J. Anim. Breed. Genet. ISSN 0931-2668
INTRODUCTION
Quantitative genetics, spread of genes and genetic improvement: papers in honour of John James
In the almost 60 years since he began to teach himself genetics, John James has come to be regarded by his many collaborators around the world as a valued and respected colleague and friend. The occasion of his 80th birthday in 2015 has provided the international genetics community with an opportunity to assemble this special issue of the Journal of Animal Breeding and Genetics, to shine some light on the breadth and depth of John’s influence and to thank him publicly for his many contributions. John was born in Rockhampton, Queensland. His performance at school was sufficient for the award of a Commonwealth Scholarship that enabled him to enrol in a Bachelor of Arts (BA) degree at the University of Queensland in Brisbane. Graduating with majors in mathematics in 1956, John’s introduction to genetics came when he responded to an advertisement for someone to analyse data from a poultry selection program being run by Glen McBride, then a Lecturer in Animal Genetics and Breeding in the Department of Animal Husbandry within the Faculty of Veterinary Science at the University of Queensland. As recounted by Glen to one of us (FN), John immediately threw himself into learning genetics, devouring every paper and book available. He also threw himself into Glen’s very demanding large-scale non-orthogonal analyses of variance, which had to be conducted on a MADAS calculating machine, for which (in Glen’s words) calculating ‘a single sum of squares could take 15 h of punching numbers into a machine’. When Glen happened to mention the possibility of tracing the genetic contribution of an individual to a population, by calculating the changes in that individual’s proportionate contribution of genes over succeeding generations, John soon realized the potential of this idea. In Glen’s own words, John ‘quickly took the concept far beyond my beginnings’, leading rapidly to the publication in July 1958 of John’s first paper (James & McBride 1958). This is the original spread-of-genes/genetic-contributions paper, which has had such a lasting effect, as summarised in this special issue by Woolliams et al. (2015). Even before the publication of this paper, Glen had decamped to Edinburgh for a quick-fire PhD in animal
© 2015 Blackwell Verlag GmbH
• J. Anim. Breed. Genet. 132 (2015) 85–88
genetics under the supervision of Alan Robertson, leaving John to continue with his analyses of the poultry data and to further develop the spread-ofgenes concept, especially in the context of control populations where changes in gene contributions are due to chance. Importantly, this enabled John to derive the relationship between genetic drift (quantified as effective population size) and variance of the spread of genes (James 1962a). By the time of Glen’s return from Edinburgh in 1960, John had extended his spread-of-genes analyses of the poultry data and was ready to apply it to Glen’s PhD Drosophila data (James 1962b; McBride & James 1965). Glen’s return from Edinburgh coincided with the publication of Douglas Falconer’s revolutionary Introduction to Quantitative Genetics, which fired John’s imagination. By this time, he was already exercising his mathematical skills in papers addressing genetical questions as disparate as selection in two environments (James 1961), the conflict between directional and intermediate-optimum selection (James 1962c), and misconceptions concerning a particular estimator of heritability (James 1962d). Genetics, however, was not the only area of knowledge in which John had become involved. Even before leaving for Edinburgh, Glen had become increasingly interested in behaviour, first in his poultry selection lines, and soon in cattle, pigs and humans as well. After Glen’s return from Edinburgh, John had a central role in the analysis of Glen’s behavioural data, leading to several important ethology papers, including one in Nature (McBride et al. 1963) and a highly influential paper on human behaviour in Journal of Psychology (McBride et al. 1965). These papers signalled Glen’s move to the University’s Department of Psychology, from where he is still publishing (aged 90) as Professor Emeritus of Social Ethology. Thus was Glen lost to genetics. He still, however, takes great pleasure in knowing that his relatively short career as a geneticist has had such a lasting legacy. In 1962, without any formal postgraduate qualification but with a wealth of research experience and some substantial publications, John was appointed
doi:10.1111/jbg.12158
Introduction
lecturer in the School of Wool Technology at the University of New South Wales in Sydney, where he remained as geneticist and statistician (under a series of school/department name changes) until formal retirement 35 years later, in 1997. Throughout this time, he continued to publish papers on a wide range of topics in quantitative genetics. In 1973, his publications earned him a DSc from the University of New South Wales. Inevitably in a School of Wool Technology, John became involved in unresolved questions to do with sheep improvement; questions that were for the most part equally applicable to selection programs in any domesticated species. An important example is his pioneering paper that formalized the concept (and introduced the name) of open-nucleus breeding systems (James 1977). Building on ideas originating with Helen Newton Turner and Neville Jackson, John showed that if a sire-breeding nucleus is opened to the regular introduction of selected females from the base population, the rate of genetic gain can be increased by 10–15% and the rate of inbreeding can be halved. This paper stimulated myriad detailed investigations of the implications of such schemes and led to many practical applications across a range of livestock, especially in the developing world (as highlighted by Mueller et al. (2015)) in this special issue. Another important contribution involved the resolution, with Charlie Smith (Scotland) and Pim Brascamp (The Netherlands), of several anomalies that had arisen in the application of profit equations for deriving economic weights in multitrait selection indexes (Smith et al. 1986). After almost three decades, this publication is still informing calculations of economic weights across the entire spectrum of improvement programs in animals and plants. Other topics for which the careful scrutiny of John and his students/colleagues added greatly to our understanding include determining breeding objectives, designing sire reference schemes, determining optimum sire purchasing strategies and determining the optimum allocation of resources in selection programs. Given all these contributions, it was very fitting, and not at all surprising, that John should have been the first recipient (in 1994) of the Helen Newton Turner Medal, which is awarded ‘from the ranks of those persons who have made an outstanding contribution to genetic improvement of Australian livestock’. The citation for his award states that by 1994 John was ‘regarded as Australia’s leading scientist in quantitative genetics and the theory of genetic improvement’. John is also a highly influential teacher. Many of the undergraduates who learned their genetics and statis86
tics from John have gone on to play important roles in animal (and plant) improvement programs in Australia and elsewhere. In addition, many of his numerous postgraduate students have become leaders in their chosen fields. One of us (CW) counts herself exceedingly fortunate to have had John as her PhD supervisor. Another of us (JS) is one of several European academics who have chosen to come to Australia to spend time working with John. JS considers himself unusually lucky in having received John’s insight into mathematical and statistical methodologies as well as gaining a better understanding of the benefits of working together with people of other countries and continents, getting a broader view: to JS (and the rest of us) John is the master of perspective. Consistent with his realization of the invaluable experience to be gained by working in other countries, John (together with his wife Patricia and daughters) took sabbaticals in Scotland, Norway, France and Germany. The first of these, in Edinburgh in 1970, led to a very fruitful collaboration with the American psychiatrist Ted Reich (described in an obituary (Nurnberger 2004) as being ‘generally regarded as one of the founders of modern psychiatric genetics’). Ted had come to Edinburgh to work on Douglas Falconer’s threshold model of liability to disease. Aided by Chris Morris, who had just started his PhD and just happened to be sharing Ted’s room in the Institute of Animal Genetics, John and Ted developed a twothreshold model of multifactorial liability (Reich et al. 1972), which (as described by Wray & Visscher (2015) in this special issue) has had, and is still having, a profound effect on human genetics. Indeed, this is by far John’s most-cited paper. After returning to the Washington University School of Medicine, St Louis, Ted continued working with John on developing and further expanding the threshold model, resulting in two more co-authored papers in the 1970s (Reich et al. 1977; Fishman et al. 1978). Part of John’s second sabbatical was at the INRA Department of Animal Genetics at Jouy-en-Josas in 1978. From then on, John maintained close links with a number of French colleagues and generously offered them his expertise. He was associate editor of Genetics Selection Evolution for over two decades, from 1981 to 2001. During that period, he was responsible for the linguistic revision of all papers submitted to the journal. Very often, taking advantage of his knowledge of the field, he went beyond his strict duties and acted as an additional, informal, referee. For more than ten years, John has also been involved in the activities of an international group, headed by Jean-Louis Foulley, exchanging solutions to the weekly mathematical © 2015 Blackwell Verlag GmbH
• J. Anim. Breed. Genet. 132 (2015) 85–88
Introduction
games offered by E Busser and G Cohen in Le Monde. In solving those problems, John again displayed the mathematical skills previously mentioned. Elegance, clarity of reasoning, extreme conciseness and accuracy were the qualities that appeared in his solutions, the same gentleman’s qualities as those he displayed in his scientific writings. After his formal retirement, John has remained actively involved in research and in mentoring postgraduate students, first with CSIRO colleagues in the Ian Clunies Ross laboratory at Prospect, and (since 2001) in the genetics laboratory of the Faculty of Veterinary Science at the University of Sydney, where he is Honorary Professor. Two of us (CW and FN), together with our colleagues Chris Moran and Peter Thomson, can vouch for the enormous benefit we and our students have gained and still gain from having John’s knowledge, understanding and experience ‘on tap’ and, of course, from being able to share extended morning coffee sessions with him. We agree completely with the citation for John’s Fellowship of the Association for the Advancement of Animal Breeding and Genetics (AAABG), in which Laurie Piper is quoted as having said ‘there are many people from whom we can obtain an answer to a question on animal quantitative genetics. However, if you want THE answer, then you automatically go to John.’ Never the first to join a debate, John generally sits back and digests the arguments from all sides, and then, if asked, quietly sorts out the issues properly. The papers in this special issue cover many, but by no means all, of the areas of knowledge to which John has contributed. The scene is nicely set by Woolliams et al. (2015), who show clearly how the concept of genetic contributions introduced in John’s very first paper (James & McBride, 1958) is the theme that unifies the two key elements of the design of breeding programs, namely genetic gain (DG) and the rate of inbreeding (DF). Indeed, as Woolliams et al. (2015) explain, the design of breeding programs (including genomic selection programs) boils down to optimizing genetic contributions over generations so as to maximize DG while constraining DF. Related to the James & McBride (1958) spread-of-genes/genetic-contributions concept is the calculation of partial inbreeding coefficients. Baumung et al. (2015) describe a software package (GRain) that calculates partial coefficients for the classical inbreeding coefficient, for ancestral inbreeding coefficients and for a new parameter, ancestral history coefficient. These parameters are useful for analysing the effects of the spread of genes of particular ancestors, inbreeding depression and purging mechanisms. The next paper (Kerr et al. © 2015 Blackwell Verlag GmbH
• J. Anim. Breed. Genet. 132 (2015) 85–88
2015) illustrates John’s partial inspiration of, and direct contribution to, the design of an overlappinggenerations breeding program for two tree species, drawing important lessons for animal breeding. The following two papers relate to genomic selection in dairy cattle. Kemper et al. (2015) investigate the age of QTL and show how QTL that are present in only one breed (and hence are relatively young) can play havoc in genomic prediction for another breed in a multibreed reference population. Boichard et al. (2015) describe the changes that need to be made in dairy selection programs in order to harvest the many benefits of genomic selection and to avoid its potential pitfalls. Building on John’s important contributions to our understanding of breeding objectives and selection indexes, Santos et al. (2015) develop a strategy for comparing alternate breeding objectives and selection indexes, such as might be used in different countries. Then follow two papers on breeding programs, showing John’s influence spreading as far as communitybased breeding programs in low-input farming systems (as mentioned previously; Mueller et al. 2015) and aquaculture species (Li & Ponzoni 2015). John’s contribution to our understanding of linkage disequilibrium (LD) in the context of selection for a trait with epistasis is highlighted by Hill & M€ aki-Tanila (2015), who, in the course of investigating the extent to which LD contributes to non-additive genetic variation, reinforce the not-yet-fully accepted reality that even in the presence of substantial epistasis, epistatic variance is typically of minor importance. This paper is neatly complemented by Ali et al. (2015) who report a genome-wide epistasis analysis (GWEA) of beef cattle data. Finally, as mentioned previously, Wray & Visscher (2015) provide an insightful and entertaining review of John’s most-cited work, namely his major contributions to the quantitative genetics of threshold traits. Never one to seek attention, John will not feel entirely comfortable with this special issue. In marking his 80th birthday in this way, the editors and authors (and many other colleagues who have not been able to contribute to this special issue) seek his indulgence for their wish to provide a permanent and public indication of their regard for him as a scientist and friend, and to thank him for his many contributions to the advancement of the knowledge and practical application of genetics. Acknowledgements We are very grateful to Asko M€ aki-Tanila, the Executive Editor of Journal of Animal Breeding and Genetics, 87
Introduction
who so enthusiastically embraced the suggestion of this special issue, and who has been heavily involved throughout its gestation. We also thank Stuart Barker, Glen McBride, Jan Nicholas, Chris Morris, Jean-Jacques Colleau, Jean-Louis Foulley, Sue Mortimer, Keith Hammond and Bill Hill for providing background information and/or feedback. F.W. Nicholas1, C.M. Wade1, L. Ollivier2 and J.S€ olkner3 1 Faculty of Veterinary Science, University of Sydney, Sydney, NSW, Australia 2Honorary Director of Research (INRA), Member of the French Academy of Agriculture, Jouy-en-Josas, France 3Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Vienna, Austria E-mail: [email protected]
References Ali A.A., Khatkar M.S., Kadarmideen H.N., Thomson P.C. (2015) Additive and epistatic genome-wide association for growth and ultrasound scan measures of carcassrelated traits in Brahman cattle. J. Anim. Breed. Genet. 132, 187–197. Baumung R., Farkas J., Boichard D., Meszaros G., S€ olkner J., Curik I. (2015) GRain: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach. J. Anim. Breed. Genet. 132, 100– 108. Boichard D., Ducrocq V., Fritz S. (2015) Sustainable dairy cattle selection in the genomic era. J. Anim. Breed. Genet. 132, 135–143. Fishman P.M., Reich T., Suarez B., James J.W. (1978) A note on the essential parameters of the two-allele autosomal locus model. Am. J. Hum. Genet., 30, 283–292. Hill W.G., M€aki-Tanila A. (2015) Expected influence of linkage disequilibrium on genetic variance caused by dominance and epistasis on quantitative traits. J. Anim. Breed. Genet. 132, 176–186. James J.W. (1961) Selection in two environments. Heredity, 16, 145–152. James J.W. (1962a) The spread of genes in random mating control populations. Genet. Res., 3, 1–10. James J.W. (1962b) The spread of genes in populations under selection. In: XIIth World’s Poultry Congress Section Papers. pp. 14–16. James J.W. (1962c) Conflict between directional and centripetal selection. Heredity, 17, 487–499. James J.W. (1962d) On Schwartz and Wearden’s method of estimating heritability. Biometrics, 18, 123–125.
88
James J.W. (1977) Open nucleus breeding systems. Anim. Prod., 24, 287–305. James J.W., McBride G. (1958) The spread of genes by natural and artificial selection in closed poultry flocks. J. Genet., 56, 55–62. Kemper K.E., Hayes B.J., Daetwyler H.D., Goddard M.E. (2015) How old are QTL and how widely do they segregate? J. Anim. Breed. Genet. 132, 121–134. Kerr R., McRae T.A., Dutkowski G.W., Tier B. (2015) Rolling front breeding strategies for the genetic improvement of plantation forest tree species in Australia. J. Anim. Breed. Genet. 132, 109–120. Li Y., Ponzoni R.W. (2015) Some aspects of design and analysis of selection programs in aquaculture species. J. Anim. Breed. Genet. 132, 169–175. McBride G., James J.W. (1965) Effects of inbreeding and bristle number on reproductive success in selected lines of Drosophila melanogaster. Heredity, 20, 474–480. McBride G., James J.W., Shoffner R.N. (1963) Social forces determining spacing and head orientation in a flock of domestic hens. Nature, 197, 1272–1273. McBride G., King M.G., James J.W. (1965) Social proximity effects on galvanic skin responses in adult humans. J. Psychol., 61, 153–157. Mueller J.P., Rischkowsky B., Haile A., Philipsson J., Mwai O., Besbes B., Valle Zarate A., Tibbo M., Mirkena T., Duguma G., S€ olkner J., Wurzinger M. (2015) Community based livestock breeding programs: essentials and examples. J. Anim. Breed. Genet. 132, 155–168. Nurnberger J. (2004) Obituary: Theodore Reich, M.D. (1938–2003). Am. J. Hum. Genet., 75, 1–2. Reich T., James J.W., Morris C.A. (1972) The use of multiple thresholds in determining the mode of transmission of semi-continuous traits. Ann. Hum. Genet., 36, 163– 184. Reich T., James J.W., Wette R., Rice J. (1977) Use of multiple thresholds and segregation analysis in analyzing the phenotypic heterogeneity of multifactorial traits. Behav. Genet., 7, 85–86. Santos B.F.S., McHugh N., Byrne T.J., Berry D.P., Amer P.R. (2015) Comparison of breeding objectives across countries with application to sheep indexes in New Zealand and Ireland. J. Anim. Breed. Genet. 132, 144–154. Smith C., James J.W., Brascamp E.W. (1986) On the derivation of economic weights in livestock improvement. Anim. Prod., 43, 545–551. Woolliams J.A., Berg P., Dagnachew B., Meuwissen T.H.E. (2015) Genetic contributions and their optimisation. J. Anim. Breed. Genet. 132, 89–99. Wray N.R., Visscher P.M. (2015) Quantitative genetics of disease traits. J. Anim. Breed. Genet. 132, 198–203.
© 2015 Blackwell Verlag GmbH
• J. Anim. Breed. Genet. 132 (2015) 85–88
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INTRODUCTION
Quantitative genetics, spread of genes and genetic improvement: papers in honour of John James
In the almost 60 years since he began to teach himself genetics, John James has come to be regarded by his many collaborators around the world as a valued and respected colleague and friend. The occasion of his 80th birthday in 2015 has provided the international genetics community with an opportunity to assemble this special issue of the Journal of Animal Breeding and Genetics, to shine some light on the breadth and depth of John’s influence and to thank him publicly for his many contributions. John was born in Rockhampton, Queensland. His performance at school was sufficient for the award of a Commonwealth Scholarship that enabled him to enrol in a Bachelor of Arts (BA) degree at the University of Queensland in Brisbane. Graduating with majors in mathematics in 1956, John’s introduction to genetics came when he responded to an advertisement for someone to analyse data from a poultry selection program being run by Glen McBride, then a Lecturer in Animal Genetics and Breeding in the Department of Animal Husbandry within the Faculty of Veterinary Science at the University of Queensland. As recounted by Glen to one of us (FN), John immediately threw himself into learning genetics, devouring every paper and book available. He also threw himself into Glen’s very demanding large-scale non-orthogonal analyses of variance, which had to be conducted on a MADAS calculating machine, for which (in Glen’s words) calculating ‘a single sum of squares could take 15 h of punching numbers into a machine’. When Glen happened to mention the possibility of tracing the genetic contribution of an individual to a population, by calculating the changes in that individual’s proportionate contribution of genes over succeeding generations, John soon realized the potential of this idea. In Glen’s own words, John ‘quickly took the concept far beyond my beginnings’, leading rapidly to the publication in July 1958 of John’s first paper (James & McBride 1958). This is the original spread-of-genes/genetic-contributions paper, which has had such a lasting effect, as summarised in this special issue by Woolliams et al. (2015). Even before the publication of this paper, Glen had decamped to Edinburgh for a quick-fire PhD in animal
© 2015 Blackwell Verlag GmbH
• J. Anim. Breed. Genet. 132 (2015) 85–88
genetics under the supervision of Alan Robertson, leaving John to continue with his analyses of the poultry data and to further develop the spread-ofgenes concept, especially in the context of control populations where changes in gene contributions are due to chance. Importantly, this enabled John to derive the relationship between genetic drift (quantified as effective population size) and variance of the spread of genes (James 1962a). By the time of Glen’s return from Edinburgh in 1960, John had extended his spread-of-genes analyses of the poultry data and was ready to apply it to Glen’s PhD Drosophila data (James 1962b; McBride & James 1965). Glen’s return from Edinburgh coincided with the publication of Douglas Falconer’s revolutionary Introduction to Quantitative Genetics, which fired John’s imagination. By this time, he was already exercising his mathematical skills in papers addressing genetical questions as disparate as selection in two environments (James 1961), the conflict between directional and intermediate-optimum selection (James 1962c), and misconceptions concerning a particular estimator of heritability (James 1962d). Genetics, however, was not the only area of knowledge in which John had become involved. Even before leaving for Edinburgh, Glen had become increasingly interested in behaviour, first in his poultry selection lines, and soon in cattle, pigs and humans as well. After Glen’s return from Edinburgh, John had a central role in the analysis of Glen’s behavioural data, leading to several important ethology papers, including one in Nature (McBride et al. 1963) and a highly influential paper on human behaviour in Journal of Psychology (McBride et al. 1965). These papers signalled Glen’s move to the University’s Department of Psychology, from where he is still publishing (aged 90) as Professor Emeritus of Social Ethology. Thus was Glen lost to genetics. He still, however, takes great pleasure in knowing that his relatively short career as a geneticist has had such a lasting legacy. In 1962, without any formal postgraduate qualification but with a wealth of research experience and some substantial publications, John was appointed
doi:10.1111/jbg.12158
Introduction
lecturer in the School of Wool Technology at the University of New South Wales in Sydney, where he remained as geneticist and statistician (under a series of school/department name changes) until formal retirement 35 years later, in 1997. Throughout this time, he continued to publish papers on a wide range of topics in quantitative genetics. In 1973, his publications earned him a DSc from the University of New South Wales. Inevitably in a School of Wool Technology, John became involved in unresolved questions to do with sheep improvement; questions that were for the most part equally applicable to selection programs in any domesticated species. An important example is his pioneering paper that formalized the concept (and introduced the name) of open-nucleus breeding systems (James 1977). Building on ideas originating with Helen Newton Turner and Neville Jackson, John showed that if a sire-breeding nucleus is opened to the regular introduction of selected females from the base population, the rate of genetic gain can be increased by 10–15% and the rate of inbreeding can be halved. This paper stimulated myriad detailed investigations of the implications of such schemes and led to many practical applications across a range of livestock, especially in the developing world (as highlighted by Mueller et al. (2015)) in this special issue. Another important contribution involved the resolution, with Charlie Smith (Scotland) and Pim Brascamp (The Netherlands), of several anomalies that had arisen in the application of profit equations for deriving economic weights in multitrait selection indexes (Smith et al. 1986). After almost three decades, this publication is still informing calculations of economic weights across the entire spectrum of improvement programs in animals and plants. Other topics for which the careful scrutiny of John and his students/colleagues added greatly to our understanding include determining breeding objectives, designing sire reference schemes, determining optimum sire purchasing strategies and determining the optimum allocation of resources in selection programs. Given all these contributions, it was very fitting, and not at all surprising, that John should have been the first recipient (in 1994) of the Helen Newton Turner Medal, which is awarded ‘from the ranks of those persons who have made an outstanding contribution to genetic improvement of Australian livestock’. The citation for his award states that by 1994 John was ‘regarded as Australia’s leading scientist in quantitative genetics and the theory of genetic improvement’. John is also a highly influential teacher. Many of the undergraduates who learned their genetics and statis86
tics from John have gone on to play important roles in animal (and plant) improvement programs in Australia and elsewhere. In addition, many of his numerous postgraduate students have become leaders in their chosen fields. One of us (CW) counts herself exceedingly fortunate to have had John as her PhD supervisor. Another of us (JS) is one of several European academics who have chosen to come to Australia to spend time working with John. JS considers himself unusually lucky in having received John’s insight into mathematical and statistical methodologies as well as gaining a better understanding of the benefits of working together with people of other countries and continents, getting a broader view: to JS (and the rest of us) John is the master of perspective. Consistent with his realization of the invaluable experience to be gained by working in other countries, John (together with his wife Patricia and daughters) took sabbaticals in Scotland, Norway, France and Germany. The first of these, in Edinburgh in 1970, led to a very fruitful collaboration with the American psychiatrist Ted Reich (described in an obituary (Nurnberger 2004) as being ‘generally regarded as one of the founders of modern psychiatric genetics’). Ted had come to Edinburgh to work on Douglas Falconer’s threshold model of liability to disease. Aided by Chris Morris, who had just started his PhD and just happened to be sharing Ted’s room in the Institute of Animal Genetics, John and Ted developed a twothreshold model of multifactorial liability (Reich et al. 1972), which (as described by Wray & Visscher (2015) in this special issue) has had, and is still having, a profound effect on human genetics. Indeed, this is by far John’s most-cited paper. After returning to the Washington University School of Medicine, St Louis, Ted continued working with John on developing and further expanding the threshold model, resulting in two more co-authored papers in the 1970s (Reich et al. 1977; Fishman et al. 1978). Part of John’s second sabbatical was at the INRA Department of Animal Genetics at Jouy-en-Josas in 1978. From then on, John maintained close links with a number of French colleagues and generously offered them his expertise. He was associate editor of Genetics Selection Evolution for over two decades, from 1981 to 2001. During that period, he was responsible for the linguistic revision of all papers submitted to the journal. Very often, taking advantage of his knowledge of the field, he went beyond his strict duties and acted as an additional, informal, referee. For more than ten years, John has also been involved in the activities of an international group, headed by Jean-Louis Foulley, exchanging solutions to the weekly mathematical © 2015 Blackwell Verlag GmbH
• J. Anim. Breed. Genet. 132 (2015) 85–88
Introduction
games offered by E Busser and G Cohen in Le Monde. In solving those problems, John again displayed the mathematical skills previously mentioned. Elegance, clarity of reasoning, extreme conciseness and accuracy were the qualities that appeared in his solutions, the same gentleman’s qualities as those he displayed in his scientific writings. After his formal retirement, John has remained actively involved in research and in mentoring postgraduate students, first with CSIRO colleagues in the Ian Clunies Ross laboratory at Prospect, and (since 2001) in the genetics laboratory of the Faculty of Veterinary Science at the University of Sydney, where he is Honorary Professor. Two of us (CW and FN), together with our colleagues Chris Moran and Peter Thomson, can vouch for the enormous benefit we and our students have gained and still gain from having John’s knowledge, understanding and experience ‘on tap’ and, of course, from being able to share extended morning coffee sessions with him. We agree completely with the citation for John’s Fellowship of the Association for the Advancement of Animal Breeding and Genetics (AAABG), in which Laurie Piper is quoted as having said ‘there are many people from whom we can obtain an answer to a question on animal quantitative genetics. However, if you want THE answer, then you automatically go to John.’ Never the first to join a debate, John generally sits back and digests the arguments from all sides, and then, if asked, quietly sorts out the issues properly. The papers in this special issue cover many, but by no means all, of the areas of knowledge to which John has contributed. The scene is nicely set by Woolliams et al. (2015), who show clearly how the concept of genetic contributions introduced in John’s very first paper (James & McBride, 1958) is the theme that unifies the two key elements of the design of breeding programs, namely genetic gain (DG) and the rate of inbreeding (DF). Indeed, as Woolliams et al. (2015) explain, the design of breeding programs (including genomic selection programs) boils down to optimizing genetic contributions over generations so as to maximize DG while constraining DF. Related to the James & McBride (1958) spread-of-genes/genetic-contributions concept is the calculation of partial inbreeding coefficients. Baumung et al. (2015) describe a software package (GRain) that calculates partial coefficients for the classical inbreeding coefficient, for ancestral inbreeding coefficients and for a new parameter, ancestral history coefficient. These parameters are useful for analysing the effects of the spread of genes of particular ancestors, inbreeding depression and purging mechanisms. The next paper (Kerr et al. © 2015 Blackwell Verlag GmbH
• J. Anim. Breed. Genet. 132 (2015) 85–88
2015) illustrates John’s partial inspiration of, and direct contribution to, the design of an overlappinggenerations breeding program for two tree species, drawing important lessons for animal breeding. The following two papers relate to genomic selection in dairy cattle. Kemper et al. (2015) investigate the age of QTL and show how QTL that are present in only one breed (and hence are relatively young) can play havoc in genomic prediction for another breed in a multibreed reference population. Boichard et al. (2015) describe the changes that need to be made in dairy selection programs in order to harvest the many benefits of genomic selection and to avoid its potential pitfalls. Building on John’s important contributions to our understanding of breeding objectives and selection indexes, Santos et al. (2015) develop a strategy for comparing alternate breeding objectives and selection indexes, such as might be used in different countries. Then follow two papers on breeding programs, showing John’s influence spreading as far as communitybased breeding programs in low-input farming systems (as mentioned previously; Mueller et al. 2015) and aquaculture species (Li & Ponzoni 2015). John’s contribution to our understanding of linkage disequilibrium (LD) in the context of selection for a trait with epistasis is highlighted by Hill & M€ aki-Tanila (2015), who, in the course of investigating the extent to which LD contributes to non-additive genetic variation, reinforce the not-yet-fully accepted reality that even in the presence of substantial epistasis, epistatic variance is typically of minor importance. This paper is neatly complemented by Ali et al. (2015) who report a genome-wide epistasis analysis (GWEA) of beef cattle data. Finally, as mentioned previously, Wray & Visscher (2015) provide an insightful and entertaining review of John’s most-cited work, namely his major contributions to the quantitative genetics of threshold traits. Never one to seek attention, John will not feel entirely comfortable with this special issue. In marking his 80th birthday in this way, the editors and authors (and many other colleagues who have not been able to contribute to this special issue) seek his indulgence for their wish to provide a permanent and public indication of their regard for him as a scientist and friend, and to thank him for his many contributions to the advancement of the knowledge and practical application of genetics. Acknowledgements We are very grateful to Asko M€ aki-Tanila, the Executive Editor of Journal of Animal Breeding and Genetics, 87
Introduction
who so enthusiastically embraced the suggestion of this special issue, and who has been heavily involved throughout its gestation. We also thank Stuart Barker, Glen McBride, Jan Nicholas, Chris Morris, Jean-Jacques Colleau, Jean-Louis Foulley, Sue Mortimer, Keith Hammond and Bill Hill for providing background information and/or feedback. F.W. Nicholas1, C.M. Wade1, L. Ollivier2 and J.S€ olkner3 1 Faculty of Veterinary Science, University of Sydney, Sydney, NSW, Australia 2Honorary Director of Research (INRA), Member of the French Academy of Agriculture, Jouy-en-Josas, France 3Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Vienna, Austria E-mail: [email protected]
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