to the fact that the accuracy of their
genomic breeding value approaches the accuracy of the breeding value of the
proven sires based on the phenotypic data of their daughters. See, figure below
where you should realize that the reliability is the (accuracy).
Within CRV breeding program genomic selection of the young bull dams
decreases also their age at selection. Today, 75 percent of the young bull dams
are one year old heifers and 25 per cent are first calved heifers. In the traditional
scheme young bull dams had at least a full lactation at the moment of selection. An
increasing percentage of young bulls with a genomic breeding value is used as sire
of the new generation of young bulls. In the traditional scheme only proven bulls
were sire of the young bulls to be tested. All these facts sharply decrease the
generation interval in the breeding program of CRV and this accelerates the
genetic improvement at least with a factor 2.
Another effect of genomic selection is the relatively small costs of genomic
testing. Therefore, every year, 2600 young bull calves are tested for their SNP
variants. Then, based on their genomic breeding value, one out of 15 is selected to
put into the breeding program. This sharp selection, even within a group of full sibs,
is very attractive. In the breeding program the number of young bulls selected for a
high breeding value increases. The number of bulls, which have to wait four years
for the milk production data of their progeny, decreases sharply. This has a very
favourable effect on the costs of the genomic selection breeding program in
comparison with the traditional scheme with a large amount of “waiting” bulls,
waiting for years before their daughters finished their first lactation.
CRV is co-operating with a lot of breeding companies in other European
countries to create a large reference population. Today (2014) the reference
population consists of approximately 30.000 progeny tested bulls that were also
screened for their SNP profile. This high number is the reason why the accuracy of
the genomic breeding value of young unproven bulls is getting very close to the
accuracy of progeny tested bulls.

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 ANIMAL BREEDING AND HUSBANDRY
Value of genomic selection within the dairy production farms
At dairy farms a large proportion of the dairy cows has to be used as dam for
the next generation of dairy cows. This low selection intensity can be increased in
two ways: 1) increase the longevity and with that the number of calvings per cow
and 2) by the use of sexed semen, because then the change to obtain a
replacement heifer calf is 90 % instead of 50%. In a situation with a higher intensity
due to a low replacement rate and the use of sexed semen, genomic selection in
young born heifer calves is calculated to be profitable for the dairy farmer.

12.5. Breeding programs with a pyramidal structure

In many breeding programs trait recording is expensive and therefore the

number of animals for which traits are recorded is rather small in relation to the
whole population. Consequently, the genetic improvement is realized for only a
limited number of animals where the selection is practiced. These animals are used
to disseminate the realized genetic improvement to the entire population. The
selection of a limited number of animals, the multiplication in the next generation
with a much larger number of animals and the production of the “production”
animals in very large numbers in the final generation, leads to a pyramidal structure
(see figure 12.4 and 12.5).

Figure 12.4. Hendrix-Genetics (ISA)’s pyramidal structure breeding program for

egg production

384 | HUTU, OLDENBROEK & WAAIJ.

STRUCTURE OF BREEDING SYSTEMS
The dissemination of the selection response depends on the structure of the
breeding programs. In commercial pigs and poultry programs, selection takes place
in the top of the breeding program. By using a few “multiplying generations” the
selection response obtained in the top is disseminated into the animals producing
meat or eggs. The figure below outlines as an example the structure of the
Hendrix-Genetics (ISA) breeding program (see figure 12.4):
Within the commercial breeding schemes, for example in poultry and pigs,
the selection response is realized in specialized lines. In commercial poultry
(broiler) breeding programs usually a four-way cross is applied. Two female lines
are selected for fertility and egg quality, the male lines for growth traits.
Crossbreeding results in a high number of healthy chicks due to the full exploitation
of heterosis. In the broiler scheme shown above, the selection takes place in the
pure lines, in a limited number of great grandparents. When the selected great
grandparents are multiplied in sufficient numbers, they are crossed. The generation
interval in poultry selection lines is very low, i. e. less than a year to accelerate the
selection response. The A*B line cross gives the A*B F1 progeny that act as
Grandparent and the C*D line cross the C*D F1 grandparent. The pure line and the
F1 animals are owned by the breeding company to protect the characteristics of
their lines and the realized genetic improvement in these lines. By maintaining
different selection lines, they keep the options to create animals which can produce
for different markets and react quickly to market changes.
In commercial pig breeding programs usually, a three-way cross is applied.
See e.g. the Hypor program in 2014:

Figura 12.4. Hybridization program for Hypor hybrid (2014)

385 | © FMVT, 2020

 ANIMAL BREEDING AND HUSBANDRY

12.6. Key issues on breeding programs

1. A breeding program or a breeding scheme is a program aiming at defined

breeding objectives for the production of a next generation of animals. It
combines a series of steps: Recording selection traits, estimating breeding
values, selecting potential parents and designing a mating program for the
selected parents including appropriate (artificial) reproduction methods.
2. In a breeding program tenacity, accuracy and discipline of the active
breeders is crucial. Tenacity with respect to the breeding goal, accuracy in
collecting phenotypes, genotypes and pedigree registration and last but not
least discipline in selection and mating. These important human factors
should be kept under control.
3. In animal species kept for companion or leisure purposes breed
association have only very loose control over the breeding program. These
programs have a flat structure: Nearly all females can be selected and in
most cases the breed association has only a strong vote in the selection of
the males.
4. In pig and poultry production (pork, eggs and broiler meat) commercial
breeding programs have full control over all breeding activities. They own a
limited number of breeding animals that are part of their selection lines. In
these lines the companies determine the breeding goal, perform the
collecting of data and the breeding value estimation, and take care for the
selection and mating of parents to produce a new generation.
5. Breeding programs with an open nucleus are in between breeding
programs with a flat and loose structure and breeding programs with a
pyramidal structure, fully in control. In open nucleus programs part of the
population is owned by a limited number of breeders and/or a breeding
company. This part is used to select the sires and to select the dams of the
sires for the next generation.

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 BIBLIOGRAPHY

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*** Concepts in Growth and Development, http://animalbiosciences. uoguelph.ca/

~swatland/ch8_1.htm
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*** http://www.gesfokwaarden.eu /en/breedingvalues/pdf/E_09_EN.pdf

TUTORIALS & BACKGROUND IN GENETICS:

1. Introduction to heredity:
https://www.khanacademy.org/science/biology/classical-genetics/mendelian--
genetics/v/introduction-to-heredity
2. Heredity 2: https://www.khanacademy.org/science/biology/classical-
genetics/mendelian--genetics/v/punnett-square-fun
3. Alleles and genes:https://www.khanacademy.org/science/biology/gene-
expression-central-dogma/central-dogma-transcription/v/alleles-and-genes
4. Allele frequency:https://www.khanacademy.org/science/biology/her/heredity-
and-genetics/v/allele-frequency
5. What are phenotypes?https://www.youtube.com/watch?v=kLpr6t4-eLI
6. Where do your genes come from? https://www.youtube.com/watch?v=-
Yg89GY61DE

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TUTORIALS & BACKGROUND IN STATISTICS:

1. Introduction: mean, median and mode:
https://www.khanacademy.org/math/probability/data-distributions-
a1/summarizing-center-distributions/v/statistics-intro-mean-median-and-mode
2. Correlation and regression: https://www.youtube.com/watch?v=jmB_wK6iLCs
3. Variance rules for statistics: https://www.youtube.com/watch?v=rsMGeseIDNg
4. Rules to calculate covariances:
https://www.youtube.com/watch?v=3Z2cngD54Qw
5. Introduction to the normal distribution:
https://www.khanacademy.org/math/statistics-probability/modeling-
distributions-of-data/normal-distributions-library/v/introduction-to-the-normal-
distribution

TUTORIALS – ANIMAL BREEDING:

1. Why Animal Breeding?

https://www.youtube.com/watch?time_continue=4&v=wbLTe_1bKVE
2. The Seven Steps of a Breeding Program -
https://www.youtube.com/watch?v=b3r30EZc3IM
3. The Value of Information in Animal Breeding
https://www.youtube.com/watch?v=tffqHe8q4eY
4. The Concept of Inbreeding
https://www.youtube.com/watch?time_continue=462&v=Fk4OpMZx0B4
5. Consequences of Inbreeding
https://www.youtube.com/watch?time_continue=280&v=7Eh21o0QLXM
6. Animation Inbreeding and Genetic Relationships
https://www.youtube.com/watch?time_continue=21&v=eRG3RSVlWIE
7. The Concept of Genetic Models
https://www.youtube.com/watch?time_continue=131&v=mN6VX4mx9z4
8. The Genotypic Value
https://www.youtube.com/watch?time_continue=19&v=FtlWZ4lDSH0
9. Heritability
https://www.youtube.com/watch?time_continue=295&v=dCkK7oiI-0o
10. The Transmission Model
https://www.youtube.com/watch?time_continue=202&v=B7PJBrn1uG8
11. Permanent and Common Environment
https://www.youtube.com/watch?time_continue=73&v=_3CiIGNx6ks
12. Breeding Values – Genetic Concept

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BIBLIOGRAPHY
https://www.youtube.com/watch?v=qqJN0t_8PeI
13. Estimating Breeding Values and Predicted Performance
https://www.youtube.com/watch?time_continue=4&v=MB7WBeF41fw
14. Using Genomic Information
https://www.youtube.com/watch?time_continue=1&v=MTN3tfBiF74
15. Animation Estimated Breeding Value
https://www.youtube.com/watch?v=X3fQ3__FLEE
16. Video: Calculating Genetic Gain
https://www.youtube.com/watch?v=Sx7JWz0FD54
17. Mating
https://www.youtube.com/watch?v=05DDmOIzBqs
18. Inbreeding at the Population Level
https://www.youtube.com/watch?time_continue=1&v=hJh491hBUjg

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PART THREE: BIBLIOGRAPY 430

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448 | HUTU, OLDENBROEK & WAAIJ

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ANIMAL BREEDING AND HUSBANDRY

Ioan Hutu, DMV, PhD, Kor Oldenbroek, Eng, PhD, Liesbeth van der Waaij , Eng, PhD
Veterinarian (1997), animal Master in Animal Husbandry Master in Animal Husbandry (1996)
science engineer (2001), master (1973) and PhD in Animal and PhD in Animal Husbandry and
in management (2012), PhD in
animal reproduction (2002) at
Breeding and Nutrition (1988)
from Wageningen University, the
Genetics (2001) from Wageningen
University, the Netherlands. Former
ANIMAL BREEDING AND
USAMVBT. Associate Professor Netherlands. Retired, associate Assistant Professor at Animal
in the Discipline of Animal
Production, Faculty of Veterinary
specialist invited to the Center for
Genetic Resources Netherlands.
Reproduction and Genomics
Center, Wageningen University, HUSBANDRY
Medicine Timisoara, Romania. The Netherland

Ioan Hutu
Kor Oldenbroek
Liesbeth van der Waaij

I. Hutu, K. Oldenbroek, L. van der Waaij

ISBN 978-606-785-148-9

AGROPRINT - TIMISOARA, 2020