Functional Plant Genomics

Abstract

As a result of the rapid accumulation of DNA sequence information, including the complete genome sequences for several plant species, plant research is focussing increasingly on analysis of gene function. A book on plant functional genomics is therefore timely and this substantial volume is to be welcomed. It is an updated and expanded version of a French edition, published in 2004 by INRA, which provides a large proportion of the contributors. Its coverage of the topic is broad and reasonably comprehensive. The book is divided into five sections, the first dealing with structural genomics, genome sequencing and the bioinformatics associated with sequence analysis and sequence databases. The second section, entitled ‘Functional Genomics: From Sequences to Function in Plants’, covers the broad range of methods that are being used to discover and characterize gene function. It includes plant transformation, reverse genetics, DNA microarrays, proteomics, metabolomics and bioimaging techniques that are being used to determine sites of gene expression. There are also chapters on metabolic flux analysis and metabolic networks, which are becoming increasingly important in analysing the complex involvement of particular genes/proteins with overall cell metabolism. The third section deals with plant model systems, with chapters on Arabidopsis and a range of crop species – rice, Medicago, tomato, grapevine and sugar cane – that are the current focus of genomics programmes. The chapters summarize the progress that has been made in gene discovery for these systems and, perhaps more importantly, describe the genetic resources that are currently available. In some cases, particularly for Arabidopsis and rice, there is some overlap with the chapter on plant genome sequencing. Nevertheless these chapters provide a useful summary of current progress, at least at the time of publishing, in 2007. The fourth section encompasses genetic analysis, including the use of molecular markers in genotyping, gene isolation and functional characterization. Methods such as map-based cloning and the identification of genes underlying QTLs are described in some detail. There is also consideration of the use of molecular markers in plant breeding with one chapter devoted to maize and wheat breeding. The final short section contains two chapters, one on macro-molecular structure which, although highly informative, seems somewhat misplaced in this volume, while the other on metabolic fingerprinting by Fourier-transformed infra-red might have been included in the functional genomics section. There is also a very useful glossary explaining the jargon and many acronyms used in this field. I found this a very useful and informative resource. Although it is not a light read, it is targeted to the non-specialist so that each chapter starts with a fairly simple and well-explained introduction to the topic, including a historical perspective that I found particularly helpful. Nevertheless, many of the topics are highly technical and I must admit to finding chapters such as that on the statistical basis of gene expression analysis quite heavy going. This does not detract from the value of the book, as such methods are becoming increasingly important in biology and it is necessary for biologists to understand their theoretical basis and, perhaps more importantly, to appreciate their limitations. I found the chapters on gene prediction and detection of protein function from DNA sequences very helpful, particularly for their cautionary messages. Incorrect annotation of genes in databases is a common problem in genomics research and is a source of considerable confusion. Some of the chapters could be better co-ordinated. In addition to the overlapping material alluded to above, I noticed some confusing discrepancies between chapters. For example, the chapters on metabolomics and metabolic fingerprinting claimed respectively 50 000 and 100 000 compounds identified from plants, citing different sources. In the context of this book this might seem a trivial point, but it may be an indication of the depth of editing. It may seem somewhat churlish to note omissions in a book of this size and breadth of coverage, but there are to my mind several notable gaps. I would have liked to have seen more detailed descriptions of DNA sequencing technology, highlighting the recent innovations in this area. Although 454 technology was mentioned in the chapter on genome sequencing, the method was dismissed as having minimal significance for full genome sequencing due to the shortness of reads. However, so-called second generation sequencing using a range of technologies is being used increasingly and will have a major impact on genomics. For example, sequencing the full genomes of all Arabidopsis ecotypes is now technically feasible in terms of time and cost and will be of profound value for relating phenotype and genotype, a prime objective in functional genomics. Such approaches could have been given more prominence. I feel a chapter on the technological basis for 1st, 2nd and 3rd generation sequencing, although this last may be too recent for inclusion, is a must for a volume of this type. I found the descriptions of the technology, as provided, for example, for microscopy or high-throughput genotyping, some of the most useful aspects of this book. The use of TILLING in reverse genetics might have been given more coverage as a non-GM approach to targeted breeding. It was discussed briefly in the chapter on tomato genomics, but it would have been better included in the functional genomics section. I am also surprised there was no mention of the recently completed genome sequence of Brachypodium distachyon, which is a closer model for temperate cereals than is rice. Despite these omissions this book makes a valuable contribution to the plant science literature and I believe that many plant biologists would benefit from reading it. Of course, a problem for works of this type that cover such rapidly advancing fields is that they are out of date almost before they are published. Nevertheless, the book provides an important historical perspective to the subject of functional genomics as well as the theoretical underpinning for most of the topics covered. Above all it is a valuable resource for those entering the field.