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Plant Genotyping II: SNP Technology ed. Robert J. Henry. ix+285 pp. Wallingford: CAB International. £65, US$130, €105 (Hardback). ISBN 978-1-84593-382-1.

Published online by Cambridge University Press:  24 November 2008

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Abstract

Type
Book Review
Copyright
Copyright © 2008 Cambridge University Press

SNP technology is fast becoming the most important methodology for discovering and detecting genetic differences between individuals. This is not just the case for plants, but for all types of organisms. In fact, the main driver for higher throughput and lower cost sequencing and SNP genotyping has come from human genetics in its relentless search for the genetic factors underlying complex diseases. This book describes the most important areas in which SNP technology has been applied in plant research, ranging from genetic mapping and dissection of complex traits, marker-assisted selection, characterization of germplasm and DNA barcoding. Chapter 1 describes methods for SNP discovery in plants and, because the emphasis is on the hexaploid wheat crop, provides a good insight into the particular challenges of genotyping in polyploid plants. It describes possible solutions to the challenge of distinguishing between true allelic, homoeologous and paralogous polymorphisms in polyploid species. Sugarcane has an even more highly polyploid genome, and chapter 5 illustrates how EcoTILLING can help in identifying SNPs in this complex genome. SNP discovery methods are described in various chapters, and in various degrees of detail. They include single strand conformation polymorphism (SSCP), TILLING/EcoTILLING, microarrays, and in silico methodology (including searching for SNPs in microsatellite containing sequences). However, it is difficult to avoid the conclusion that whatever the method used, validation and confirmation of SNPs have to involve sequencing. Sequencing should thus feature prominently in a book on SNP technology. The widely used Applied Biosystems capillary electrophoresis sequencing platform is described on pages 120–121, with one or two inaccuracies, such as exchanging cathode with anode. Pyrosequencing is described in several places, including its use in the ‘454’ sequencing system, which was the first of the next generation sequencing technologies. The Solexa system is only mentioned, and since then ABI has launched its SOLID system. It illustrates the pace with which this technology is developing and the difficulty of keeping a book on this subject completely up to date. However, chapter 9 does provide fascinating insight into emerging nanotechnology-based sequencing and genotyping methods, promising further miniaturization and lower cost per assay. There are a host of existing SNP detection systems available. The MassARRAY system, pyrosequencing and allele-specific PCR are well described. I am surprised that the Illumina Bead Array system is not mentioned, but I can appreciate that it is difficult to give an exhaustive treatment of all available technologies. There is an example of marker use for selecting rice genotypes with improved fragrance qualities, but no comparable examples given for complex traits. This is still to come. This book is slightly expensive, given that all figures are in black and white. Nevertheless, it gives a flavour of many of the current technologies, and their potential applications in plant-based research, and the distinct impression that affordable marker-assisted selection and breeding is within reach as the next generation sequencing and genotyping technologies become widely available.