Dr. Sushil Neupane's notes on "Introductory Genetics and Animal Breeding" for the 2nd year, 1st semester of the Diploma in Animal Science (latest syllabus of CTEVT) provide a comprehensive overview of key concepts and principles related to genetics and animal breeding. The notes cover fundamental topics in genetics and their practical applications in livestock production and breeding programs.

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PREPARED BY DR. SUSHIL NEUPANE (B.V.SC. AND A.H., IAAS, TU)
Unit 9: Breeding Strategies 9 Hrs.
9.1 Define breeding goal and objectives and their basis
9.2 Open Nucleus and Close nucleus Breeding Systems
9.3 Formulation of Breeding Plans for Different Livestock Species
9.4 Community Breeding Systems
A breeding goal is the specification of the traits to be improved including the emphasis
given to each trait. It gives the direction in which the population should improve.
A breeding program is a program aiming at defined breeding objectives for the production
of a next generation of animals. It is the combination of recording selected traits, the
estimation of breeding values, the selection of potential parents and a mating programme for
the selected parents including appropriate (artificial) reproduction methods.
Figure: Breeding program
Genetic Improvement
Genetic improvement aims for an active use of the genetic variation available, both within
breeds and between breeds of livestock. The animal genetic variation can be used to
accommodate interests and wishes of farmers to make livestock even more efficient in using
available resources to produce human food and other agricultural products. Genetic
improvement focuses at a directional improvement in genetics of animals in coming

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PREPARED BY DR. SUSHIL NEUPANE (B.V.SC. AND A.H., IAAS, TU)
generations such that they will produce the desired products more efficiently under the
(expected) future economic, social and ecological production environment. This direction of
the improvement is formalized in a ‘breeding goal’.
Genetic Improvement Strategies
1. Breeding goal definition is the first step to be made in designing genetic
improvement strategies. The breeding goal identifies the animal traits that farmers
would like to be improved. To be able to identify the animal traits, the development
objective of agricultural production in the country is to be defined and the animal
production system is to be characterized.
2. Then, a second step is to implement a structure of gathering information, a recording
system, to identify those animals that have the highest breeding value for traits in
the breeding goal. This step of identifying high genetic merit animals is called
‘breeding value prediction’.
3. A third step is to make a well-organized structure for:
 the use of animals with highest predicted breeding value; and
 the dissemination of superior genes through the population, a quick and
widespread use of selected animals
The improvement objective has six essential characteristics. Basically, the objective of
improvement is characterized by the fact that:
i) Aims at the challenges of the future
ii) Includes all the desired features in the improvement objective
iii) Contains breeding values grouped in "genotypic aggregations"
iv) Allows the weighting of the characters subject to improvement v) includes all the desired
features in a single criterion (index)
vi) May include not only economic values, but also non-economic aspects

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PREPARED BY DR. SUSHIL NEUPANE (B.V.SC. AND A.H., IAAS, TU)
An example. Goal traits in genetic improvement of chickens
• General
 Disease resistance
 Adaptation to heat stress
 Utilisation of poor quality feeds
• Breeding stock
 Productive life
 Fecundity
 Quality of eggs (fertilisation, hatchability)
• Growers
 Growth rate
 Feed conversion
 Carcass quality
The breeding objective is the overall goal of the genetic improvement program. This might
be to maximise profit, or to maximise economic efficiency or to minimise economic risk.
The aggregate genotype is mathematical function of genetically controlled traits that when
maximised will achieve the breeding objective.
The selection index is a mathematical function of traits that are recorded or for which there
are genetic evaluations available, that when used for selecting animals for breeding will
maximize the aggregate genotype which will achieve the breeding objective.

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PREPARED BY DR. SUSHIL NEUPANE (B.V.SC. AND A.H., IAAS, TU)
What is a breeding objective?
The breeding objective is the overall goal of our breeding program. By setting a clear
breeding objective it is possible to then make objective decisions in breeding programs, such
as:
1) Choice of animals as parents in within-line or within-breed selection
2) Choice of which lines or breeds to introduce to the production system
3) Evaluation of different investments in breeding programs and design of alternative
breeding programs. The breeding objective provides the criterion to quantify and then
maximize the return on investments in the breeding program.
Selection index
 The selection index is a tool that lists all the observations for making the selection
decisions;
 In the selection index, observations are weighed by their index co-efficient;
 These index co-efficients are calculated to maximize the correlation between the
breeding goal and the selection index.
Basis of breeding goal and objectives
The basis of breeding goals and objectives is determined by a combination of factors, which
may include:
a. Economic Considerations: Breeding goals and objectives are often influenced by
economic factors. Traits that directly impact production efficiency, profitability, or
market value are typically prioritized. For example, in livestock breeding, traits like
growth rate, feed efficiency, meat quality, and milk production are often considered
important because they have a direct impact on the economic returns of the
enterprise.
b. Stakeholder Preferences: The preferences and needs of various stakeholders, such
as farmers, producers, consumers, and industry organizations, play a crucial role in
shaping breeding goals and objectives. Input from these stakeholders can be gathered
through surveys, focus groups, or market research to understand their priorities and
ensure that breeding programs align with their expectations.

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PREPARED BY DR. SUSHIL NEUPANE (B.V.SC. AND A.H., IAAS, TU)
c. Environmental Sustainability: With growing concerns about environmental
sustainability, breeding goals and objectives may incorporate traits that reduce the
environmental impact of the animals or improve their adaptation to changing
environmental conditions. For example, traits like lower greenhouse gas emissions,
reduced water usage, or increased heat tolerance may be targeted to address
environmental challenges.
d. Health and Welfare: Breeding goals and objectives often include traits related to
the health and welfare of the animals. This can involve selecting for disease
resistance, parasite tolerance, robustness, longevity, or traits that promote good
animal welfare practices. By breeding for improved health and welfare, breeders aim
to enhance the overall well-being and productivity of the animals.
e. Genetic Diversity and Conservation: In some cases, breeding goals and objectives
are driven by the need to maintain or enhance genetic diversity within a population
or to conserve rare or endangered breeds. These goals may prioritize traits related to
genetic variability, adaptability, or unique breed characteristics to preserve genetic
resources for future generations.
f. Scientific Knowledge and Technological Advancements: Advances in scientific
knowledge and technology can influence breeding goals and objectives. New
research findings, genomic tools, or breeding technologies may uncover previously
unknown traits or enable more accurate selection for desired traits. Breeding
programs often incorporate the latest scientific advancements to maximize genetic
gain and improve the efficiency of selection.
g. Regulatory Requirements: Breeding goals and objectives may also be influenced
by regulatory frameworks or industry standards. Certain traits or characteristics may
be mandated by regulations or required to meet specific certification programs,
ensuring compliance with quality, safety, or animal welfare standards.
Open Nucleus and Close nucleus Breeding Systems
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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PREPARED BY DR. SUSHIL NEUPANE (B.V.SC. AND A.H., IAAS, TU)
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 System:
The Open Nucleus Breeding System is a method used in animal breeding programs,
particularly in livestock breeding. In this system, the breeding program involves a central
nucleus herd and satellite herds. The nucleus herd consists of elite animals selected for
desirable traits, such as high milk production, fast growth, or disease resistance. The satellite
herds, located on different farms or locations, are used for commercial production.
The main goal of the Open Nucleus Breeding System is to improve the overall genetic
quality of the commercial herd through selective breeding. The nucleus herd serves as the
source of genetically superior animals that are bred with the animals in the satellite herds.
Offspring from these crosses are evaluated and selected based on predetermined criteria, and
the best animals are then incorporated back into the nucleus herd.
This system allows for genetic progress to be made within the nucleus herd while also
disseminating improved genetics to the commercial herds. By periodically incorporating

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superior animals from the satellite herds into the nucleus herd, the genetic diversity within
the nucleus is maintained, and the overall performance of the commercial herds can be
enhanced over time.
Close Nucleus Breeding System:
The Close Nucleus Breeding System is a variant of the Open Nucleus Breeding System. In
this system, the nucleus herd is maintained in isolation, and there is no incorporation of
genetic material from satellite herds or outside sources. The main objective of the Close
Nucleus Breeding System is to develop and maintain a genetically pure and homogeneous
population with specific desirable traits.
In the Close Nucleus Breeding System, all breeding activities take place within the nucleus
herd. The animals are carefully selected based on strict criteria and bred with each other to
propagate the desired traits. This system is often employed when there is a need to maintain
the genetic purity of a particular breed or to develop a highly specialized population for
research or production purposes.
The Close Nucleus Breeding System allows for a high degree of control over the genetic
composition of the population. However, it can also lead to a reduction in genetic diversity
over time if not managed properly. To mitigate this risk, periodic introduction of new genetic
material from external sources may be necessary to maintain genetic variation and prevent
inbreeding depression.

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PREPARED BY DR. SUSHIL NEUPANE (B.V.SC. AND A.H., IAAS, TU)
Formulation of Breeding Plans for Different Livestock Species
Formulating breeding plans for different livestock species involves considering various
factors such as breed goals, selection criteria, mating strategies, and genetic management
techniques. While the specific details may vary depending on the species, here are some
general guidelines for formulating breeding plans for different livestock:
1. Define breed goals: Start by clearly defining the breeding objectives for the specific
livestock species. Identify the traits that are economically important and align with
market demands. Examples may include growth rate, meat quality, milk production,
fertility, disease resistance, or specific traits for specialized breeds (e.g., fiber quality
for sheep). Prioritize the traits based on their importance to the breeding program.
2. Establish a breeding system: Choose an appropriate breeding system that suits the
objectives of the breeding program and the species' reproductive characteristics.
Common breeding systems include:
a. Purebred breeding: Emphasizes the production of animals with desirable traits
within a specific breed.
b. Crossbreeding: Utilizes the benefits of hybrid vigor by crossing different breeds
to improve specific traits or overall performance.
c. Composite breeding: Develops new breeds by combining genetics from multiple
breeds or populations to achieve specific objectives.

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3. Selection criteria: Determine the selection criteria for identifying superior animals
for breeding. Selection can be based on various methods:
a. Phenotypic selection: Based on observable traits, such as visual appearance or
performance records.
b. Genomic selection: Utilizes DNA markers and genomic information to estimate
the genetic potential of individuals.
c. Progeny testing: Evaluates the performance of offspring to determine the genetic
merit of their parents.
4. Breeding strategies:
a. Inbreeding: Used selectively to concentrate desirable genes and reinforce
uniformity within a breed. Care should be taken to avoid inbreeding depression.
b. Outcrossing: Introduces genetic diversity by mating unrelated individuals within
the same breed.
c. Line breeding: A form of selective inbreeding that maintains a high genetic
relationship to a particular ancestor while avoiding excessive inbreeding.
d. Rotational crossbreeding: A systematic approach that involves rotating sire
breeds to maintain hybrid vigor while retaining desirable traits.
5. Genetic management:
a. Record keeping: Maintain accurate and detailed records of pedigree,
performance, and reproductive data to make informed breeding decisions.
b. Breeding value estimation: Utilize statistical methods to estimate the genetic
merit of animals, allowing for more precise selection.
c. Artificial insemination (AI) and embryo transfer (ET): Implement advanced
reproductive technologies to accelerate genetic progress and enable the use of
elite genetics.
d. Genomic technologies: Utilize genetic markers and genomic data to identify
superior individuals at an early age and improve accuracy of selection.
6. Monitoring and evaluation: Regularly evaluate the performance of breeding
animals, assess the progress towards breeding goals, and adjust the breeding plan
accordingly.

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PREPARED BY DR. SUSHIL NEUPANE (B.V.SC. AND A.H., IAAS, TU)
Example
To help make the right, long term decisions it is worth investing time in the production of a
simple breeding plan. Here are some of the steps in creating that plan.
1. Review the current enterprise performance
 Assess your strengths and weaknesses
 Compare your performance to national benchmarks.
2. Define the market you will be producing for in the future
3. Determine your breeding objectives
 For breeding females
 For the slaughter generation
 Recognising the antagonisms that may exist between them
4. Assess your current genetic resources
 What type of sheep and cattle do you have at the moment?
5. Define the main resource constraints for your system
 In terms of labour, feed, land and buildings
6. Consider how performance can be enhanced through breeding
 Within breed selection (EBVs)
 Using a different breed – Crossbreeding/Breed Substitution
 Selection/Culling within the herd or flock
7. Consider how changes will be introduced
 Grading up existing breeding stock
 Buying in/using AI to introduce new genetics
8. Develop a strategy to monitor changes in performance and assess your success over
time.

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PREPARED BY DR. SUSHIL NEUPANE (B.V.SC. AND A.H., IAAS, TU)
Figure: Breeding Program
Figure: breeding plans for ruminant livestock in the tropics

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Community Breeding Systems for livestock in Nepal
In Nepal, community-based breeding systems have been successfully implemented to
improve livestock productivity and meet the needs of local communities. These systems
involve active participation and collaboration among community members, government
agencies, and other stakeholders. Here are some key elements and examples of community
breeding systems for livestock in Nepal:
1. Formation of community-based organizations: Community groups or
organizations are established to facilitate collective decision-making, resource
management, and implementation of breeding programs. These groups may include
farmers, local leaders, extension workers, and representatives from relevant
government agencies.
2. Identification of breed priorities: Communities assess their livestock production
systems, identify breeding goals, and prioritize traits that are important for their
specific needs. This could include traits such as milk production, draught power,
disease resistance, adaptability, or market suitability.
3. Conservation of local breeds: Community breeding systems in Nepal often
emphasize the conservation and utilization of indigenous livestock breeds. Local
breeds are valued for their adaptation to local conditions, resilience to diseases, and
ability to produce products that meet the demands of local markets.
4. Breed improvement programs:
a. Selection and breeding: Community members are trained in basic animal selection
techniques, including visual appraisal and phenotypic evaluation. Local animals that exhibit
desirable traits are selected as breeding stock, ensuring the retention of important genetic
diversity.
b. Breeding infrastructure: Community-based breeding systems may establish community
breeding centers or breeding herds where superior males, known as community bulls, are
managed and used for natural service or artificial insemination. These centers provide access
to high-quality genetics and promote controlled breeding.
c. Community-based artificial insemination (AI): Trained community members or para-
veterinarians perform AI services within the community. This approach ensures access to
improved genetics and allows for the rapid dissemination of superior traits.

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5. Capacity building and training: Community members are provided with training
and technical support on livestock management, breeding practices, record-keeping,
and animal health. This empowers them to take an active role in the breeding program
and enhances their knowledge and skills.
6. Monitoring and evaluation: Regular monitoring and evaluation of the breeding
program are conducted to assess the progress and impact on livestock productivity.
This helps identify areas for improvement and guides future decision-making.
7. Collaboration and institutional support: Successful community breeding systems
often involve collaboration with local government agencies, research institutions,
and non-governmental organizations. These partnerships provide technical expertise,
resources, and support to sustain and scale up the breeding programs.
Examples of community breeding systems in Nepal include the "Community-Based
Livestock Breeding Program" implemented by the Department of Livestock Services and
the "Community-Based Dairy Cattle Breeding Program" supported by Heifer International
Nepal. These programs have shown positive results in improving livestock productivity,
increasing income for farmers, and enhancing the overall well-being of rural communities.