Enhancing Gain from Long-Term Forest Tree Breeding while Conserving Genetic Diversity

ACTA UNIVERSITATIS AGRICULTURAE SUECIAE SILVESTRIA 109 Enhancing Gain from Long-Term Forest Tree Breeding while Conserving Genetic Diversity Ola Rosvall Department of Forest Genetics and Plant Physiology UMEÅ SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES Enhancing Gain from Long-Term Forest Tree Breeding while Conserving Genetic Diversity Ola Rosvall Department of Forest Genetics and Plant Physiology UMEÅ Doctoral Thesis Swedish University of Agricultural Sciences Umeå 1999 ACTA UNIVERSITATIS AGRICULTURAE SUECIAE Silvestria 109 ISSN 1401-6230 ISBN 91-576-5643-6  1999 Ola Rosvall, Sävar Printed by: SLU, Grafiska enheten, Umeå, Sweden, 1999 ABSTRACT Rosvall, O 1999 Enhancing gain from long-term forest tree breeding while conserving genetic diversity Doctor’s dissertation ISSN 1401-6230, ISBN 91-576-5643-6 Long-term genetic diversity in a breeding population (BP), and gain in production populations (PP) arising from it, were analysed by stochastic computer simulation for different management strategies (population size and structure, selection and mating) and genetic parameters (variance components and inbreeding depression) The simulations were based on the infinitesimal genetic model and comparisons made over a range of gene diversity The Swedish Norway spruce improvement program, featuring the use of clonal testing, was used as a baseline It is suggested that the merit of a tree breeding strategy should be evaluated primarily on the basis of the BP’s long-term capacity to supply improved material to PPs Under this objective, it is more important to conserve gene diversity in the BP, than when the objective is to improve the breeding value of the BP itself The level of acceptable inbreeding is dependent on test methodology and the type of PP to be supported When the effects of increased selection accuracy by clonal testing, positive assortative mating and inbreeding depression on PP net gain are considered together, balanced within-family selection appears favourable First, clonal testing considerably improves the response from within-family selection, while decreasing family variance under more aggressive index-selection scenarios Second, under within-family selection, the greatest family variance is maintained and the greatest enhancement of family variance is reached by positive assortative mating, maximising additional gain from intensively selected PPs at maximum BP gene diversity Third, if inbreeding depression is considered, the net gain under within-family selection becomes even more equal to net gain under more aggressive selection strategies, since the lowest relatedness is also maintained Inbreeding depression is counteracted by mating designs with two crosses per parent instead of only one Fourth, the efficiency of clonal testing is greatest under low inbreeding depression Consequently, short-term genetic gain in PPs is enhanced by methods that also conserve the greatest gene diversity for long-term breeding Under these conditions, the exploitation of the small additional gain available from among-family selection in the BP, involves a large loss of gene diversity per unit increase in net gain The optimal imbalance in parent contributions depends on the type of PP, but it usually seems worthwhile only to increase contributions from a small number of the very best parents In general, imbalance is best achieved by a restricted increase in contributions per parent, giving a structure similar to an open nucleus BP Key words: artificial selection, breeding population, breeding strategy, effective population size, gene diversity, genetic gain, genetic variance, inbreeding, inbreeding depression, status number, group coancestry, group-merit selection Author’s address: Ola Rosvall, The Forestry Research Institute of Sweden, SkogForsk, SE-918 21 Sävar, Sweden CONTENTS Abstract _ ContentS _ Appendix List of publications included Introduction Tree breeding strategies _7 Problems addressed Objectives _10 theoretical context 10 The model system 10 Genetic diversity 11 Genetic response and gain 17 Selection for both genetic improvement and diversity 22 Methods 23 Baseline breeding strategy 23 Alternative breeding strategies _23 Summary of the publications included _ 25 discussion 29 High net gain at high genetic diversity _29 Compromising genetic diversity for increased gain _38 Consequences for the breeding strategy 40 Measuring loss of genetic diversity _42 The genetic model and assumptions _46 Conclusions _ 48 Practical implications 48 Future research _49 Literature CITED 50 Acknowledgements _66 APPENDIX In the thesis, publications are referred to by their roman numerals LIST OF PUBLICATIONS INCLUDED I ROSVALL, O., LINDGREN, D and MULLIN, T.J 1999 Sustainability robustness and efficiency of a multi-generation breeding strategy based on within-family clonal selection Silvae Genetica: 47(5−6), 307−321 II ROSVALL, O., and ANDERSSON, E.W 1999 Group-merit selection compared to conventional restricted selection for trade-offs between genetic gain and diversity Forest Genetics 6(1):11−24 III ROSVALL, O., and MULLIN, T.J 1999 Positive assortative mating with selection restrictions on group coancestry enhances gain while conserving genetic diversity in long-term forest tree breeding Manuscript IV R OSVALL, O., MULLIN, T.J., and LINDGREN, D 1999 Controlling parent contributions during positive assortative mating and selection increases gain in long-term forest tree breeding Manuscript All publications are reproduced with the publisher’s permission INTRODUCTION Tree breeding strategies The design of an optimal breeding programme with selection over several generations must reconcile the trade-off between gains achieved in the short term and those subsequently possible in the longer term The conflict between short- and long-term gains occurs because genetic improvement is accompanied by a loss of genetic diversity (Robertson 1961; Dempfle 1975) and therefore less genetic variability is available for future improvement A variety of breeding strategies and techniques addressing both genetic improvement and conservation are available for advanced-generation breeding (as reviewed by White 1993; Williams and Hamrick 1996; see also Burdon and Shelbourne 1971; Lindgren and Gregorius 1976; Burdon 1986; Kang and Nienstaedt 1987; Kang 1991), and described for a number of applied long-term tree breeding programmes, e.g., Chamaecyparis nootkatensis (Russell 1993); Larix decidua, L leptolepis (Li and Wyckoff, 1994); Picea glauca (Beaulieu 1996); Picea mariana (Park et al 1993); Picea sitchensis (Fletcher 1992); Pinus banksiana (Joyce and Nitschke 1993; Klein 1998); Pinus elliottii (White et al 1993); Pinus radiata (Cotterill 1984; Shelbourne et al 1986); Pinus taeda (McKeand and Bridgewater 1998); Pseudotsuga menziesii (Woods 1993); and in Sweden for Pinus sylvestris, Pinus contorta, Picea abies, and Betula pendula (Danell 1991a, 1993a) Recent advances in long-term forest breeding strategies involve comparisons and optimisation with help from advanced analytical models and computer simulation (e.g., Mahalovich 1990; King and Johnson 1993; Bridgewater et al 1992; Kerr et al 1998; Gea et al 1997; McKeand and Bridgewater 1998; Borralho and Dutkowski 1998; Wei et al 1998) Continuous development in biotechnology provides tree breeders with new means to domesticate, modify, propagate and conserve trees, offering new promises for resource management, but also potential threats to genetic diversity (van Buijtenen and Lowe 1989; Bonga et al 1997; Mullin and Bertrand 1998; Park et al 1998a, b) Part of the solution to the built-in conflict in tree breeding is met by a structuring of the breeding population (BP), both physically and conceptually (Gullberg and Kang 1985) A hierarchical structure and sublining of the BP will keep selection intensity high, control loss of diversity, and reduce inbreeding in production populations (PP) (Burdon et al 1977; Danell 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they did my ordinary work in addition to their own Laila Andersson, Jörgen Hajek, Birger Eriksson, Bengt Andersson and Tore Ericsson must be mentioned for support, but all the staff contributed to create my opportunity This project was not free of cost I first acknowledge, with great appreciation, a personal grant from the Jacob Wallenberg Foundation The project was also supported by the Swedish Institute, Carl Tryggers Stiftelse För Vetenskaplig Forskning and Föreningen Skogsträdsförädling It also involved co-operation with EU project FAIR5 PL97 3823 "Wood quality in Birch" concerning breeding strategies using clonal multiplication for testing I have had a great support in my circle of acquaintances, family, parents, relatives, and friends Ragnar Burman came to my rescue many times when constructing a new house (my second project that I hope Dag will forgive) Berndt and Emmy Johansson provided the infrastructure for my laptop when finding peace and quiet at the oldfashioned family cottage, on our island paradise, where the most productive weeks took place But most of my friends have experienced a never-present person Probably my children have taken advantage of my becoming so absorbed; hopefully, they are sufficiently mature not to have been seriously hurt The inexhaustible patience of my wife, Gunnel, is admirable I thank you all! Genetic improvement Clone mix Seed orchard Breeding popolation Genetic diversity Breeding cycle Figure The tree improvement model system Additive and dominance mean and variance are managed within the breeding population to support high net gain in future seed orchard and clone mix production populations Simulation Deterministic simulations are based on algebraic equations that predict the likely outcome of sampling, while stochastic (Monte Carlo) simulation models mimic random processes Stochastic simulation is particularly suitable for genetic systems, as meiosis and genetic recombination are random processes Although well developed and rapid, deterministic prediction and simulation cannot deal with the same level of complexity over many generations as can stochastic simulation (Lacy, 1987; Mullin and Park 1995) Stochastic simulation is commonly used to verify accuracy when prediction equations are developed (e.g., Verrier et al 1990; Shepherd and Kinghorne 1994) Monte Carlo simulation can easily handle cumulative changes in variances and mean values, and can cope with departures from normality Sampling distributions for the outcome make it possible to perform statistical comparisons to study robustness This type of simulation model can also easily accommodate any management practice, which may not be readily accomplished by mathematical analysis Stochastic genetic models may mimic events at individual loci, so-called finite loci or allelic models, or may be parameter based, describing average genetic effects according to quantitative genetics theory The choice between using allelic- or parameter-based models depends on assumptions regarding the nature of gene action and on the objective of the study (e.g., Jorjani et al 1997a) Whatever the choice, models are necessarily simplifications of a real system Simulation has long been used in theoretical Enhancing Gain from Long-Term Forest Tree Breeding while Conserving Genetic Diversity Ola Rosvall Akademisk avhandling som för vinnande av skoglig doktorsexamen kommer att offentligen försvaras i hörsal Björken, SLU, Umeå, fredagen den september 1999, kl 13 00 Abstract Long-term genetic diversity in a breeding population (BP), and gain in production populations (PP) arising from it, were analysed by stochastic computer simulation for different management strategies (population size and structure, selection and mating) and genetic parameters (variance components and inbreeding depression) The simulations were based on the infinitesimal genetic model and comparisons made over a range of gene diversity The Swedish Norway spruce improvement program, featuring the use of clonal testing, was used as a baseline It is suggested that the merit of a tree breeding strategy should be evaluated primarily on the basis of the BP’s long-term capacity to supply improved material to PPs Under this objective, it is more important to conserve gene diversity in the BP, than when the objective is to improve the breeding value of the BP itself The level of acceptable inbreeding is dependent on test methodology and the type of PP to be supported When the effects of increased selection accuracy by clonal testing, positive assortative mating and inbreeding depression on PP net gain are considered together, balanced within-family selection appears favourable First, clonal testing considerably improves the response from within-family selection, while decreasing family variance under more aggressive indexselection scenarios Second, under within-family selection, the greatest family variance is maintained and the greatest enhancement of family variance is reached by positive assortative mating, maximising additional gain from intensively selected PPs at maximum BP gene diversity Third, if inbreeding depression is considered, the net gain under within-family selection becomes even more equal to net gain under more aggressive selection strategies, since the lowest relatedness is also maintained Inbreeding depression is counteracted by mating designs with two crosses per parent instead of only one Fourth, the efficiency of clonal testing is greatest under low inbreeding depression Consequently, short-term genetic gain in PPs is enhanced by methods that also conserve the greatest gene diversity for long-term breeding Under these conditions, the exploitation of the small additional gain available from amongfamily selection in the BP, involves a large loss of gene diversity per unit increase in net gain The optimal imbalance in parent contributions depends on the type of PP, but it usually seems worthwhile only to increase contributions from a small number of the very best parents In general, imbalance is best achieved by a restricted increase in contributions per parent, giving a structure similar to an open nucleus BP Key words: artificial selection, breeding population, breeding strategy, effective population size, gene diversity, genetic gain, genetic variance, inbreeding, inbreeding depression, status number, group coancestry, group-merit selection Distribution: Swedish University of Agricultural Sciences Department of Forest Genetics and Plant Physiology Umeå 1999 ISSN 1401- 6230 S-901 83 UMEÅ, Sweden ISBN 91-576-5643-6