Module GENE-422-522-11

Topic 01: Introduction to Animal Breeding Programs

On completion of this topic you should be able to:

• Understand the different aspects involved in animal breeding programs;
• Analyse animal breeding programs as a logical order of decisions to be made; and
• Put the different aspects of animal breeding in the right context, and understand the knowledge needed about making certain investments.

This introductory topic aims to show that all animal breeding activity forms a framework of logically ordered decisions. Understanding this framework will help you fit together the material in the rest of the unit. It is important to realise that this framework is applicable at all levels: individual farm, breed, industry, and nation, and that it forms a sensible basis for approaching research and extension/advisory activity.

Topic 02: Principles of Estimation of Breeding Values

On completion of this topic you should be able to:

• Understand the principle of estimation of breeding value (EBV);
• Understand accuracy of EBV • Predict how much EBVs vary among individuals;
• Predict how much EBV might change with new information; and
• Predict response to selection based on EBV.

In this topic we will discuss the principle of estimation of breeding value. First we present how phenotypic information is turned into an EBV. The heritability of the trait is important here. Second, we discuss the accuracy of EBV, how it is calculated, and why it is important. Basically, the higher the accuracy, the higher the response to selection based on EBV. Closely related to accuracy are the variance of the EBV and the Prediction Error Variance of EBV. The variance of the EBV indicates how much difference in EBV values we can expect. This is relevant if we want to predict the EBV of a selected group of individuals.

Topic 03: Selection Index Theory: Relatives

On completion of this topic you should be able to:

• Assess the value of relative’s information in EBV accuracy;
• Derive the weights on relative’s information in estimating breeding value;
• Understand the value of progeny testing; and
• Know the relationship between progeny test size and accuracy of sire’s EBV.

This topic will present selection index theory, particularly when applied to combining information from one trait only.

Topic 04: The Use of Linear Models

The purpose of this topic is to familiarise you with linear models. Based on a simple example, we will present a linear model as the statistical method to estimate fixed effects. Understanding such examples is important for understanding how BLUP corrects for fixed effects in genetic evaluation procedures.

On completion of this topic you should be able to:

• Understand the power of linear models;
• Set up a simple example of linear models; and
• Understand how BLUP can correct for fixed effects.

Topic 05

Part 1: Best Linear Unbiased Prediction

On completion of Part 1 you should be able to:

• Understand the principle of mixed models;
• Understand how in BLUP, different effects can be taken into account;
• Understand how BLUP uses additive genetic relationships; and
• Know that BLUP uses optimal selection index weights for the different sources of information to estimate the breeding value of an animal.

Part 2: Properties of BLUP

In this second part , we present a mixed model, where random and fixed effects are jointly fitted and estimated. The solutions of the mixed model are BLUP EBV for individual animals, and an example will demonstrate that these solutions make sense based on what we have learned so far.

On completion of Part 2 you should be able to:

• Understand how BLUP accounts for selection of parents and non-random mating;
• Understand how BLUP can estimate genetic trends;
• Calculate accuracy from mixed model equations;
• Understand accuracy from BLUP-EBV, in particular in relation to the contemporary group size and the ‘effective information’ about each animal; and
• Understand the effects of BLUP selection on genetic progress and inbreeding.

Part 3: Evaluation of Animals in Practice

On completion of Part 3 you should be able to:

• Understand the level of complexity of commercial genetic evaluation programs;
• Understand the requirements about data quality and the quality of the models used for genetic evaluation;
• Know about the different extensions that are possible based on the animal model;
• Understand across breed evaluation; and
• Be aware of computational methods used to solve large scale genetic evaluation systems.

Topic 06: Multiple Trait Genetic Evaluation

This topic will present the main advantages of multiple trait genetic evaluation as well as details of multiple trait mixed model equations. Knowledge of the mechanics of such equations is important for developing an understanding of the practical implementation of multiple trait genetic evaluation. The importance of having the correct genetic parameters is also discussed.

On completion of this topic you should be able to:

• Understand the benefits of multiple trait genetic evaluation and when it is mostly advantageous;
• Understand how multiple trait mixed models are set up and have an idea about computational aspects; and
• Understand the importance of correct genetic parameters.

Topic 07: Estimation of Genetic Parameters

On completion of this topic you should:

• Understand the importance of estimation of genetic parameters in animal breeding;
• Know when estimation of genetic parameters may be required;
• Understand the principles of estimation of variance components;
• Estimate heritability from sib analysis;
• Estimate heritability from parent-offspring regression; and
• Have an understanding of the different methods that can be used to estimate genetic parameters.

Topic 08: Molecular Markers

This topic introduces molecular markers, focusing on the common types of markers used in animal genetics and their properties relevant to QTL mapping.

On completion of this topic you should have an understanding:

• that molecular markers detect variations at the DNA level;
• of the three main types of molecular markers: RFLPs, microsatellites and SNPs;
• of molecular biology procedures used for typing molecular markers; and
• of the statistical considerations of marker choice for QTL mapping.

Topic 09: Genetic and Physical Maps

Genetic and physical maps are used in QTL mapping and gene discovery experiments. These maps show the location of genetic markers, genes, and other features (such as repeat sequences) on the genome. This topic overviews the features of these maps and how they are constructed.

By the end of this topic, you should have:

• an understanding of the terms genetic and physical maps, and the units used to measure distances on these maps;
• the ability to construct a simple genetic map from three-point testcross data;
• the ability to relate observed recombination frequencies to map distances through mapping functions;
• an understanding of the concept that multi-locus linkage maps from complex pedigree can be constructed by the maximum likelihood approach;
• an understanding of the different types of physical maps and how they are constructed;
• conceptualised how genetic and physical maps can be linked together; and
• an overview of the current genome sequencing status for a number of livestock species.

Topic 10: Detection of QTL

On completion of this topic you should be able to:

• Understand how markers can be used to trace the probability of inheritance of a genomic region from one generation to the next;
• Understand how tracing a genomic region can lead to a test of whether that region influences a trait of interest;
• Understand the different information available from interval mapping compared to single marker mapping;
• Understand the effects of multiple QTL in QTL detection; and
• Understand the issues of multiple testing in QTL detection.

Topic 11: Marker Assisted and Genomic Selection

On completion of this topic you should be able to:

• Understand how markers can be used to gain information on QTL genotype of individuals;
• Understand how a gene can be introgressed from a donor to recipient population using markers;
• Understand Genomic Selection;
• Understand how MAS can be applied in different situations; and
• Understand how EBV can be calculated with the knowledge of QTL .

Topic 12: Gene Discovery

Gene discovery refers to the identification of gene(s) controlling a trait of interest, and the associated mutation(s) responsible for the altered phenotype.

By the end of this topic, you should have an understanding of:

• the basic steps to gene discovery for a quantitative trait;
• the limitations of linkage and linkage disequilibrium analysis in relation to refining a QTL position;
• the term ‘positional candidate gene’, and how these genes can be identified; and
• how the identification of functional mutations can be used to prove the candidate gene is actually the gene of interest.

Topic 13: Breeding Objectives

Breeding objectives provide the foundations for a successful breeding program by creating direction and focus for the breeder. This topic will give you a detailed understanding of breeding objectives and why they are important in animal breeding programs. The economic issues associated with breeding objectives will be covered which is particularly important where multiple traits are concerned. Some methods of developing a breeding objective will be illustrated in this topic along with some discussion of the complications that may occur when using these methods.

On completion of this topic you should be able to answer the following questions:

• What is a breeding objective?
• Why is it important to define the breeding objective?
• How is the breeding objective used for selection of animals?

Topic 14: Multiple Trait Selection

Improvement in the efficiency and quality of animal production can be achieved by improving several characteristics simultaneously.

On completion of this topic you should know:

• How to derive selection criteria for multiple traits;
• How to predict multiple trait selection response;
• How to manipulate multiple trait selection response; and
• Considerations in order to make optimal genetic change.

Topic 15: Breeding Program Design Principles

Animal breeders aim to bring about genetic change in their livestock, with a view to increasing profitability, ease of management and sustainability.

On completion of this topic you should be able to:

• Understand the issues involved in breeding program design
• Predict rates of genetic improvement for breeding programs
• Design and compare alternative breeding programs

Topic 16: Designs to Exploit Reproductive Technology

Reproductive technologies such as AI and MOET can be used to greatly increase fecundity. This increases selection intensity and, in turn, genetic gains

On completion of this topic you should:

• Have an understanding of the different reproductive technologies available to animal breeders; and
• Have an understanding of how each technology can affect genetic progress.

Topic 17: Balancing Selection and Inbreeding

This topic is in fact a pre-cursor to Topic 19 “Mate Selection for the tactical implementation of breeding programs”. In this topic we deal with the animal breeding issues of selection and inbreeding whilst Topic 18 covers selection and crossbreeding. Topic 15 introduced all the key issues in animal breeding, including technical issues, logistical issues and cost issues.

On completion of this topic you should:

• Understand the issues that affect which is the best crossing system to adopt
• Have a good feel for what makes dominance good and epistasis bad in crossing systems

Topic 18: Breed Utilisation and Crossbreeding

Selection and crossbreeding are two key tools for animal breeders. This topic gives sufficient theoretical background on crossbreeding to show how we can exploit it. It also introduces us to integrating crossbreeding with other issues in animal breeding.

On completion of this topic you should:

• Understand the issues that affect which is the best crossing system to adopt; and
• Have a good feel for what makes dominance good and epistasis bad in crossing systems.

Topic 19: Mate Selection for the tactical implementation of breeding programs

Breeding program design can be pre-determined and implemented through sets of rules, or it can emerge as a consequence of decisions made at the level of individual matings. This latter approach is the tactical approach, with decisions made tactically in the face of prevailing animals and other resources.

Tactical implementation of breeding programs provides a practical means to integrate technical, logistical and cost issues facing animal breeders. Moreover, tactical implementation benefits from opportunistically optimal use of prevailing animals and other resources, resulting in better outcomes.

On completion of this topic you should be able to understand:

• That specifying matings to be made covers a very wide range of animal breeding issues – technical, economic and logistical issues; and
• We now have evolutionary algorithms that can find the best mating set, or something close to best.

Topic 20: Breeding Practices in the Merino Industry

In this topic we explore genetic improvement programs in the Merino industry. We start by looking at breeding trends in the commercial production sector, which are strongly related to market signals for the two main sheep products, wool and meat. We also briefly touch on the structure of the ram breeding sector which is the driver of genetic change for the industry.

On completion of this topic you should understand:

• The structure of the commercial and ram breeding sectors of the industry;
• The traits which influence production and how to include them in a breeding objective; and
• Merino genetic evaluation and breeding systems.

Topic 21: Breeding Practices in the Lamb Industry

In this topic we explore genetic improvement programs in the Lamb industry. The history of this industry in Australia is interesting. While the Merino industry in Australia fared well and was wealthy a few decades ago, the lamb production was more or less seen as a poor cousin. This disadvantage was turned into an advantage in the early 1990s when an across flock genetic evaluation system was initiated by Meat and Livestock Australia: LAMBPLAN. Since then, the genetic trends achieved by Terminal Sire breeds have been significant and this has impacted on phenotypic progress and market share.

At the end of this topic you should:

• The structure of the commercial and ram breeding sectors of the industry
• The traits which influence production and how to include them in a breeding objective
• Understand and describe the way in which Sheep Genetics has improved sheepmeat production
• Understand the relevance of genetic correlation to ASBV
• Be able to separate environmental from genetic effects
• Understand the measures of accuracy for ASBV and FBUS

Topic 22: Practical Breeding Program Issues – Beef Industry

The beef industry is a vital component of Australian agriculture, valued at approximately $4.3 billion, with over 2 million tonnes of product produced in 2002. The profitability of beef enterprises is strongly influenced by genetic improvement but there are many practical breeding program issues that beef producers need to address in order to ensure such improvement.

On completion of this topic you should be able to:

• Demonstrate understanding of the structure of the beef industry, and its impact on genetic improvement;
• Demonstrate understanding of the three primary components of genetic improvement (breeding objectives, genetic evaluation and breeding program design);
• Discuss relevant issues associated with these key components in the beef industry;
• Appreciate and discuss the tools available for genetic improvement in the beef industry, and have used their web applications.
• Discuss uptake of genetic technology in the beef industry; and
• Discuss future developments in genetic improvement in the beef industry.

Topic 23: Summary

To actually achieve results in genetic improvement is challenging, especially in low input systems, where there are relatively many independent decision makers. However, whether a multi-player Merino sheep program or a pig breeding program of a multinational company, a lot of the same principles apply and systematic analysis and application of good breeding practice is achievable. This last topic tries to summarise the main aspects of genetic improvement programs and put them in perspective, such that decision making in breeding programs can be rationalised and put in the appropriate context.

On completion of this topic you should:

• Be able to put together the different topics from this unit in a unifying framework;
• Understand the place of each topic of this unit in the context of an animal breeding program;
• Be able to analyse an animal breeding problem in a breeding program context, and to know the tools available to help implementing such programs: and
• Understand new developments and evaluate them in the right context.

Appendix: An Introduction to Matrix Algebra and Linear Models

Matrices take a lot of the tedium out of both presenting algebra and calculating results. They are widely used in scientific animal breeding, particularly in selection indices and BLUP. This topic provides a basic introduction to matrices.