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Association mapping in plants.
NC Oraguzie, EHA Rikkerink, SE Gardiner, HN de Silva. eds. 2007.
New York: Springer Science+Business Media. $139 (hardback). 277 pp.
Association genetics is a relatively new approach to dissect complex traits that is based on the establishment of causal relationships between genotypes and phenotypes in natural or breeding populations. The use of new high-throughput techniques, which allow in a single assay genotyping of thousands of single nucleotide polymorphisms (SNPs), has boosted the application of this approach both in animal and plant research. Originating in human genetics, association genetics is now widely used in plant breeding, in particular in undomesticated organisms such as forest trees. The main advantage of association mapping in comparison with other common approaches (e.g. QTL mapping) is that the multiple generations of recombination that have taken place in natural populations result in a tight linkage of causal polymorphisms with nearby genomic regions, avoiding the large blocks of linkage that are often obtained from two- or three-generation pedigrees and facilitating the identification of polymorphisms that are associated with quantitative traits.
Association mapping in plants is a timely, well-planned book that covers most topics related to association mapping in plants, from introductory aspects about linkage disequilibrium and SNP genotyping techniques, to sampling and data analysis issues, as well as giving insights into the potential impact of association mapping in plant breeding programmes. The book is structured into 11 chapters and four sections. Section 1 (chapters 1 and 2, 39 pp.) introduces the basic principles of association mapping, including an exhaustive literature review; Section 2 (chapters 3–6, 62 pp.) provides technical details on SNP genotyping, describing classical methods and new technologies (such as the 454 technology); Section 3 (chapters 7 and 8, 94 pp.), in our opinion the most remarkable part of the book, is devoted to detailed discussion of sampling strategies and statistical methodologies for the development of association mapping studies; finally, Section 4 (chapters 9–11, 73 pp.) consists of three chapters dealing with the application of association mapping to breeding of forage species, forest trees and perennial horticultural crops, respectively.
Despite some irregularity in the quality of content and some redundancy in the most general chapters, both difficult to avoid in collective books such as this one, Association mapping in plants is an excellent overview of this fast-advancing discipline that can be used both as an introductory book for students and as a manual to design experiments and analyse genetic association data by experienced researchers or breeding program managers. Indeed, one of the merits of this book is the combination of general literature-review chapters with chapters providing detailed statistical developments and insights into the usefulness of association genetics in operative breeding. Statistical issues are presented in a relatively accessible way, accompanied by informative tables and figures, although a background on quantitative genetics would be helpful to the reader. The authors also provide several case studies and examples, reanalyses of published data and, most interesting of all, R and BUGS codes that can be used as presented or adapted to the readers' needs. The statistical part of the book covers the main approaches used in plant association genetics: case-control studies, general (GLMs) and mixed (MLMs) linear models and transmission disequilibrium tests (TDTs), with a focus also on the application of Bayesian methods. Although the case for the use of Bayesian methods presented in the book is convincing, we miss a more thorough treatment of GLMs and MLMs, as these methods are nowadays one of the most common ways of analysing association genetic data for complex quantitative traits.
Some other merits of this book are: (1) the insights on sampling issues, in particular the very useful discussion on the power to detect association and optimal sample size of association populations taking into account Bayes factors and genetic control of traits; (2) the treatment of common flaws in association studies, including the provision of alternatives such as STRAT to deal with the common issue of population structure; and (3) the specific discussion of methods to confront multiple-testing issues, in particular the false discovery rate (FDR) and related methods.
The three last chapters of the book are well worth a comment. In them, the authors give a well-balanced view of the future of genetic association in plant breeding. For example, the chapter about forest trees begins with an exhaustive literature review and evaluation of progress in applied forest genomics and quantitative genetics in forest trees. Then, the advantages of gene-based selection (GAS) based on association genetics with respect to traditional marker-assisted selection (MAS) are discussed. The chapter continues with reporting requirements and conditions for integrating association genetics within operational forest tree breeding and finishes with a list of sensible conclusions on applicability, limitations and challenges. The information contained in these three final chapters give the reader the knowledge and tools needed to assess from a cost–risk perspective the use of association genetics in specific plant breeding programs.
Association genetics has a broad, multidisciplinary scope and can be used not only in plant breeding (i.e. with focus on commercially interesting genes and traits) but also to advance knowledge in disciplines such as evolutionary biology or population genetics that aim at understanding evolutionary processes in nature. Association genetics, from this point of view, can provide insights into the molecular basis of adaptive traits and on the role of natural selection and other evolutionary forces in shaping genetic variation patterns in plants. In conclusion, we recommend Association mapping in plants as an excellent book to researchers and professionals (population and evolutionary biologists, plant breeders, quantitative geneticists, among others) who have an interest in plant genetics and evolution.