Inbreeding and brood stock management

Douglas Tave
Urania Unlimited
Coos Bay, Oregon

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This document has been prepared within the framework of the Regular Programme activities of the Inland Water Resources and Aquaculture Service of the Fishery Resources Division. The primar objective of this document is to outline how inbreeding can be avoided or minimized and thus prevent genetic problems in cultured populations of fish at fish farms and fish culture stations. A secondary objective is to outline how inbreeding can be used to improve cultured populations of food fish. This document is directed to extension personnel, aquaculturists, and those who plan natural resource management programmes.

The original manuscript was prepared by Douglas Tave of Urania Unlimited, Coos Bay, Oregon, USA. It was reviewed by Gray Thorgaard, Daryl Kuhlers, Devin M. Bartley, and Katherine Bruner Tave. The figures were prepared by Sally Rader under the supervision of Douglas Tave.

Tave, D.
Inbreeding and brood stock management.
Fisheries Technical Paper. No. 392. Rome, FAO. 1999. 122p.


This manual, written for extension workers, aquaculturists, and those who work with natural resource management programmes, primarily deals with the problems caused by unwanted inbreeding in cultured fish populations and describes management techniques that can be used to prevent or minimize inbreeding. The manual also describes how inbreeding can be used to improve captive populations of fish. The manual contains chapters on: basic genetics and the genetics of inbreeding; how to determine individual inbreeding values when pedigrees are known; how to determine the average inbreeding value in a population when pedigrees are not known; genetic drift, which is random changes in gene frequency; how inbreeding programmes can be used to improve cultured populations of food fish; how to prevent inbreeding depression and loss of genetic variance in farmed populations; and recommendations on how to manage cultured populations of fish to prevent unwanted inbreeding and genetic drift from depressing productivity, profits, and survival. One of the most important aspects of managing a closed population of fish at a fish farm or fish culture station is the management of the population's effective breeding number, because inbreeding is inversely related to the effective breeding number. Techniques to determine and manage the effective breeding number are described, and recommended minimum effective breeding numbers are provided for a variety of farm sizes and fish culture goals. A number of culture techniques can affect inbreeding, and ways to modify them so there is minimal impact on inbreeding are discussed. Finally, ways to minimize inbreeding during selective breeding programmes are described.


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I first became interested in the problems of inbreeding (the mating of relatives) in hatchery populations when I was at Auburn University working on my dissertation: a study on heritability for growth in Nile tilapia. The results were disappointing because the heritabilities were small, so I studied the population's history to see if I could explain why the heritabilities were smaller than expected. What I found surprised me. The population had been transferred across three continents, and each time the size of the population had been severely reduced. I surmised that these reductions in population size produced inbreeding and genetic drift (random changes in gene frequency, resulting in the loss of genetic variance), and that this combination ruined the population genetically. Subsequent studies by other students found that the population could not be improved by selection and that there was no heterozygosity at loci that were examined electrophoretically, which confirmed my conclusion the population's gene pool had been severely damaged by improper brood stock management.

At the same time, I discovered “saddleback,” a bizarre deformity in the Auburn population of blue tilapia; I also saw orders for foundation brood stock that were being filled by collecting and shipping offspring produced by a single mating. This led me to the conclusion that inbreeding and genetic drift caused by small hatchery populations could explain a variety of problems.

Ironically, even though the Auburn University population of blue tilapia is highly inbred because it was founded by a single female and three males, the saddleback phenotype had nothing to do with inbreeding. But research on this phenotype and others has led me on a quixotic 19-year adventure to discover effective ways to explain inbreeding and genetic drift to farmers, hatchery managers, and fisheries administrators and to try and show them how to manage hatchery populations so that inbreeding and genetic drift do not cause inbreeding depression or rob their populations of valuable alleles and genetic variance. This manual is the culmination of those efforts.

This manual is a full-sib companion to Selective Breeding Programmes for Medium-sized Fish Farms (FAO Fisheries Technical Paper 352). As was the case in that manual, this one arbitrarily defines medium-sized farms as those with 2 ha of ponds; small and large farms are obviously those on the lesser and greater side of 2 ha. Additionally, a fourth category was created for this manual: public hatcheries that produce fish for stocking lakes and rivers.

The goal of this manual is two-fold: The first part is to provide easy-to-understand and easy-to-follow recommendations about how to avoid the accumulation of inbreeding and genetic drift so these twin problems do not reduce growth rate, viability, fecundity, etc. This manual was written to educate extension agents and university-trained aquaculturists so that they would be able to understand what inbreeding and genetic drift are and to illustrate how uncontrolled accumulations of both can decrease growth rate, fecundity, viability, and survival; increase the percentage of deformed fish; and make future selective breeding programmes ineffective.

Often, what is considered to be “normal” hatchery management is, in reality, the type of brood stock mismanagement that causes inbreeding and genetic drift to accumulate to levels that cause problems. The biggest culprit is the genetic size of the breeding population, a concept called the “effective breeding number.” When no selection is occurring, managing a population's effective breeding number is the most important aspect of brood stock management, because it is inversely related to both inbreeding and genetic drift. Techniques that can be used to manage a population's effective breeding number are described, along with recommended minimum effective breeding numbers that can easily be incorporated into yearly work plans.

Unfortunately, there is an appalling lack of information about how specific levels of inbreeding affect growth, viability, disease resistance, fecundity, survival, and other production phenotypes for important cultured species of fish. What information does exist has been generated by a handful of studies that, for the most, part simply skip across the surface of the sea of knowledge. The prime reason for this lack of information is short-sighted bureaucrats and administrators who are unwilling to fund long-term studies that will generate the kind of data that are readily available to other animal breeders. This is somewhat understandable, because short-term projects that provide immediate benefits are needed. However, breeding programmes are long-term investments, and they should be funded before they are necessary, so that information will be waiting and available when it will be needed in the future.

The second part of the goal of this manual is to illustrate how inbreeding can be used to improve a population. Inbreeding is a powerful breeding tool that has been used to improve livestock and grains, but most fish farmers and hatchery managers do not know how it can be used; they only want to avoid it. Although most fish farmers and hatchery managers will probably never use inbreeding in their breeding programmes, if they know how it can be used, they will have a better appreciation of how it can be prevented or controlled.

This manual is not a genetics textbook; it is written for aquaculturists who do not have a good background in genetics but who are interested in applying genetics and breeding principles to brood stock management. It is written in a simple, straightforward manner. I have tried to use as little jargon as possible, but when it was unavoidable, I defined each term when it was first used. In addition, there is a glossary that defines many of the terms.

Many of the ideas and recommendations in this manual have to be developed mathematically. In all cases, the math that was used is simple elementary-school arithmetic. No calculus was used. All math can be solved with pencil and paper or can be done with inexpensive hand-held calculators; every example in this manual and the values that appear in every table were derived using a $12 hand-held calculator. It is not necessary to do the math or to understand it in order to understand how inbreeding works and to comprehend how it can be avoided. The math was provided for those who wanted to see how the recommendations were determined and to enable others to create their own recommendations, since they are site-specific and are based on species, hatchery size, budget, goals, manpower, etc.

The manual was written so that each chapter is self-contained. Those who already know a subject or those who are not interested in a particular topic can read only those chapters that interest them.

Chapter 1 is an introduction that explains what the manual is about and gives a brief explanation of what inbreeding is, in relation to other breeding programmes.

Chapter 2 is a totally abridged discussion about selected concepts in genetics. The only topics that are covered are those needed to help explain what inbreeding is and to show how it works.

Chapter 3 explains how individual inbreeding values are calculated. Individual inbreeding values can be determined if fish can be marked and if family pedigrees can be determined. Two methods are discussed: path analysis and covariance analysis.

Chapter 4 explains how the average inbreeding value in a population is determined. This approach must be used when individuals cannot be identified. This chapter introduces the concept of effective breeding number. When managing a hatchery population, managing its effective breeding number may be the most important aspect of brood stock management, because inbreeding is inversely related to effective breeding number.

Chapter 5 is a brief explanation of genetic drift. Like inbreeding, it too is inversely related to effective breeding number. Genetic drift is random changes in gene frequency due to sampling error. In aquaculture, this is caused by the transfer of fish from one hatchery to another; choice of which brood fish will be allowed to spawn; or sudden decreases in population size because of disease, dissolved oxygen depletion, etc.

The major thrust of this manual is to discuss inbreeding, explain what it can do to a population when it inadvertently reaches high levels, and to prescribe palatable management plans that can be used to prevent inbreeding depression (decreased growth rate, etc.). Consequently, some may feel that genetic drift is simply a sideline topic and not understand why it needs to be included. Its inclusion is necessary because inbreeding and genetic drift are inextricably linked by effective breeding number. Additionally, if you manage only to prevent unwanted inbreeding, unwanted genetic drift can cause similar problems. Consequently, a prudent farmer or hatchery manager will try and manage both, especially since managing both requires little extra effort.

Chapter 6 explains how inbreeding can be used to improve a population. Inbreeding is one of the three major types of breeding programmes. Although it is not as appreciated as selection and crossbreeding, it has been used to produce outstanding animals and plants, and the crops and livestock it produces help feed a hungry world. Inbreeding is extremely important in breed or strain development. Inbreeding can be used to improve response to selection when heritability is small. And inbreeding is the classic way to improve the results of crossbreeding programmes. Consequently, any farmer or hatchery manager who wants to manage the genetics of his population should know how inbreeding works and what it can do. In order to use inbreeding to improve a population, a farmer or hatchery manager must know how to design and maintain regular systems of inbreeding. Several regular systems of inbreeding are illustrated, along with the levels of inbreeding that they produce.

Chapters 7 and 8 are the heart and soul of the manual and are the chapters that will interest most farmers and hatchery managers. Chapter 7 discusses ways to prevent inbreeding in hatchery populations and shows the methods that can be used to determine the effective breeding numbers that are needed to prevent inbreeding from accumulating to levels that cause inbreeding depression and that will prevent genetic drift from robbing the population of needed genetic variance.

The single most important aspect of brood stock management under these circumstances is to prevent bottlenecks. A bottleneck is a drastic reduction in effective breeding number. A single bottleneck can cause permanent genetic damage to the population by producing high levels of inbreeding and by producing high levels of genetic drift. A single bottleneck can ruin years of excellent brood stock management.

In addition, several spawning and breeding techniques that can be used to increase effective breeding number are presented.

Chapter 8 presents a series of recommendations that farmers and hatchery managers can use to prevent inbreeding depression and the loss of genetic variance via genetic drift. This is a key aspect of brood stock management when no selective breeding programme will be used to improve growth rate or other phenotypes. For most farmers and hatchery managers this means managing effective breeding number at a pre-determined size. Recommended effective breeding numbers are made for small, medium, and large farms and for public hatcheries. Several recommendations are made for all four situations, based on a farmer's or hatchery manager's goals, the type of fish culture that is being done, and the level of genetic risk that is acceptable. The process by which a farmer or hatchery manager can determine the effective breeding number that he needs for a customized set of goals is also presented.

Recommendations are also made about mating protocols that can be used to minimize inbreeding during a selective breeding programme. Inbreeding is inevitable when a farmer conducts a selective breeding programme. Selection produces inbreeding because each act of selection creates a bottleneck; additionally, when only the best are allowed to mate, the mating of relatives is inevitable. Inbreeding is of secondary importance during a selective breeding programme, because the major genetic goal is to alter the genetics of the population in order to improve productivity. However, inbreeding needs to be monitored and it should be minimized, or selection will be used only to counteract inbreeding depression.

Genetic drift will also occur during a selective breeding programme. In fact, genetic drift can accumulate at a faster rate during a selective breeding programme because each act of selection creates a bottleneck and the number of families is often reduced. The major effect of genetic drift under these circumstances will be on genes that are not affected by the selective breeding programme. Genetic drift will minimally effect the genes which control phenotypes that are undergoing selection or that are undergoing indirect selection. The problems caused by genetic drift can generally be ignored during a selective breeding programme, because selection and conservation of genetic variance are diametrically opposed breeding programmes.

I did not include any citations in the text or tables. This was not done to slight the contributions by others; it was done to make the manual uncluttered and more readable. I have included a list of recommended reading at the end of the manual for those who wish to pursue one of the topics discussed in this manual in greater detail.

I thank Gary Thorgaard, Daryl Kuhlers, and Katherine Bruner Tave for critical review of the manuscript. Once again, Sally Rader has turned my preliminary sketches into works of art. I would also like to thank Devin Bartley for giving me the opportunity to synthesize my thoughts in this area.

This book is for Katherine and Kai, the Sancho and Panza of my life, who never fail to put me back on my Rozinante when the windmills get too fierce.

Douglas Tave
July, 1998

Food and Agriculture Organization of the United Nations
Rome, 1999 © FAO

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Chapter 1: Introduction

Chapter 2: Genetics

Genes and chromosomes
Phenotype and genotype
Genetics of qualitative phenotypes
Genetics of quantitative phenotypes

Uses of inbreeding
Inbreeding depression

Inbreeding studies in fish

Chapter 3: Calculating individual inbreeding values

Creating a pedigree
Path analysis
Covariance analysis

Chapter 4: Calculating average inbreeding values in hatchery population

Effective breeding number (Ne)

Chapter 5: Genetic drift

Effective breeding number and genetic drift

Chapter 6: Using inbreeding to improve growth and other phenotypes

Inbreeding programmes

Creation of new breeds
Use of a herd bull
Inbreeding to expose and cull detrimental recessive alleles
Inbreeding to improve the results of between-family selection
Creation of inbred lines for crossbreeding programmes

Inbreeding produced when relatives mate
Regular systems of inbreeding

Parent-offspring inbreeding programme
Full-sib inbreeding programme
Half-sib inbreeding programme
Double first cousin inbreeding programme

Chromosomal manipulation

Mitotic gynogenesis
Mitotic androgenesis
Meiotic gynogenesis


Chapter 7: Preventing inbreeding depression and loss of genetic variance in hatchery populations

Preventing inbreeding depression

If fish are marked
If fish are not marked

Preventing genetic drift
Techniques that can be used to manage effective breeding number

Stretching generations
Pedigreed mating
Altering spawning techniques

Increasing the spawning population
Spawn a more equal sex ratio
Fertilization techniques


Chapter 8: Recommendations

Acquisition of a population
When no selective breeding programme will be conducted

Small farms
Medium-sized farms
Large farms
Public hatcheries
Customizing recommendations

When selective breeding programmes will be conducted

Individual selection
Family selection



Recommended reading